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Enriquez-Felix EE, Pérez-Salazar C, Rico-Ruiz JG, Calheiros de Carvalho A, Cruz-Morales P, Villalobos-Escobedo JM, Herrera-Estrella A. Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism. Microbiol Spectr 2024; 12:e0316523. [PMID: 38441469 DOI: 10.1128/spectrum.03165-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 04/06/2024] Open
Abstract
Trichoderma species are known for their mycoparasitic activity against phytopathogenic fungi that cause significant economic losses in agriculture. During mycoparasitism, Trichoderma spp. recognize molecules produced by the host fungus and release secondary metabolites and hydrolytic enzymes to kill and degrade the host's cell wall. Here, we explored the participation of the Trichoderma atroviride RNAi machinery in the interaction with six phytopathogenic fungi of economic importance. We determined that both Argonaute-3 and Dicer-2 play an essential role during mycoparasitism. Using an RNA-Seq approach, we identified that perception, detox, and cell wall degradation depend on the T. atroviride-RNAi when interacting with Alternaria alternata, Rhizoctonia solani AG2, and R. solani AG5. Furthermore, we constructed a gene co-expression network that provides evidence of two gene modules regulated by RNAi, which play crucial roles in essential processes during mycoparasitism. In addition, based on small RNA-seq, we conclude that siRNAs regulate amino acid and carbon metabolism and communication during the Trichoderma-host interaction. Interestingly, our data suggest that siRNAs might regulate allorecognition (het) and transport genes in a cross-species manner. Thus, these results reveal a fine-tuned regulation in T. atroviride dependent on siRNAs that is essential during the biocontrol of phytopathogenic fungi, showing a greater complexity of this process than previously established.IMPORTANCEThere is an increasing need for plant disease control without chemical pesticides to avoid environmental pollution and resistance, and the health risks associated with the application of pesticides are increasing. Employing Trichoderma species in agriculture to control fungal diseases is an alternative plant protection strategy that overcomes these issues without utilizing chemical fungicides. Therefore, understanding the biocontrol mechanisms used by Trichoderma species to antagonize other fungi is critical. Although there has been extensive research about the mechanisms involved in the mycoparasitic capability of Trichoderma species, there are still unsolved questions related to how Trichoderma regulates recognition, attack, and defense mechanisms during interaction with a fungal host. In this work, we report that the Argonaute and Dicer components of the RNAi machinery and the small RNAs they process are essential for gene regulation during mycoparasitism by Trichoderma atroviride.
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Affiliation(s)
- Eli Efrain Enriquez-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - Camilo Pérez-Salazar
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | - José Guillermo Rico-Ruiz
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
| | | | - Pablo Cruz-Morales
- Novo Nordisk Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
- Plant and Microbial Biology Department, University of California, Berkeley, Carlifornia, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, Carlifornia, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav Campus Guanajuato, Irapuato, Guanajuato, Mexico
- The LatAmBio Initiative, Irapuato, Guanajuato, Mexico
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2
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García-López R, Taboada B, Zárate S, Muñoz-Medina JE, Salas-Lais AG, Herrera-Estrella A, Boukadida C, Vazquez-Perez JA, Gómez-Gil B, Sanchez-Flores A, Arias CF. Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover. Microb Genom 2024; 10:001220. [PMID: 38512312 PMCID: PMC11004493 DOI: 10.1099/mgen.0.001220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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3
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Vega-Arroy JD, Herrera-Estrella A, Ovando-Vázquez C, Casas-Flores S. Inferring co-expression networks of Arabidopsis thaliana genes during their interaction with Trichoderma spp. Sci Rep 2024; 14:2466. [PMID: 38291044 PMCID: PMC10827721 DOI: 10.1038/s41598-023-48332-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/25/2023] [Indexed: 02/01/2024] Open
Abstract
Fungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The transcriptional landscape of the plant during the interaction with these fungi showed a reduction in functions such as reactive oxygen species production, defense mechanisms against pathogens, and hormone signaling. T. virens, as opposed to T. atroviride, was more effective at downregulating genes related to terpenoid metabolism, root development, and chemical homeostasis. Through gene co-expression analysis, we found functional gene modules that closely link plant defense with hypoxia. Notably, we found a transcription factor (locus AT2G47520) with two functional domains of interest: a DNA-binding domain and an N-terminal cysteine needed for protein stability under hypoxia. We hypothesize that the transcription factor can bind to the promoter sequence of the GCC-box that is connected to pathogenesis by positioned weight matrix analysis.
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Affiliation(s)
- Javier-David Vega-Arroy
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, Camino a la Presa San José 2055. Col. Lomas 4 Sección, 78216, San Luis Potosí, SLP, Mexico
- IPICYT, CONAHCYT, Centro Nacional de Supercomputo, Laboratorio de Inteligencia Artificial y Bioinformática, Camino a la Presa San José 2055. Col. Lomas 4 sección, 78216, San Luis Potosí, SLP, Mexico
| | - Alfredo Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, unidad de Genómica Avanzada-Langebio, Libramiento Norte carretera Irapuato-León km 9.6, 36824, Irapuato, GTO, Mexico
| | - Cesaré Ovando-Vázquez
- IPICYT, CONAHCYT, Centro Nacional de Supercomputo, Laboratorio de Inteligencia Artificial y Bioinformática, Camino a la Presa San José 2055. Col. Lomas 4 sección, 78216, San Luis Potosí, SLP, Mexico.
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Laboratorio de Genómica Funcional y Comparativa, Camino a la Presa San José 2055. Col. Lomas 4 Sección, 78216, San Luis Potosí, SLP, Mexico.
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Camargo-Escalante MO, Balcázar-López E, Albores Méndez EM, Winkler R, Herrera-Estrella A. LOX1- and PLP1-dependent transcriptional reprogramming is essential for injury-induced conidiophore development in a filamentous fungus. Microbiol Spectr 2023; 11:e0260723. [PMID: 37943049 PMCID: PMC10714772 DOI: 10.1128/spectrum.02607-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE In addition to being considered a biocontrol agent, the fungus Trichoderma atroviride is a relevant model for studying mechanisms of response to injury conserved in plants and animals that opens a new landscape in relation to regeneration and cell differentiation mechanisms. Here, we reveal the co-functionality of a lipoxygenase and a patatin-like phospholipase co-expressed in response to wounding in fungi. This pair of enzymes produces oxidized lipids that can function as signaling molecules or oxidative stress signals that, in ascomycetes, induce asexual development. Furthermore, we determined that both genes participate in the regulation of the synthesis of 13-HODE and the establishment of the physiological responses necessary for the formation of reproductive aerial mycelium ultimately leading to asexual development. Our results suggest an injury-induced pathway to produce oxylipins and uncovered physiological mechanisms regulated by LOX1 and PLP1 to induce conidiation, opening new hypotheses for the novo regeneration mechanisms of filamentous fungi.
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Affiliation(s)
- Martín O. Camargo-Escalante
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Edgar Balcázar-López
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Exsal M. Albores Méndez
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Robert Winkler
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
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5
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Taboada BI, Zárate S, García-López R, Muñoz-Medina JE, Gómez-Gil B, Herrera-Estrella A, Sanchez-Flores A, Salas-Lais AG, Roche B, Martínez-Morales G, Domínguez Zárate H, Duque Molina C, Avilés Hernández R, López S, Arias CF. SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico. Microb Genom 2023; 9:001120. [PMID: 38112714 PMCID: PMC10763511 DOI: 10.1099/mgen.0.001120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/09/2023] [Indexed: 12/21/2023] Open
Abstract
In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants' abundance, distribution, and genetic diversity in Mexico from April to August 2022. Over 35 % of the sequenced genomes in this period corresponded to the BA.2 variant, 8 % to the BA.4 and 56 % to the BA.5 variant. Multiple subvariants were identified, but the most abundant, BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1 and BA.4.1, circulated across the entire country, not forming geographical clusters. Contrastingly, other subvariants exhibited a geographically restricted distribution, most notably in the Southeast region, which showed a distinct subvariant dynamic. This study supports previous results showing that this region may be a significant entry point and contributed to introducing and evolving novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States through time, which may have contributed to the overall increased diversity observed during this wave compared to the previous ones. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.
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Affiliation(s)
- Blanca Itzelt Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36824, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Gabriela Martínez-Morales
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Hermilo Domínguez Zárate
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Célida Duque Molina
- Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Ciudad de México 06700, Mexico
| | - Ricardo Avilés Hernández
- Unidad de Planeación e Innovación en Salud, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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6
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García-López R, Rivera-Gutiérrez X, Rosales-Rivera M, Zárate S, Muñoz-Medina JE, Roche B, Herrera-Estrella A, Gómez-Gil B, Sanchez-Flores A, Taboada B, Arias CF. SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations. Infection 2023; 51:1549-1555. [PMID: 37058241 PMCID: PMC10103656 DOI: 10.1007/s15010-023-02034-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE The swift expansion of the BW.1 SARS-CoV-2 variant coincided with a rapid increase of COVID-19 cases occurring in Southeast Mexico in October, 2022, which marked the start of Mexico's sixth epidemiological wave. In Yucatan, up to 92% (58 of 73) of weekly sequenced genomes between epidemiological week 42 and 47 were identified as either BW.1 or its descendant, BW.1.1 in the region, during the last trimester of 2022. In the current study, a comprehensive genomic comparison was carried out to characterize the evolutionary history of the BW lineage, identifying its origins and its most important mutations. METHODS An alignment of all the genomes of the BW lineage and its parental BA.5.6.2 variant was carried out to identify their mutations. A phylogenetic and ancestral sequence reconstruction analysis with geographical inference, as well as a longitudinal analysis of point mutations, were performed to trace back their origin and contrast them with key RBD mutations in variant BQ.1, one of the fastest-growing lineages to date. RESULTS Our ancestral reconstruction analysis portrayed Mexico as the most probable origin of the BW.1 and BW.1.1 variants. Two synonymous substitutions, T7666C and C14599T, support their Mexican origin, whereas other two mutations are specific to BW.1: S:N460K and ORF1a:V627I. Two additional substitutions and a deletion are found in its descending subvariant, BW.1.1. Mutations found in the receptor binding domain, S:K444T, S:L452R, S:N460K, and S:F486V in BW.1 have been reported to be relevant for immune escape and are also key mutations in the BQ.1 lineage. CONCLUSIONS BW.1 appears to have arisen in the Yucatan Peninsula in Southeast Mexico sometime around July 2022 during the fifth COVID-19 wave. Its rapid growth may be in part explained by the relevant escape mutations also found in BQ.1.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Xaira Rivera-Gutiérrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Benjamin Roche
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para La Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
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7
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Alder-Rangel A, Bailão AM, Herrera-Estrella A, Rangel AEA, Gácser A, Gasch AP, Campos CBL, Peters C, Camelim F, Verde F, Gadd GM, Braus G, Eisermann I, Quinn J, Latgé JP, Aguirre J, Bennett JW, Heitman J, Nosanchuk JD, Partida-Martínez LP, Bassilana M, Acheampong MA, Riquelme M, Feldbrügge M, Keller NP, Keyhani NO, Gunde-Cimerman N, Nascimento R, Arkowitz RA, Mouriño-Pérez RR, Naz SA, Avery SV, Basso TO, Terpitz U, Lin X, Rangel DEN. The IV International Symposium on Fungal Stress and the XIII International Fungal Biology Conference. Fungal Biol 2023; 127:1157-1179. [PMID: 37495306 DOI: 10.1016/j.funbio.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 04/24/2023] [Indexed: 07/28/2023]
Abstract
For the first time, the International Symposium on Fungal Stress was joined by the XIII International Fungal Biology Conference. The International Symposium on Fungal Stress (ISFUS), always held in Brazil, is now in its fourth edition, as an event of recognized quality in the international community of mycological research. The event held in São José dos Campos, SP, Brazil, in September 2022, featured 33 renowned speakers from 12 countries, including: Austria, Brazil, France, Germany, Ghana, Hungary, México, Pakistan, Spain, Slovenia, USA, and UK. In addition to the scientific contribution of the event in bringing together national and international researchers and their work in a strategic area, it helps maintain and strengthen international cooperation for scientific development in Brazil.
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Affiliation(s)
| | - Alexandre Melo Bailão
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Alfredo Herrera-Estrella
- Unidad de Genómica Avanzada-Langebio, Centro de Investigación y de Estudios Avanzados Del IPN, Irapuato, Guanajuato, Mexico
| | | | - Attila Gácser
- HCEMM-USZ Fungal Pathogens Research Group, Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin Madison, Madison, WI, USA
| | - Claudia B L Campos
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José Dos Campos, SP, Brazil
| | - Christina Peters
- Deutsche Forschungsgemeinschaft (DFG), Office Latin America, São Paulo, SP, Brazil
| | - Francine Camelim
- German Academic Exchange Service (DAAD), DWIH, Sao Paulo, SP, Brazil
| | - Fulvia Verde
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Gerhard Braus
- Institute for Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, Goettingen, Germany
| | - Iris Eisermann
- The Sainsbury Laboratory, University of East Anglia, Norwich, England, UK
| | - Janet Quinn
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, England, UK
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology FORTH and School of Medicine, University of Crete Heraklion, Greece
| | - Jesus Aguirre
- Departamento de Biología Celular y Del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autonoma de México, Mexico City, Mexico
| | - Joan W Bennett
- Department of Plant Biology, Rutgers, State University of New Jersey, New Brunswick, NJ, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Joshua D Nosanchuk
- Departments of Medicine and Microbiology and Immunology, Albert Einstein College of Medicine, The Bronx, NY, USA
| | | | - Martine Bassilana
- Institute of Biology Valrose, University Côte D'Azur, CNRS, INSERM, Nice, France
| | | | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Michael Feldbrügge
- Institute of Microbiology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Nancy P Keller
- Department of Medical Microbiology, Department of Plant Pathology, University of Wisconsin, Madison, WI, USA
| | - Nemat O Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Raquel Nascimento
- Deutsche Forschungsgemeinschaft (DFG), Office Latin America, São Paulo, SP, Brazil
| | - Robert A Arkowitz
- Institute of Biology Valrose, University Côte D'Azur, CNRS, INSERM, Nice, France
| | - Rosa Reyna Mouriño-Pérez
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Sehar Afshan Naz
- Lab of Applied Microbiology and Clinical Mycology, Department of Microbiology, Federal Urdu University of Arts, Science and Technology, Gulshan Iqbal, Karachi, Pakistan
| | - Simon V Avery
- School of Life and Environmental Sciences, University of Nottingham, Nottingham, England, UK
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Theodor-Boveri-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Wuerzburg, Germany
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Vega-Muñoz I, Herrera-Estrella A, Martínez-de la Vega O, Heil M. ATM and ATR, two central players of the DNA damage response, are involved in the induction of systemic acquired resistance by extracellular DNA, but not the plant wound response. Front Immunol 2023; 14:1175786. [PMID: 37256140 PMCID: PMC10225592 DOI: 10.3389/fimmu.2023.1175786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/27/2023] [Indexed: 06/01/2023] Open
Abstract
Background The plant immune response to DNA is highly self/nonself-specific. Self-DNA triggered stronger responses by early immune signals such as H2O2 formation than nonself-DNA from closely related plant species. Plants lack known DNA receptors. Therefore, we aimed to investigate whether a differential sensing of self-versus nonself DNA fragments as damage- versus pathogen-associated molecular patterns (DAMPs/PAMPs) or an activation of the DNA-damage response (DDR) represents the more promising framework to understand this phenomenon. Results We treated Arabidopsis thaliana Col-0 plants with sonicated self-DNA from other individuals of the same ecotype, nonself-DNA from another A. thaliana ecotype, or nonself-DNA from broccoli. We observed a highly self/nonself-DNA-specific induction of H2O2 formation and of jasmonic acid (JA, the hormone controlling the wound response to chewing herbivores) and salicylic acid (SA, the hormone controlling systemic acquired resistance, SAR, to biotrophic pathogens). Mutant lines lacking Ataxia Telangiectasia Mutated (ATM) or ATM AND RAD3-RELATED (ATR) - the two DDR master kinases - retained the differential induction of JA in response to DNA treatments but completely failed to induce H2O2 or SA. Moreover, we observed H2O2 formation in response to in situ-damaged self-DNA from plants that had been treated with bleomycin or SA or infected with virulent bacteria Pseudomonas syringae pv. tomato DC3000 or pv. glycinea carrying effector avrRpt2, but not to DNA from H2O2-treated plants or challenged with non-virulent P. syringae pv. glycinea lacking avrRpt2. Conclusion We conclude that both ATM and ATR are required for the complete activation of the plant immune response to extracellular DNA whereas an as-yet unknown mechanism allows for the self/nonself-differential activation of the JA-dependent wound response.
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Affiliation(s)
- Isaac Vega-Muñoz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato, GTO, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato, GTO, Mexico
| | - Octavio Martínez-de la Vega
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato, GTO, Mexico
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato, GTO, Mexico
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9
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Sarrocco S, Herrera-Estrella A, Collinge DB. Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II. Front Microbiol 2023; 14:1203870. [PMID: 37234538 PMCID: PMC10208526 DOI: 10.3389/fmicb.2023.1203870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Affiliation(s)
- Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alfredo Herrera-Estrella
- National Laboratory of Genomics for Biodiversity, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato, Mexico
| | - David B. Collinge
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
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González-Lemes I, Acosta-Maspons A, Cetz-Chel JE, Polania JA, Acosta-Gallegos JA, Herrera-Estrella A, Covarrubias AA. Carbon-concentrating mechanisms in pods are key elements for terminal drought resistance in Phaseolus vulgaris. J Exp Bot 2023; 74:1642-1658. [PMID: 36546370 DOI: 10.1093/jxb/erac504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is one of the most consumed legumes in the human diet and a substantial source of dietary protein. A major problem for this rainfed crop is the decrease in grain yield caused by prolonged drought periods during the reproductive stage of plant development (terminal drought). Terminal drought remains a prevailing threat to the farming of this staple, with losses reaching >80%. Based on the high correlation between the resistance of common bean to terminal drought and efficient photoassimilate mobilization and biomass accumulation in seeds, we aimed to identify mechanisms implicated in its resistance to this stress. We used two representative Durango race common bean cultivars with contrasting yields under terminal drought, grown under well-watered or terminal drought conditions. Using comparative transcriptomic analysis focused on source leaves, pods, and seeds from both cultivars, we provide evidence indicating that under terminal drought the resistant cultivar promotes the build-up of transcripts involved in recycling carbon through photosynthesis, photorespiration, and CO2-concentrating mechanisms in pod walls, while in seeds, the induced transcripts participate in sink strength and respiration. Physiological data support this conclusion, implicating their relevance as key processes in the plant response to terminal drought.
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Affiliation(s)
- Ingrid González-Lemes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Alexis Acosta-Maspons
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - José E Cetz-Chel
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
| | - José A Polania
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jorge A Acosta-Gallegos
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Bajío, Celaya, Guanajuato, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Zárate S, Taboada B, Rosales-Rivera M, García-López R, Muñoz-Medina JE, Sanchez-Flores A, Herrera-Estrella A, Gómez-Gil B, Selem Mojica N, Salas-Lais AG, Vazquez-Perez JA, Cabrera-Gaytán DA, Fernandes-Matano L, Uribe-Noguez LA, Chale-Dzul JB, Maldonado Meza BI, Mejía-Nepomuceno F, Pérez-Padilla R, Gutiérrez-Ríos RM, Loza A, Roche B, López S, Arias CF. Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants. Viruses 2023; 15:243. [PMID: 36680283 PMCID: PMC9863047 DOI: 10.3390/v15010243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. METHODS The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. RESULTS BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. CONCLUSIONS Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36821, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia 58089, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Joel Armando Vazquez-Perez
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - David Alejandro Cabrera-Gaytán
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Larissa Fernandes-Matano
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Luis Antonio Uribe-Noguez
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City, 02990, Mexico
| | - Juan Bautista Chale-Dzul
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Merida 97150, Mexico
| | | | - Fidencio Mejía-Nepomuceno
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rogelio Pérez-Padilla
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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12
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Loza A, Wong-Chew RM, Jiménez-Corona ME, Zárate S, López S, Ciria R, Palomares D, García-López R, Iša P, Taboada B, Rosales M, Boukadida C, Herrera-Estrella A, Mojica NS, Rivera-Gutierrez X, Muñoz-Medina JE, Salas-Lais AG, Sanchez-Flores A, Vazquez-Perez JA, Arias CF, Gutiérrez-Ríos RM. Two-year follow-up of the COVID-19 pandemic in Mexico. Front Public Health 2023; 10:1050673. [PMID: 36711379 PMCID: PMC9880891 DOI: 10.3389/fpubh.2022.1050673] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Background After the initial outbreak in China (December 2019), the World Health Organization declared COVID-19 a pandemic on March 11th, 2020. This paper aims to describe the first 2 years of the pandemic in Mexico. Design and methods This is a population-based longitudinal study. We analyzed data from the national COVID-19 registry to describe the evolution of the pandemic in terms of the number of confirmed cases, hospitalizations, deaths and reported symptoms in relation to health policies and circulating variants. We also carried out logistic regression to investigate the major risk factors for disease severity. Results From March 2020 to March 2022, the coronavirus disease 2019 (COVID-19) pandemic in Mexico underwent four epidemic waves. Out of 5,702,143 confirmed cases, 680,063 were hospitalized (11.9%), and 324,436 (5.7%) died. Even if there was no difference in susceptibility by gender, males had a higher risk of death (CFP: 7.3 vs. 4.2%) and hospital admission risk (HP: 14.4 vs. 9.5%). Severity increased with age. With respect to younger ages (0-17 years), the 60+ years or older group reached adjusted odds ratios of 9.63 in the case of admission and 53.05 (95% CI: 27.94-118.62) in the case of death. The presence of any comorbidity more than doubled the odds ratio, with hypertension-diabetes as the riskiest combination. While the wave peaks increased over time, the odds ratios for developing severe disease (waves 2, 3, and 4 to wave 1) decreased to 0.15 (95% CI: 0.12-0.18) in the fourth wave. Conclusion The health policy promoted by the Mexican government decreased hospitalizations and deaths, particularly among older adults with the highest risk of admission and death. Comorbidities augment the risk of developing severe illness, which is shown to rise by double in the Mexican population, particularly for those reported with hypertension-diabetes. Factors such as the decrease in the severity of the SARS-CoV2 variants, changes in symptomatology, and advances in the management of patients, vaccination, and treatments influenced the decrease in mortality and hospitalizations.
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Affiliation(s)
- Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de Mexico, Ciudad de México, Mexico
| | | | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ricardo Ciria
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Diego Palomares
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Mauricio Rosales
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Alfredo Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Irapuato, Guanajuato, Mexico
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Michoacan, Mexico
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - José Esteba Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico,*Correspondence: Rosa María Gutiérrez-Ríos ✉
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13
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Molina-Mora JA, Reales-González J, Camacho E, Duarte-Martínez F, Tsukayama P, Soto-Garita C, Brenes H, Cordero-Laurent E, Ribeiro dos Santos A, Guedes Salgado C, Santos Silva C, Santana de Souza J, Nunes G, Negri T, Vidal A, Oliveira R, Oliveira G, Muñoz-Medina JE, Salas-Lais AG, Mireles-Rivera G, Sosa E, Turjanski A, Monzani MC, Carobene MG, Remes Lenicov F, Schottlender G, Fernández Do Porto DA, Kreuze JF, Sacristán L, Guevara-Suarez M, Cristancho M, Campos-Sánchez R, Herrera-Estrella A. Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021. Front Public Health 2023; 11:1095202. [PMID: 36935725 PMCID: PMC10018007 DOI: 10.3389/fpubh.2023.1095202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.
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Affiliation(s)
- Jose Arturo Molina-Mora
- Centro de investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- *Correspondence: Jose Arturo Molina-Mora
| | | | - Erwin Camacho
- Investigaciones Biomédicas, Universidad de Sucre, Sincelejo, Colombia
| | - Francisco Duarte-Martínez
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Pablo Tsukayama
- Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Claudio Soto-Garita
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Hebleen Brenes
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | - Estela Cordero-Laurent
- Laboratorio de Genómica y Biología Molecular, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Tres Ríos, Cartago, Costa Rica
| | | | | | - Caio Santos Silva
- Instituto de Ciências Biológica, Universidade Federal do Pará, Belém, Brazil
| | | | - Gisele Nunes
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Tatianne Negri
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Amanda Vidal
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Renato Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Environmental Genomics, Vale Institute of Technology, Belém, Pará, Brazil
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Guadalupe Mireles-Rivera
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
| | - Ezequiel Sosa
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Adrián Turjanski
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Cecilia Monzani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauricio G. Carobene
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Federico Remes Lenicov
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gustavo Schottlender
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Luisa Sacristán
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | | | - Marco Cristancho
- Vicerrectoria de Investigación y Creación, Universidad de Los Andes, Bogotá, Colombia
| | - Rebeca Campos-Sánchez
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Irapuato, Mexico
- Alfredo Herrera-Estrella
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14
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Parker TA, Cetz J, de Sousa LL, Kuzay S, Lo S, Floriani TDO, Njau S, Arunga E, Duitama J, Jernstedt J, Myers JR, Llaca V, Herrera-Estrella A, Gepts P. Loss of pod strings in common bean is associated with gene duplication, retrotransposon insertion and overexpression of PvIND. New Phytol 2022; 235:2454-2465. [PMID: 35708662 DOI: 10.1111/nph.18319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Fruit development has been central in the evolution and domestication of flowering plants. In common bean (Phaseolus vulgaris), the principal global grain legume staple, two main production categories are distinguished by fibre deposition in pods: dry beans, with fibrous, stringy pods; and stringless snap/green beans, with reduced fibre deposition, which frequently revert to the ancestral stringy state. Here, we identify genetic and developmental patterns associated with pod fibre deposition. Transcriptional, anatomical, epigenetic and genetic regulation of pod strings were explored through RNA-seq, RT-qPCR, fluorescence microscopy, bisulfite sequencing and whole-genome sequencing. Overexpression of the INDEHISCENT ('PvIND') orthologue was observed in stringless types compared with isogenic stringy lines, associated with overspecification of weak dehiscence-zone cells throughout the pod vascular sheath. No differences in DNA methylation were correlated with this phenotype. Nonstringy varieties showed a tandemly direct duplicated PvIND and a Ty1-copia retrotransposon inserted between the two repeats. These sequence features are lost during pod reversion and are predictive of pod phenotype in diverse materials, supporting their role in PvIND overexpression and reversible string phenotype. Our results give insight into reversible gain-of-function mutations and possible genetic solutions to the reversion problem, of considerable economic value for green bean production.
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Affiliation(s)
- Travis A Parker
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Jose Cetz
- National Laboratory of Genomics for Biodiversity, CINVESTAV, Irapuato, Guanajuato, C.P. 36821, Mexico
| | - Lorenna Lopes de Sousa
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Saarah Kuzay
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Sassoum Lo
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - Talissa de Oliveira Floriani
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
- Department of Genetics, Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Serah Njau
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
- Department of Water and Agricultural Resource Management, University of Embu, Embu, 60100, Kenya
| | - Esther Arunga
- Department of Water and Agricultural Resource Management, University of Embu, Embu, 60100, Kenya
| | - Jorge Duitama
- Department of Systems and Computing Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Judy Jernstedt
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
| | - James R Myers
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Alfredo Herrera-Estrella
- National Laboratory of Genomics for Biodiversity, CINVESTAV, Irapuato, Guanajuato, C.P. 36821, Mexico
| | - Paul Gepts
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616-8780, USA
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15
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Zárate S, Taboada B, Muñoz-Medina JE, Iša P, Sanchez-Flores A, Boukadida C, Herrera-Estrella A, Selem Mojica N, Rosales-Rivera M, Gómez-Gil B, Salas-Lais AG, Santacruz-Tinoco CE, Montoya-Fuentes H, Alvarado-Yaah JE, Molina-Salinas GM, Espinoza-Ayala GE, Enciso-Moreno JA, Gutiérrez-Ríos RM, Loza A, Moreno-Contreras J, García-López R, Rivera-Gutierrez X, Comas-García A, Wong-Chew RM, Jiménez-Corona ME, del Angel RM, Vazquez-Perez JA, Matías-Florentino M, Pérez-García M, Ávila-Ríos S, Castelán-Sánchez HG, Delaye L, Martínez-Castilla LP, Escalera-Zamudio M, López S, Arias CF. The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico. Microbiol Spectr 2022; 10:e0224021. [PMID: 35389245 PMCID: PMC9045257 DOI: 10.1128/spectrum.02240-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, México
| | - Mauricio Rosales-Rivera
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlám, Mazatlán, México
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Héctor Montoya-Fuentes
- Centro de Investigación Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, México
| | - Julio Elias Alvarado-Yaah
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | | | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Zacatecas, México
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Andreu Comas-García
- Facultad de Medicna y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Rosa María del Angel
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav, Ciudad de México, México
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Marissa Pérez-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Hugo G. Castelán-Sánchez
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Guanajuato, México
| | - León P. Martínez-Castilla
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | | | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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16
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Garduño-Rosales M, Callejas-Negrete OA, Medina-Castellanos E, Bartnicki-García S, Herrera-Estrella A, Mouriño-Pérez RR. F-actin dynamics following mechanical injury of Trichoderma atroviride and Neurospora crassa hyphae. Fungal Genet Biol 2022; 159:103672. [PMID: 35150841 DOI: 10.1016/j.fgb.2022.103672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 11/04/2022]
Abstract
We investigated hyphae regeneration in Trichoderma atroviride and Neurospora crassa, with particular focus on determining the role of the actin cytoskeleton after mechanical injury. Filamentous actin (F-actin) dynamics were observed by live-cell confocal microscopy in both T. atroviride and N. crassa strains expressing Lifeact-GFP. In growing hyphae of both fungi, F-actin localized in three different structural forms: patches, cables and actomyosin rings. Most patches were conspicuously arranged in a collar in the hyphal subapex. A strong F-actin signal, likely actin filaments, colocalized with the core of the Spitzenkörper. Filaments and cables of F-actin we observed along the cortex throughout hyphae. Following mechanical damage at the margin of growing mycelia of T. atroviride and N. crassa, the severed hyphae lost their cytoplasmic contents, but plugging of the septal pore by a Woronin body, the rest of the hyphal tube remained whole. In both fungi, patches of F-actin began accumulating next to the plugged septum. Regeneration was attained by the emergence of a new hyphal tube as an extension of the plugged septum wall. The septum wall was gradually remodeled into the apical wall of the emerging hypha. Whereas in T. atroviride the re-initiation of polarized growth took about ∼1 h, in N. crassa, actin patch accumulation began almost immediately, and new growing hyphae were observed ∼30 min after injury. By confocal microscopy, we found that chitin synthase 1 (CHS-1), a microvesicle (chitosome) component, accumulated next to the plugged septum in regenerating hyphae of N. crassa. We concluded that the actin cytoskeleton plays a key role in hyphal regeneration by supporting membrane remodeling, helping to facilitate transport of vesicles responsible for new wall growth and organization of the new tip-growth apparatus.
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Affiliation(s)
- Marisela Garduño-Rosales
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., México
| | - Olga A Callejas-Negrete
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., México
| | - Elizabeth Medina-Castellanos
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., México; Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato. Irapuato, Gto., México
| | - Salomon Bartnicki-García
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato. Irapuato, Gto., México
| | - Rosa R Mouriño-Pérez
- Departamento de Microbiología. Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, B.C., México.
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17
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Pola-Sánchez E, Villalobos-Escobedo JM, Carreras-Villaseñor N, Martínez-Hernández P, Beltrán-Hernández EB, Esquivel-Naranjo EU, Herrera-Estrella A. A Global Analysis of Photoreceptor-Mediated Transcriptional Changes Reveals the Intricate Relationship Between Central Metabolism and DNA Repair in the Filamentous Fungus Trichoderma atroviride. Front Microbiol 2021; 12:724676. [PMID: 34566928 PMCID: PMC8456097 DOI: 10.3389/fmicb.2021.724676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
Light provides critical information for the behavior and development of basically all organisms. Filamentous fungi sense blue light, mainly, through a unique transcription factor complex that activates its targets in a light-dependent manner. In Trichoderma atroviride, the BLR-1 and BLR-2 proteins constitute this complex, which triggers the light-dependent formation of asexual reproduction structures (conidia). We generated an ENVOY photoreceptor mutant and performed RNA-seq analyses in the mutants of this gene and in those of the BLR-1, CRY-1 and CRY-DASH photoreceptors in response to a pulse of low intensity blue light. Like in other filamentous fungi BLR-1 appears to play a central role in the regulation of blue-light responses. Phenotypic characterization of the Δenv-1 mutant showed that ENVOY functions as a growth and conidiation checkpoint, preventing exacerbated light responses. Similarly, we observed that CRY-1 and CRY-DASH contribute to the typical light-induced conidiation response. In the Δenv-1 mutant, we observed, at the transcriptomic level, a general induction of DNA metabolic processes and strong repression of central metabolism. An analysis of the expression level of DNA repair genes showed that they increase their expression in the absence of env-1. Consistently, photoreactivation experiments showed that Δenv-1 had increased DNA repair capacity. Our results indicate that light perception in T. atroviride is far more complex than originally thought.
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Affiliation(s)
- Enrique Pola-Sánchez
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | | | - Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Emma Beatriz Beltrán-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Edgardo Ulises Esquivel-Naranjo
- Laboratorio de Microbiología Molecular, Unidad de Microbiología Básica y Aplicada, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
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18
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Esparza-Reynoso S, Ruíz-Herrera LF, Pelagio-Flores R, Macías-Rodríguez LI, Martínez-Trujillo M, López-Coria M, Sánchez-Nieto S, Herrera-Estrella A, López-Bucio J. Trichoderma atroviride-emitted volatiles improve growth of Arabidopsis seedlings through modulation of sucrose transport and metabolism. Plant Cell Environ 2021; 44:1961-1976. [PMID: 33529396 DOI: 10.1111/pce.14014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
Plants host a diverse microbiome and differentially react to the fungal species living as endophytes or around their roots through emission of volatiles. Here, using divided Petri plates for Arabidopsis-T. atroviride co-cultivation, we show that fungal volatiles increase endogenous sugar levels in shoots, roots and root exudates, which improve Arabidopsis root growth and branching and strengthen the symbiosis. Tissue-specific expression of three sucrose phosphate synthase-encoding genes (AtSPS1F, AtSPS2F and AtSPS3F), and AtSUC2 and SWEET transporters revealed that the gene expression signatures differ from those of the fungal pathogens Fusarium oxysporum and Alternaria alternata and that AtSUC2 is largely repressed either by increasing carbon availability or by perception of the fungal volatile 6-pentyl-2H-pyran-2-one. Our data point to Trichoderma volatiles as chemical signatures for sugar biosynthesis and exudation and unveil specific modulation of a critical, long-distance sucrose transporter in the plant.
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Affiliation(s)
- Saraí Esparza-Reynoso
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - León Francisco Ruíz-Herrera
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Ramón Pelagio-Flores
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | | | | | - Montserrat López-Coria
- Departamento de Bioquímica, Facultad de Bioquímica, Conjunto E, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sobeida Sánchez-Nieto
- Departamento de Bioquímica, Facultad de Bioquímica, Conjunto E, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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19
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Esquivel-Naranjo EU, Herrera-Estrella A. Strong preference for the integration of transforming DNA via homologous recombination in Trichoderma atroviride. Fungal Biol 2020; 124:854-863. [PMID: 32948273 DOI: 10.1016/j.funbio.2020.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/17/2020] [Accepted: 07/02/2020] [Indexed: 11/15/2022]
Abstract
Trichoderma species play important roles in nature as plant growth promotors and antagonists of phytopathogenic fungi, and are used as models to study photomorphogenesis. Molecular tools have been implemented to manipulate and improve these fungi. However, instability of transformants or very low frequency of homologous recombination has been reported. Here, we report the fate of transforming DNA, demonstrating that it can follow two different fates. When a vector contains sequences also present in the Trichodermaatroviride genome, it mainly integrates by homologous recombination generating stable recombinant strains. In contrast, vectors with no sequence homology to the T. atroviride genome generate unstable transformants, losing the transforming DNA in the first generation of conidia produced without selection where, surprisingly, the vector behaves as autoreplicative. Integration by homologous recombination was demonstrated when transformants were generated with a truncated version of the blr2 gene, resulting in insertional mutants with phenotypes identical to those of knockout mutants. Our results indicate that T. atroviride is highly efficient in integrating DNA by homologous recombination and that plasmid vectors with no sequence homology to the genome are maintained for several generations in T. atroviride if kept under selective pressure even though they lacked fungal autonomous replication sequences.
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Affiliation(s)
- Edgardo Ulises Esquivel-Naranjo
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Autonomous University of Querétaro, Querétaro, 76140, Mexico; Laboratorio Nacional de Genómica para La Biodiversidad, CINVESTAV-Irapuato, 36824, rapuato, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para La Biodiversidad, CINVESTAV-Irapuato, 36824, rapuato, Mexico.
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20
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Villalobos-Escobedo JM, Esparza-Reynoso S, Pelagio-Flores R, López-Ramírez F, Ruiz-Herrera LF, López-Bucio J, Herrera-Estrella A. The fungal NADPH oxidase is an essential element for the molecular dialog between Trichoderma and Arabidopsis. Plant J 2020; 103:2178-2192. [PMID: 32578269 DOI: 10.1111/tpj.14891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Members of the fungal genus Trichoderma stimulate growth and reinforce plant immunity. Nevertheless, how fungal signaling elements mediate the establishment of a successful Trichoderma-plant interaction is largely unknown. In this work, we analyzed growth, root architecture and defense in an Arabidopsis-Trichoderma co-cultivation system, including the wild-type (WT) strain of the fungus and mutants affected in NADPH oxidase. Global gene expression profiles were assessed in both the plant and the fungus during the establishment of the interaction. Trichoderma atroviride WT improved root branching and growth of seedling as previously reported. This effect diminished in co-cultivation with the ∆nox1, ∆nox2 and ∆noxR null mutants. The data gathered of the Arabidopsis interaction with the ∆noxR strain showed that the seedlings had a heightened immune response linked to jasmonic acid in roots and shoots. In the fungus, we observed repression of genes involved in complex carbohydrate degradation in the presence of the plant before contact. However, in the absence of NoxR, such repression was lost, apparently due to a poor ability to adequately utilize simple carbon sources such as sucrose, a typical plant exudate. Our results unveiled the critical role played by the Trichoderma NoxR in the establishment of a fine-tuned communication between the plant and the fungus even before physical contact. In this dialog, the fungus appears to respond to the plant by adjusting its metabolism, while in the plant, fungal perception determines a delicate growth-defense balance.
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Affiliation(s)
- José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.6 libramiento Norte Carretera Irapuato-León, Irapuato, C. P. 36824, México
| | - Saraí Esparza-Reynoso
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, Morelia, C. P. 58030, México
| | - Ramón Pelagio-Flores
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.6 libramiento Norte Carretera Irapuato-León, Irapuato, C. P. 36824, México
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, C. P. 58240, México
| | - Fabiola López-Ramírez
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.6 libramiento Norte Carretera Irapuato-León, Irapuato, C. P. 36824, México
| | - León F Ruiz-Herrera
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, Morelia, C. P. 58030, México
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, Morelia, C. P. 58030, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Km. 9.6 libramiento Norte Carretera Irapuato-León, Irapuato, C. P. 36824, México
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21
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Estrada-Rivera M, Hernández-Oñate MÁ, Dautt-Castro M, Gallardo-Negrete JDJ, Rebolledo-Prudencio OG, Uresti-Rivera EE, Arenas-Huertero C, Herrera-Estrella A, Casas-Flores S. IPA-1 a Putative Chromatin Remodeler/Helicase-Related Protein of Trichoderma virens Plays Important Roles in Antibiosis Against Rhizoctonia solani and Induction of Arabidopsis Systemic Disease Resistance. Mol Plant Microbe Interact 2020; 33:808-824. [PMID: 32101077 DOI: 10.1094/mpmi-04-19-0092-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, either indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma spp. emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to cocultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell wall-degrading enzymes putatively relevant for root colonization. Repression of such genes reached their basal levels at later times in the interaction, when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell wall-degrading enzymes with the auxiliary activities class. RNA-Seq analyses showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (increased protection of Arabidopsis-1). Sequence analyses of IPA-1 showed its closest relatives to be members of the Rad5/Rad16 and SNF2 subfamilies; however, it grouped into a different clade. Although deletion of IPA-1 in T. virens did not affect its growth, the antibiotic activity of Δipa-1 culture filtrates against Rhizoctonia solani diminished but it remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared with the wild type.
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Affiliation(s)
- Magnolia Estrada-Rivera
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - Miguel Ángel Hernández-Oñate
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, Carretera Gustavo Enrique Astiazarán Rosas No. 46, La Victoria, C.P. 83304. Hermosillo, Sonora, Mexico
| | - Mitzuko Dautt-Castro
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | - José de Jesús Gallardo-Negrete
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
| | | | - Edith Elena Uresti-Rivera
- Facultad de Ciencias Químicas, Departamento de Inmunología y Biología Celular y Molecular, Universidad Autónoma de San Luis Potosí, Av. Salvador Nava s/n, Zona Universitaria, 78290, San Luis Potosí, Mexico
| | - Catalina Arenas-Huertero
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec No. 1570. Priv. del Pedregal 78295, San Luis Potosí, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, C.P. 36824, Irapuato, Gto., México
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la presa San José No. 2055, Colonia Lomas 4a sección, C.P. 78216, San Luis Potosí, Mexico
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22
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Carreras-Villaseñor N, Rico-Ruiz JG, Chávez Montes RA, Yong-Villalobos L, López-Hernández JF, Martínez-Hernández P, Herrera-Estrella L, Herrera-Estrella A, López-Arredondo D. Assessment of the ptxD gene as a growth and selective marker in Trichoderma atroviride using Pccg6, a novel constitutive promoter. Microb Cell Fact 2020; 19:69. [PMID: 32188455 PMCID: PMC7081547 DOI: 10.1186/s12934-020-01326-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/08/2020] [Indexed: 01/08/2023] Open
Abstract
Background Trichoderma species are among the most effective cell factories to produce recombinant proteins, whose productivity relies on the molecular toolkit and promoters available for the expression of the target protein. Although inducible promoter systems have been developed for producing recombinant proteins in Trichoderma, constitutive promoters are often a desirable alternative. Constitutive promoters are simple to use, do not require external stimuli or chemical inducers to be activated, and lead to purer enzyme preparations. Moreover, most of the promoters for homologous and heterologous expression reported in Trichoderma have been commonly evaluated by directly assessing production of industrial enzymes, requiring optimization of laborious protocols. Results Here we report the identification of Pccg6, a novel Trichoderma atroviride constitutive promoter, that has similar transcriptional strength as that of the commonly used pki1 promoter. Pccg6 displayed conserved arrangements of transcription factor binding sites between promoter sequences of Trichoderma ccg6 orthologues genes, potentially involved in their regulatory properties. The predicted ccg6-encoded protein potentially belongs to the SPE1/SPI1 protein family and shares high identity with CCG6 orthologue sequences from other fungal species including Trichoderma reesei, Trichoderma virens, Trichoderma asperellum, and to a lesser extent to that of Neurospora crassa. We also report the use of the Pccg6 promoter to drive the expression of PTXD, a phosphite oxidoreductase of bacterial origin, which allowed T. atroviride to utilize phosphite as a sole source of phosphorus. We propose ptxD as a growth reporter gene that allows real-time comparison of the functionality of different promoters by monitoring growth of Trichoderma transgenic lines and enzymatic activity of PTXD. Finally, we show that constitutive expression of ptxD provided T. atroviride a competitive advantage to outgrow bacterial contaminants when supplied with phosphite as a sole source of phosphorus. Conclusions A new constitutive promoter, ccg6, for expression of homologous and heterologous proteins has been identified and tested in T. atroviride to express PTXD, which resulted in an effective and visible phenotype to evaluate transcriptional activity of sequence promoters. Use of PTXD as a growth marker holds great potential for assessing activity of other promoters and for biotechnological applications as a contamination control system.
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Affiliation(s)
- Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico.,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C, Xalapa, 91070, Mexico
| | - José Guillermo Rico-Ruiz
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico.,Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Ricardo A Chávez Montes
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Lenin Yong-Villalobos
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - José Fabricio López-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico.,Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico.,Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500, Irapuato, Guanajuato, Mexico
| | - Damar López-Arredondo
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico. .,Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX, 79409, USA.
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23
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Sarrocco S, Herrera-Estrella A, Collinge DB. Editorial: Plant Disease Management in the Post-genomic Era: From Functional Genomics to Genome Editing. Front Microbiol 2020; 11:107. [PMID: 32117135 PMCID: PMC7010928 DOI: 10.3389/fmicb.2020.00107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/17/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alfredo Herrera-Estrella
- National Laboratory of Genomics for Biodiversity, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato, Mexico
| | - David B Collinge
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Copenhagen, Denmark
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24
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Bojórquez-Velázquez E, Barrera-Pacheco A, Espitia-Rangel E, Herrera-Estrella A, Barba de la Rosa AP. Protein analysis reveals differential accumulation of late embryogenesis abundant and storage proteins in seeds of wild and cultivated amaranth species. BMC Plant Biol 2019; 19:59. [PMID: 30727945 PMCID: PMC6366027 DOI: 10.1186/s12870-019-1656-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/16/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Amaranth is a plant naturally resistant to various types of stresses that produces seeds of excellent nutritional quality, so amaranth is a promising system for food production. Amaranth wild relatives have survived climate changes and grow under harsh conditions, however no studies about morphological and molecular characteristics of their seeds are known. Therefore, we carried out a detailed morphological and molecular characterization of wild species A. powellii and A. hybridus, and compared them with the cultivated amaranth species A. hypochondriacus (waxy and non-waxy seeds) and A. cruentus. RESULTS Seed proteins were fractionated according to their polarity properties and were analysed in one-dimensional gel electrophoresis (1-DE) followed by nano-liquid chromatography coupled to tandem mass spectrometry (nLC-MS/MS). A total of 34 differentially accumulated protein bands were detected and 105 proteins were successfully identified. Late embryogenesis abundant proteins were detected as species-specific. Oleosins and oil bodies associated proteins were observed preferentially in A. cruentus. Different isoforms of the granule-bound starch synthase I, and several paralogs of 7S and 11S globulins were also identified. The in silico structural analysis from different isoforms of 11S globulins was carried out, including new types of 11S globulin not reported so far. CONCLUSIONS The results provide novel information about 11S globulins and proteins related in seed protection, which could play important roles in the nutritional value and adaptive tolerance to stress in amaranth species.
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Affiliation(s)
- Esaú Bojórquez-Velázquez
- Instituto Potosino de Investigación Científica y Tecnológica, A.C, 78216 San Luis Potosí, Mexico
| | - Alberto Barrera-Pacheco
- Instituto Potosino de Investigación Científica y Tecnológica, A.C, 78216 San Luis Potosí, Mexico
| | - Eduardo Espitia-Rangel
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, 56250 Texcoco, Estado de México Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, 36821 Guanajuato, Mexico
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25
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Cruz-Magalhães V, Nieto-Jacobo MF, van Zijll de Jong E, Rostás M, Padilla-Arizmendi F, Kandula D, Kandula J, Hampton J, Herrera-Estrella A, Steyaert JM, Stewart A, Loguercio LL, Mendoza-Mendoza A. The NADPH Oxidases Nox1 and Nox2 Differentially Regulate Volatile Organic Compounds, Fungistatic Activity, Plant Growth Promotion and Nutrient Assimilation in Trichoderma atroviride. Front Microbiol 2019; 9:3271. [PMID: 30728815 PMCID: PMC6351448 DOI: 10.3389/fmicb.2018.03271] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/17/2018] [Indexed: 12/04/2022] Open
Abstract
In eukaryotic systems, membrane-bound NADPH oxidases (Nox) generate reactive oxygen species (ROS) as a part of normal physiological functions. In the soil-borne mycoparasitic and plant facultative symbiont Trichoderma atroviride, Nox1 and the regulator NoxR are involved in differentiation induced by mechanical damage, while the role of Nox2 has not been determined. The knock-out strains Δnox1, ΔnoxR and Δnox2 were compared to the parental strain (WT) in their ability to grow and conidiate under a series of stress conditions (osmotic, oxidative, membrane, and cell-wall stresses). All three genes were differentially involved in the stress-response phenotypes. In addition, several interactive experiments with biotic factors (plant seedlings and other fungi) were performed comparing the mutant phenotypes with the WT, which was used as the reference strain. Δnox1 and ΔnoxR significantly reduced the antagonistic activity of T. atroviride against Rhizoctonia solani and Sclerotinia sclerotiorum in direct confrontation assays, but Δnox2 showed similar activity to the WT. The Δnox1, ΔnoxR, and Δnox2 mutants showed quantitative differences in the emission of several volatile organic compounds (VOCs). The effects of a blend of these volatiles on plant-growth promotion of Arabidopsis thaliana seedlings were determined in closed-chamber experiments. The increase in root and shoot biomass induced by T. atroviride VOCs was significantly lowered by ΔnoxR and Δnox1, but not by Δnox2. In terms of fungistatic activity at a distance, Δnox2 had a significant reduction in this trait against R. solani and S. sclerotiorum, while fungistasis was highly increased by ΔnoxR and Δnox1. Identification and quantification of individual VOCs in the blends emitted by the strains was performed by GC-MS and the patterns of variation observed for individual volatiles, such as 6-Pentyl-2H-pyran-2-one (6PP-1) and (E)-6-Pent-1-enylpyran-2-one (6PP-2) were consistent with their negative effects in plant-growth promotion and positive effects in fungistasis at a distance. Nox1 and NoxR appear to have a ubiquitous regulatory role of in a variety of developmental and interactive processes in T. atroviride either as positive or negative modulators. Nox2 may also have a role in regulating production of VOCs with fungistatic activity.
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Affiliation(s)
- Valter Cruz-Magalhães
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand.,Department of Biological Sciences (DCB), State University of Santa Cruz (UESC), Ilhéus, Brazil
| | | | | | - Michael Rostás
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | | | - Diwakar Kandula
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Janaki Kandula
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - John Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | | | | | - Alison Stewart
- The Foundation for Arable Research (FAR), Christchurch, New Zealand
| | - Leandro Lopes Loguercio
- Department of Biological Sciences (DCB), State University of Santa Cruz (UESC), Ilhéus, Brazil
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26
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Abstract
Because of the need to provide food for the growing population, agricultural activity is faced with the huge challenge of counteracting the negative effects generated by adverse environmental factors and diseases caused by pathogens on crops, while avoiding environmental pollution due to the excessive use of agrochemicals. The exploitation of biological systems that naturally increase plant vigor, preparing them against biotic and abiotic stressors that also promote their growth and productivity represents a useful and viable strategy to help face these challenges. Fungi from the genus Trichoderma have been widely used in agriculture as biocontrol agents because of their mycoparasitic capacity and ability to improve plant health and protection against phytopathogens, which makes it an excellent plant symbiont. The mechanisms employed by Trichoderma include secretion of effector molecules and secondary metabolites that mediate the beneficial interaction of Trichoderma with plants, providing tolerance to biotic and abiotic stresses. Here we discuss the most recent advances in understanding the mechanisms employed by this opportunistic plant symbiont as biocontrol agent and plant growth promoter. In addition, through genome mining we approached a less explored factor that Trichoderma could be using to become successful plant symbionts, the production of phytohormones-auxins, cytokinins, abscisic acid, gibberellins, among others. This approach allowed us to detect sets of genes encoding proteins potentially involved in phytohormone biosynthesis and signaling. We discuss the implications of these findings in the physiology of the fungus and in the establishment of its interaction with plants.
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Affiliation(s)
- Paulina Guzmán-Guzmán
- First and third authors: Departamento de Biología, DCNyE Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n. CP 36050, Guanajuato, Gto., México; and second and fourth authors: Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824, Irapuato, Gto., México
| | - María Daniela Porras-Troncoso
- First and third authors: Departamento de Biología, DCNyE Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n. CP 36050, Guanajuato, Gto., México; and second and fourth authors: Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824, Irapuato, Gto., México
| | - Vianey Olmedo-Monfil
- First and third authors: Departamento de Biología, DCNyE Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n. CP 36050, Guanajuato, Gto., México; and second and fourth authors: Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824, Irapuato, Gto., México
| | - Alfredo Herrera-Estrella
- First and third authors: Departamento de Biología, DCNyE Campus Guanajuato, Universidad de Guanajuato, Noria Alta s/n. CP 36050, Guanajuato, Gto., México; and second and fourth authors: Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824, Irapuato, Gto., México
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27
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Medina-Castellanos E, Villalobos-Escobedo JM, Riquelme M, Read ND, Abreu-Goodger C, Herrera-Estrella A. Danger signals activate a putative innate immune system during regeneration in a filamentous fungus. PLoS Genet 2018; 14:e1007390. [PMID: 30500812 PMCID: PMC6291166 DOI: 10.1371/journal.pgen.1007390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/12/2018] [Accepted: 10/19/2018] [Indexed: 01/24/2023] Open
Abstract
The ability to respond to injury is a biological process shared by organisms of different kingdoms that can even result in complete regeneration of a part or structure that was lost. Due to their immobility, multicellular fungi are prey to various predators and are therefore constantly exposed to mechanical damage. Nevertheless, our current knowledge of how fungi respond to injury is scarce. Here we show that activation of injury responses and hyphal regeneration in the filamentous fungus Trichoderma atroviride relies on the detection of two danger or alarm signals. As an early response to injury, we detected a transient increase in cytosolic free calcium ([Ca2+]c) that was promoted by extracellular ATP, and which is likely regulated by a mechanism of calcium-induced calcium-release. In addition, we demonstrate that the mitogen activated protein kinase Tmk1 plays a key role in hyphal regeneration. Calcium- and Tmk1-mediated signaling cascades activated major transcriptional changes early following injury, including induction of a set of regeneration associated genes related to cell signaling, stress responses, transcription regulation, ribosome biogenesis/translation, replication and DNA repair. Interestingly, we uncovered the activation of a putative fungal innate immune response, including the involvement of HET domain genes, known to participate in programmed cell death. Our work shows that fungi and animals share danger-signals, signaling cascades, and the activation of the expression of genes related to immunity after injury, which are likely the result of convergent evolution. The idea of regenerating lost body parts has always fascinated humans due to its impact on human health. Recently, the study of the response to damage has gained importance not only in regenerative medicine, but also in organ transplantation. We have established a microbial model that given its relative simplicity and ease to work with, promises to accelerate the advance of our understanding of damage responses and regeneration. We show that activation of injury responses and hyphal regeneration in a filamentous fungus relies on the detection of danger (also called alarm) signals also used by plants and animals. Finally, we discovered a set of genes that become active in response to injury, including those putatively participating in the immune response.
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Affiliation(s)
- Elizabeth Medina-Castellanos
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Libramiento Norte Carretera Irapuato-León, Irapuato, Gto, Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Libramiento Norte Carretera Irapuato-León, Irapuato, Gto, Mexico
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana No. 3918, Ensenada, Baja California, Mexico
| | - Nick D. Read
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Libramiento Norte Carretera Irapuato-León, Irapuato, Gto, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav, Libramiento Norte Carretera Irapuato-León, Irapuato, Gto, Mexico
- * E-mail:
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28
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Abstract
A recent study identifies a locus controlling seed dormancy – a key trait of the ‘domestication syndrome’ – that has been selected for in parallel across multiple crop families.
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Affiliation(s)
- Martha Rendón-Anaya
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7080, SE-750 07, Uppsala, Sweden
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821 Irapuato, Guanajuato, Mexico.
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29
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López-Muñoz A, Nicolás FE, García-Moreno D, Pérez-Oliva AB, Navarro-Mendoza MI, Hernández-Oñate MA, Herrera-Estrella A, Torres-Martínez S, Ruiz-Vázquez RM, Garre V, Mulero V. An Adult Zebrafish Model Reveals that Mucormycosis Induces Apoptosis of Infected Macrophages. Sci Rep 2018; 8:12802. [PMID: 30143654 PMCID: PMC6109148 DOI: 10.1038/s41598-018-30754-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Mucormycosis is a life-threatening fungal infection caused by various ubiquitous filamentous fungi of the Mucorales order, although Rhizopus spp. and Mucor spp. are the most prevalent causal agents. The limited therapeutic options available together with a rapid progression of the infection and a difficult early diagnosis produce high mortality. Here, we developed an adult zebrafish model of Mucor circinelloides infection which allowed us to confirm the link between sporangiospore size and virulence. Transcriptomic studies revealed a local, strong inflammatory response of the host elicited after sporangiospore germination and mycelial tissue invasion, while avirulent and UV-killed sporangiospores failed to induce inflammation and were rapidly cleared. Of the 857 genes modulated by the infection, those encoding cytokines, complement factors, peptidoglycan recognition proteins, and iron acquisition are particularly interesting. Furthermore, neutrophils and macrophages were similarly recruited independently of sporangiospore virulence and viability, which results in a robust depletion of both cell types in the hematopoietic compartment. Strikingly, our model also reveals for the first time the ability of mucormycosis to induce the apoptosis of recruited macrophages but not neutrophils. The induction of macrophage apoptosis, therefore, might represent a key virulence mechanism of these fungal pathogens, providing novel targets for therapeutic intervention in this lethal infection.
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Affiliation(s)
- Azucena López-Muñoz
- Department of Cell Biology and Histology, University of Murcia, IMIB-Arrixaca, 30100, Murcia, Spain
| | - Francisco E Nicolás
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100, Murcia, Spain
| | - Diana García-Moreno
- Department of Cell Biology and Histology, University of Murcia, IMIB-Arrixaca, 30100, Murcia, Spain
| | - Ana B Pérez-Oliva
- Department of Cell Biology and Histology, University of Murcia, IMIB-Arrixaca, 30100, Murcia, Spain
| | - María I Navarro-Mendoza
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100, Murcia, Spain
| | | | | | - Santiago Torres-Martínez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100, Murcia, Spain
| | - Rosa M Ruiz-Vázquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100, Murcia, Spain
| | - Victoriano Garre
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, 30100, Murcia, Spain.
| | - Victoriano Mulero
- Department of Cell Biology and Histology, University of Murcia, IMIB-Arrixaca, 30100, Murcia, Spain.
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Riquelme M, Aguirre J, Bartnicki-García S, Braus GH, Feldbrügge M, Fleig U, Hansberg W, Herrera-Estrella A, Kämper J, Kück U, Mouriño-Pérez RR, Takeshita N, Fischer R. Fungal Morphogenesis, from the Polarized Growth of Hyphae to Complex Reproduction and Infection Structures. Microbiol Mol Biol Rev 2018; 82:e00068-17. [PMID: 29643171 PMCID: PMC5968459 DOI: 10.1128/mmbr.00068-17] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Filamentous fungi constitute a large group of eukaryotic microorganisms that grow by forming simple tube-like hyphae that are capable of differentiating into more-complex morphological structures and distinct cell types. Hyphae form filamentous networks by extending at their tips while branching in subapical regions. Rapid tip elongation requires massive membrane insertion and extension of the rigid chitin-containing cell wall. This process is sustained by a continuous flow of secretory vesicles that depends on the coordinated action of the microtubule and actin cytoskeletons and the corresponding motors and associated proteins. Vesicles transport cell wall-synthesizing enzymes and accumulate in a special structure, the Spitzenkörper, before traveling further and fusing with the tip membrane. The place of vesicle fusion and growth direction are enabled and defined by the position of the Spitzenkörper, the so-called cell end markers, and other proteins involved in the exocytic process. Also important for tip extension is membrane recycling by endocytosis via early endosomes, which function as multipurpose transport vehicles for mRNA, septins, ribosomes, and peroxisomes. Cell integrity, hyphal branching, and morphogenesis are all processes that are largely dependent on vesicle and cytoskeleton dynamics. When hyphae differentiate structures for asexual or sexual reproduction or to mediate interspecies interactions, the hyphal basic cellular machinery may be reprogrammed through the synthesis of new proteins and/or the modification of protein activity. Although some transcriptional networks involved in such reprogramming of hyphae are well studied in several model filamentous fungi, clear connections between these networks and known determinants of hyphal morphogenesis are yet to be established.
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Affiliation(s)
- Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Jesús Aguirre
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Salomon Bartnicki-García
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Ursula Fleig
- Institute for Functional Genomics of Microorganisms, Heinrich Heine University Düsseldorf, Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Wilhelm Hansberg
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Jörg Kämper
- Karlsruhe Institute of Technology-South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
| | - Ulrich Kück
- Ruhr University Bochum, Lehrstuhl für Allgemeine und Molekulare Botanik, Bochum, Germany
| | - Rosa R Mouriño-Pérez
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Norio Takeshita
- University of Tsukuba, Faculty of Life and Environmental Sciences, Tsukuba, Japan
| | - Reinhard Fischer
- Karlsruhe Institute of Technology-South Campus, Institute for Applied Biosciences, Karlsruhe, Germany
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31
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Pelagio-Flores R, Esparza-Reynoso S, Garnica-Vergara A, López-Bucio J, Herrera-Estrella A. Trichoderma-Induced Acidification Is an Early Trigger for Changes in Arabidopsis Root Growth and Determines Fungal Phytostimulation. Front Plant Sci 2017; 8:822. [PMID: 28567051 PMCID: PMC5434454 DOI: 10.3389/fpls.2017.00822] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/02/2017] [Indexed: 05/03/2023]
Abstract
Trichoderma spp. are common rhizosphere inhabitants widely used as biological control agents and their role as plant growth promoting fungi has been established. Although soil pH influences several fungal and plant functional traits such as growth and nutrition, little is known about its influence in rhizospheric or mutualistic interactions. The role of pH in the Trichoderma-Arabidopsis interaction was studied by determining primary root growth and lateral root formation, root meristem status and cell viability, quiescent center (QC) integrity, and auxin inducible gene expression. Primary root growth phenotypes in wild type seedlings and STOP1 mutants allowed identification of a putative root pH sensing pathway likely operating in plant-fungus recognition. Acidification by Trichoderma induced auxin redistribution within Arabidopsis columella root cap cells, causing root tip bending and growth inhibition. Root growth stoppage correlated with decreased cell division and with the loss of QC integrity and cell viability, which were reversed by buffering the medium. In addition, stop1, an Arabidopsis mutant sensitive to low pH, was oversensitive to T. atroviride primary root growth repression, providing genetic evidence that a pH root sensing mechanism reprograms root architecture during the interaction. Our results indicate that root sensing of pH mediates the interaction of Trichoderma with plants.
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Affiliation(s)
- Ramón Pelagio-Flores
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPNIrapuato, México
| | - Saraí Esparza-Reynoso
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de HidalgoMorelia, México
| | - Amira Garnica-Vergara
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de HidalgoMorelia, México
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de HidalgoMorelia, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPNIrapuato, México
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32
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Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol 2017; 18:60. [PMID: 28356141 PMCID: PMC5370463 DOI: 10.1186/s13059-017-1190-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1190-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Josaphat M Montero-Vargas
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Soledad Saburido-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José Juan Ordaz-Ortiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | | | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, 95616-8780, USA
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
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33
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Polaino S, Villalobos-Escobedo JM, Shakya VPS, Miralles-Durán A, Chaudhary S, Sanz C, Shahriari M, Luque EM, Eslava AP, Corrochano LM, Herrera-Estrella A, Idnurm A. A Ras GTPase associated protein is involved in the phototropic and circadian photobiology responses in fungi. Sci Rep 2017; 7:44790. [PMID: 28322269 PMCID: PMC5359613 DOI: 10.1038/srep44790] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 02/14/2017] [Indexed: 01/09/2023] Open
Abstract
Light is an environmental signal perceived by most eukaryotic organisms and that can have major impacts on their growth and development. The MadC protein in the fungus Phycomyces blakesleeanus (Mucoromycotina) has been postulated to form part of the photosensory input for phototropism of the fruiting body sporangiophores, but the madC gene has remained unidentified since the 1960s when madC mutants were first isolated. In this study the madC gene was identified by positional cloning. All madC mutant strains contain loss-of-function point mutations within a gene predicted to encode a GTPase activating protein (GAP) for Ras. The madC gene complements the Saccharomyces cerevisiae Ras-GAP ira1 mutant and the encoded MadC protein interacts with P. blakesleeanus Ras homologs in yeast two-hybrid assays, indicating that MadC is a regulator of Ras signaling. Deletion of the homolog in the filamentous ascomycete Neurospora crassa affects the circadian clock output, yielding a pattern of asexual conidiation similar to a ras-1 mutant that is used in circadian studies in N. crassa. Thus, MadC is unlikely to be a photosensor, yet is a fundamental link in the photoresponses from blue light perceived by the conserved White Collar complex with Ras signaling in two distantly-related filamentous fungal species.
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Affiliation(s)
- Silvia Polaino
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, USA
| | - José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Irapuato, Guanajuato, Mexico
| | - Viplendra P S Shakya
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, USA
| | | | - Suman Chaudhary
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, USA
| | - Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Mahdi Shahriari
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Eva M Luque
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain
| | - Arturo P Eslava
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Irapuato, Guanajuato, Mexico
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, USA.,School of BioSciences, University of Melbourne, Australia
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Guzmán-Guzmán P, Alemán-Duarte MI, Delaye L, Herrera-Estrella A, Olmedo-Monfil V. Identification of effector-like proteins in Trichoderma spp. and role of a hydrophobin in the plant-fungus interaction and mycoparasitism. BMC Genet 2017; 18:16. [PMID: 28201981 PMCID: PMC5310080 DOI: 10.1186/s12863-017-0481-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 02/07/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic interactions. Such interactions depend on signal exchange between both participants and can be mediated by effector proteins that alter the host cell structure and function, allowing the establishment of the relationship. The main purpose of this work was to identify, using computational methods, candidates of effector proteins from T. virens, T. atroviride and T. reesei, validate the expression of some of the genes during a beneficial interaction and mycoparasitism and to define the biological function for one of them. RESULTS We defined a catalogue of putative effector proteins from T. virens, T. atroviride and T. reesei. We further validated the expression of 16 genes encoding putative effector proteins from T. virens and T. atroviride during the interaction with the plant Arabidopsis thaliana, and with two anastomosis groups of the phytopathogenic fungus Rhizoctonia solani. We found genes which transcript levels are modified in response to the presence of both plant fungi, as well as genes that respond only to either a plant or a fungal host. Further, we show that overexpression of the gene tvhydii1, a Class II hydrophobin family member, enhances the antagonistic activity of T. virens against R. solani AG2. Further, deletion of tvhydii1 results in reduced colonization of plant roots, while its overexpression increases it. CONCLUSIONS Our results show that Trichoderma is able to respond in different ways to the presence of a plant or a fungal host, and it can even distinguish between different strains of fungi of a given species. The putative effector proteins identified here may play roles in preventing perception of the fungus by its hosts, favoring host colonization or protecting it from the host's defense response. Finally, the novel effector protein TVHYDII1 plays a role in plant root colonization by T, virens, and participates in its antagonistic activity against R. solani.
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Affiliation(s)
- Paulina Guzmán-Guzmán
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Gto, Mexico
| | - Mario Iván Alemán-Duarte
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
- Unidad Irapuato, Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Luis Delaye
- Unidad Irapuato, Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Gto, Mexico
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35
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Villalobos-Escobedo JM, Herrera-Estrella A, Carreras-Villaseñor N. The interaction of fungi with the environment orchestrated by RNAi. Mycologia 2017; 108:556-71. [DOI: 10.3852/15-246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad. Cinvestav Campus Guanajuato. Km 9.6 Libramiento Norte, carretera Irapuato-León. 36821 Irapuato, Guanajuato, Mexico
| | - Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato S/N, 36821 Irapuato, Guanajuato, Mexico
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36
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Garrido-Bazán V, Téllez-Téllez M, Herrera-Estrella A, Díaz-Godínez G, Nava-Galicia S, Villalobos-López MÁ, Arroyo-Becerra A, Bibbins-Martínez M. Effect of textile dyes on activity and differential regulation of laccase genes from Pleurotus ostreatus grown in submerged fermentation. AMB Express 2016; 6:93. [PMID: 27718214 PMCID: PMC5055507 DOI: 10.1186/s13568-016-0263-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/28/2016] [Indexed: 09/01/2023] Open
Abstract
This research was conducted to extend the knowledge on the differential regulation of laccase genes in response to dyes. In order to accomplish this, we analyzed both, the expression of five laccase genes by real time RT-qPCR, and also the laccase activity and isoforms patterns during the time-course of a Pleurotus ostreatus submerged fermentation supplemented with either acetyl yellow G (AYG) or remazol brilliant blue R (RBBR) dyes. For the purpose of obtaining a stable reference gene for optimal normalization of RT-quantitative PCR gene expression assays, we tested four candidate reference genes. As a result of this analysis, gpd was selected as reference index for data normalization. The addition of dyes had an induction effect on the enzymatic activity and also modified the zymogram profile. Fermentation with RBBR showed the highest laccase activity and number of isoforms along the course of the fermentation. Laccase gene expression profiles displayed up/down regulation along the fermentation time in four laccase genes (pox4, pox3, poxa1b and pox2), while pox1 was not expressed in either of the fermentation conditions. AYG addition caused the highest induction and repression levels for genes pox3 and poxa1b respectively. The expression level for all genes in the presence of RBBR were lower than in AYG, being in both conditions this response growth time dependent. These results show the influence of the nature of dyes on the induction level of laccase activity and on the differential regulation of the laccase genes expression in P. ostreatus.
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37
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Paolinelli-Alfonso M, Villalobos-Escobedo JM, Rolshausen P, Herrera-Estrella A, Galindo-Sánchez C, López-Hernández JF, Hernandez-Martinez R. Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response. BMC Genomics 2016; 17:615. [PMID: 27514986 PMCID: PMC4981995 DOI: 10.1186/s12864-016-2952-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lasiodiplodia theobromae is a fungus of the Botryosphaeriaceae that causes grapevine vascular disease, especially in regions with hot climates. Fungi in this group often remain latent within their host and become virulent under abiotic stress. Transcriptional regulation analysis of L. theobromae exposed to heat stress (HS) was first carried out in vitro in the presence of grapevine wood (GW) to identify potential pathogenicity genes that were later evaluated for in planta expression. RESULTS A total of 19,860 de novo assembled transcripts were obtained, forty-nine per cent of which showed homology to the Botryosphaeriaceae fungi, Neofusicoccum parvum or Macrophomina phaseolina. Three hundred ninety-nine have homology with genes involved in pathogenic processes and several belonged to expanded gene families in others fungal grapevine vascular pathogens. Gene expression analysis showed changes in fungal metabolism of phenolic compounds; where genes encoding for enzymes, with the ability to degrade salicylic acid (SA) and plant phenylpropanoid precursors, were up-regulated during in vitro HS response, in the presence of GW. These results suggest that the fungal L-tyrosine catabolism pathway could help the fungus to remove phenylpropanoid precursors thereby evading the host defense response. The in planta up-regulation of salicylate hydroxylase, intradiol ring cleavage dioxygenase and fumarylacetoacetase encoding genes, further supported this hypothesis. Those genes were even more up-regulated in HS-stressed plants, suggesting that fungus takes advantage of the increased phenylpropanoid precursors produced under stress. Pectate lyase was up-regulated while a putative amylase was down-regulated in planta, this could be associated with an intercellular growth strategy during the first stages of colonization. CONCLUSIONS L. theobromae transcriptome was established and validated. Its usefulness was demonstrated through the identification of genes expressed during the infection process. Our results support the hypothesis that heat stress facilitates fungal colonization, because of the fungus ability to use the phenylpropanoid precursors and SA, both compounds known to control host defense.
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Affiliation(s)
- Marcos Paolinelli-Alfonso
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
| | - José Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Philippe Rolshausen
- Department of Botany and Plant Sciences,University of California Riverside, Riverside, 92521 CA USA
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Clara Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
| | - José Fabricio López-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del I. P. N., Irapuato, Gto 36821 Mexico
| | - Rufina Hernandez-Martinez
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, BC 22860 Mexico
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Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol 2016; 26:1577-1584. [PMID: 27238284 DOI: 10.1016/j.cub.2016.04.038] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 02/03/2023]
Abstract
Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.
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Affiliation(s)
- Luis M Corrochano
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Polaino
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - M Isabel Álvarez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Javier Avalos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gertraud Burger
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - Lola P Camino
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - David Cánovas
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Enrique Cerdá-Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Angel Domínguez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Arturo P Eslava
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Fabian Glaser
- Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Gabriel Gutiérrez
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enrique A Iturriaga
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - B Franz Lang
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Wenjun Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Sergio López-García
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Eva M Luque
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Ana T Marcos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA
| | - Humberto R Medina
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | | | - Atsushi Miyazaki
- Department of Biological Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki 986-8580, Japan
| | - Elisa Muñoz-Torres
- Departamento de Biología Celular y Patología, Facultad de Medicina, Universidad de Salamanca, Avenida Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José A Oguiza
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - María Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | - Lucila Ortiz-Castellanos
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Antonio G Pisabarro
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Julio Rodríguez-Romero
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Rosa Ruiz-Vázquez
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mahdi Shahriari
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Ekaterina Shelest
- Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Fátima Silva-Franco
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Khajamohiddin Syed
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Víctor G Tagua
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Nicholas J Talbot
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Michael R Thon
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Hope Tice
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jagjit S Yadav
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Edward L Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611-8525, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | | | - Alexander Idnurm
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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Cetz-Chel JE, Balcázar-López E, Esquivel-Naranjo EU, Herrera-Estrella A. The Trichoderma atroviride putative transcription factor Blu7 controls light responsiveness and tolerance. BMC Genomics 2016; 17:327. [PMID: 27142227 PMCID: PMC4855978 DOI: 10.1186/s12864-016-2639-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 04/22/2016] [Indexed: 11/23/2022] Open
Abstract
Background Most living organisms use sunlight as a source of energy and/or information about their environment. Consequently, they have developed mechanisms to sense light quality and quantity. In the fungus Trichoderma atroviride blue-light is perceived through the Blue Light Regulator Complex, which in turn up-regulates a set of genes (blu) and down-regulates another set (bld), triggering asexual reproduction. To gain insight into this process, we characterized the blu7 gene, which encodes a protein containing a C2H2 zinc finger domain. Results Δblu7 mutants show reduced conidiation at low light fluences, which is still clear even when exposed to saturating light. For the first time we show a genome wide survey of light regulated gene expression in T. atroviride, including RNA-seq analyses of the wild type and the Δblu7 strains after brief exposure to blue-light. Our data show a reduction in the number of induced genes and an increase in down-regulated genes in the mutant. Light activates stress responses and several metabolic processes in the wild type strain that are no longer activated in the mutant. In agreement with the misregulation of metabolic processes, continuous exposure to white light strongly inhibited growth of the ∆blu7 mutant, in a carbon source dependent fashion. RNA-seq analyses under constant white light using glucose as sole carbon source revealed that localization and transport process present the opposite regulation pattern in the ∆blu7 and wild type strains. Genes related to amino acid, sugar and general transporters were enriched in the induced genes in the mutant and the repressed genes of the wild type. Peptone supplemented in the media restored growth of the ∆blu7 mutant in constant light, suggesting a role of Blu7 in the regulation of nitrogen metabolism in the presence of light. Conclusions Blu7 appears to regulate light sensitivity in terms of induction of conidiation, and to play a major role in supporting growth under continuous exposure to light. The diminished conidiation observed in ∆blu7 mutants is likely due to misregulation of the cAMP signaling pathway and ROS production, whereas their low tolerance to continuous exposure to light indicates that Blu7 is required for adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2639-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José E Cetz-Chel
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
| | - Edgar Balcázar-López
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico.,Present Address: Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, 76230, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Sede Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, 36821, Irapuato, Guanajuato, Mexico.
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Esquivel-Naranjo EU, García-Esquivel M, Medina-Castellanos E, Correa-Pérez VA, Parra-Arriaga JL, Landeros-Jaime F, Cervantes-Chávez JA, Herrera-Estrella A. A Trichoderma atroviride stress-activated MAPK pathway integrates stress and light signals. Mol Microbiol 2016; 100:860-76. [PMID: 26878111 DOI: 10.1111/mmi.13355] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2016] [Indexed: 11/27/2022]
Abstract
Cells possess stress-activated protein kinase (SAPK) signalling pathways, which are activated practically in response to any cellular insult, regulating responses for survival and adaptation to harmful environmental changes. To understand the function of SAPK pathways in T. atroviride, mutants lacking the MAPKK Pbs2 and the MAPK Tmk3 were analysed under several cellular stresses, and in their response to light. All mutants were highly sensitive to cellular insults such as osmotic and oxidative stress, cell wall damage, high temperature, cadmium, and UV irradiation. Under oxidative stress, the Tmk3 pathway showed specific roles during development, which in conidia are essential for tolerance to oxidant agents and appear to play a minor role in mycelia. The function of this pathway was more evident in Δpbs2 and Δtmk3 mutant strains when combining oxidative stress or cell wall damage with light. Light stimulates tolerance to osmotic stress through Tmk3 independently of the photoreceptor Blr1. Strikingly, photoconidiation and expression of blue light regulated genes was severally affected in Δtmk3 and Δpbs2 strains, indicating that this pathway regulates light responses. Furthermore, Tmk3 was rapidly phosphorylated upon light exposure. Thus, our data indicate that Tmk3 signalling cooperates with the Blr photoreceptor complex in the activation of gene expression.
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Affiliation(s)
- Edgardo Ulises Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, Irapuato, México.,Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, México
| | - Mónica García-Esquivel
- Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV-Irapuato, Irapuato, México
| | | | - Víctor Alejandro Correa-Pérez
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, México
| | - Jorge Luis Parra-Arriaga
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, México
| | - Fidel Landeros-Jaime
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, México
| | - José Antonio Cervantes-Chávez
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Querétaro, Querétaro, México
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
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Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
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García-Esquivel M, Esquivel-Naranjo EU, Hernández-Oñate MA, Ibarra-Laclette E, Herrera-Estrella A. The Trichoderma atroviride cryptochrome/photolyase genes regulate the expression of blr1-independent genes both in red and blue light. Fungal Biol 2016; 120:500-512. [PMID: 27020152 DOI: 10.1016/j.funbio.2016.01.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/10/2015] [Accepted: 01/08/2016] [Indexed: 12/11/2022]
Abstract
Quantitative transcriptome analysis led to the identification of 331 transcripts regulated by white light. Evaluation of the response to white light in mutants affected in the previously characterized blue-light receptor Blr1, demonstrated the existence of both Blr1-dependent and independent responses. Functional categorization of the light responsive genes indicated the effect of light on regulation of various transcription factors, regulators of chromatin structure, signaling pathways, genes related to different kinds of stress, metabolism, redox adjustment, and cell cycle among others. In order to establish the participation of other photoreceptors, gene expression was validated in response to different wavelengths. Gene regulation by blue and red light suggests the involvement of several photoreceptors in integrating light signals of different wavelengths in Trichoderma atroviride. Functional analysis of potential blue light photoreceptors suggests that several perception systems for different wavelengths are involved in the response to light. Deletion of cry1, one of the potential photoreceptors, resulted in severe reduction in the photoreactivation capacity of the fungus, as well as a change in gene expression under blue and red light.
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Affiliation(s)
- Mónica García-Esquivel
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Gto., Mexico
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Gto., Mexico
| | - Miguel A Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Gto., Mexico
| | - Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Gto., Mexico; Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Ver., Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Gto., Mexico.
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Ibarra-Laclette E, Zamudio-Hernández F, Pérez-Torres CA, Albert VA, Ramírez-Chávez E, Molina-Torres J, Fernández-Cortes A, Calderón-Vázquez C, Olivares-Romero JL, Herrera-Estrella A, Herrera-Estrella L. De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. BMC Genomics 2015; 16:657. [PMID: 26330142 PMCID: PMC4557841 DOI: 10.1186/s12864-015-1821-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 08/07/2015] [Indexed: 12/04/2022] Open
Abstract
Background Lophophora williamsii (commonly named peyote) is a small, spineless cactus with psychoactive alkaloids, particularly mescaline. Peyote utilizes crassulacean acid metabolism (CAM), an alternative form of photosynthesis that exists in succulents such as cacti and other desert plants. Therefore, its transcriptome can be considered an important resource for future research focused on understanding how these plants make more efficient use of water in marginal environments and also for research focused on better understanding of the overall mechanisms leading to production of plant natural products and secondary metabolites. Results In this study, two cDNA libraries were generated from L. williamsii. These libraries, representing buttons (tops of stems) and roots were sequenced using different sequencing platforms (GS-FLX, GS-Junior and PGM, respectively). A total of 5,541,550 raw reads were generated, which were assembled into 63,704 unigenes with an average length of 564.04 bp. A total of 25,149 unigenes (62.19 %) was annotated using public databases. 681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots. Some of the major alkaloids, including mescaline, were identified by GC-MS and relevant metabolic pathways were reconstructed using the Kyoto encyclopedia of genes and genomes database (KEGG). Subsequently, the expression patterns of preferentially expressed genes putatively involved in mescaline production were examined and validated by qRT-PCR. Conclusions High throughput transcriptome sequencing (RNA-seq) analysis allowed us to efficiently identify candidate genes involved in mescaline biosynthetic pathway in L. williamsii; these included tyrosine/DOPA decarboxylase, hydroxylases, and O-methyltransferases. This study sets the theoretical foundation for bioassay design directed at confirming the participation of these genes in mescaline production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1821-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Claudia Anahí Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México. .,Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México. .,Investigador Cátedra CONACyT, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, México.
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, 14260, USA.
| | - Enrique Ramírez-Chávez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Jorge Molina-Torres
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36821, Irapuato, Guanajuato, México.
| | - Araceli Fernández-Cortes
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Carlos Calderón-Vázquez
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Instituto Politécnico Nacional, 81000, Guasave, Sinaloa, México.
| | | | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, México.
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Salas-Marina MA, Isordia-Jasso MI, Islas-Osuna MA, Delgado-Sánchez P, Jiménez-Bremont JF, Rodríguez-Kessler M, Rosales-Saavedra MT, Herrera-Estrella A, Casas-Flores S. The Epl1 and Sm1 proteins from Trichoderma atroviride and Trichoderma virens differentially modulate systemic disease resistance against different life style pathogens in Solanum lycopersicum. Front Plant Sci 2015; 6:77. [PMID: 25755658 PMCID: PMC4337343 DOI: 10.3389/fpls.2015.00077] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/30/2015] [Indexed: 05/07/2023]
Abstract
Fungi belonging to the genus Trichoderma, commonly found in soil or colonizing plant roots, exert beneficial effects on plants, including the promotion of growth and the induction of resistance to disease. T. virens and T. atroviride secrete the proteins Sm1 and Epl1, respectively, which elicit local and systemic disease resistance in plants. In this work, we show that these fungi promote growth in tomato (Solanum lycopersicum) plants. T. virens was more effective than T. atroviride in promoting biomass gain, and both fungi were capable of inducing systemic protection in tomato against Alternaria solani, Botrytis cinerea, and Pseudomonas syringae pv. tomato (Pst DC3000). Deletion (KO) of epl1 in T. atroviride resulted in diminished systemic protection against A. solani and B. cinerea, whereas the T. virens sm1 KO strain was less effective in protecting tomato against Pst DC3000 and B. cinerea. Importantly, overexpression (OE) of epl1 and sm1 led to an increase in disease resistance against all tested pathogens. Although the Trichoderma WT strains induced both systemic acquired resistance (SAR)- and induced systemic resistance (ISR)-related genes in tomato, inoculation of plants with OE and KO strains revealed that Epl1 and Sm1 play a minor role in the induction of these genes. However, we found that Epl1 and Sm1 induce the expression of a peroxidase and an α-dioxygenase encoding genes, respectively, which could be important for tomato protection by Trichoderma spp. Altogether, these observations indicate that colonization by beneficial and/or infection by pathogenic microorganisms dictates many of the outcomes in plants, which are more complex than previously thought.
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Affiliation(s)
- Miguel A. Salas-Marina
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | - María I. Isordia-Jasso
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | - María A. Islas-Osuna
- Laboratorio de Genética y Biología Molecular, Centro de Investigación en Alimentación y Desarrollo, Dirección Tecnología de Alimentos de Origen VegetalHermosillo, Mexico
| | - Pablo Delgado-Sánchez
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | - Juan F. Jiménez-Bremont
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | - Margarita Rodríguez-Kessler
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | - María T. Rosales-Saavedra
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
| | | | - Sergio Casas-Flores
- Laboratorio de Genómica Funcional y Comparativa, División de Biología Molecular, Instituto Potosino de Investigación Científica y TecnológicaSan Luis Potosí, Mexico
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Guzmán-Moreno J, Flores-Martínez A, Brieba LG, Herrera-Estrella A. The Trichoderma reesei Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity. PLoS One 2014; 9:e100625. [PMID: 24964051 PMCID: PMC4070973 DOI: 10.1371/journal.pone.0100625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/28/2014] [Indexed: 12/24/2022] Open
Abstract
DNA-photolyases use UV-visible light to repair DNA damage caused by UV radiation. The two major types of DNA damage are cyclobutane pyrimidine dimers (CPD) and 6–4 photoproducts (6-4PP), which are repaired under illumination by CPD and 6–4 photolyases, respectively. Cryptochromes are proteins related to DNA photolyases with strongly reduced or lost DNA repair activity, and have been shown to function as blue-light photoreceptors and to play important roles in circadian rhythms in plants and animals. Both photolyases and cryptochromes belong to the cryptochrome/photolyase family, and are widely distributed in all organisms. Here we describe the characterization of cry1, a member of the cryptochrome/photolyase protein family of the filamentous fungus Trichoderma reesei. We determined that cry1 transcript accumulates when the fungus is exposed to light, and that such accumulation depends on the photoreceptor Blr1 and is modulated by Envoy. Conidia of cry1 mutants show decreased photorepair capacity of DNA damage caused by UV light. In contrast, strains over-expressing Cry1 show increased repair, as compared to the parental strain even in the dark. These observations suggest that Cry1 may be stimulating other systems involved in DNA repair, such as the nucleotide excision repair system. We show that Cry1, heterologously expressed and purified from E. coli, is capable of binding to undamaged and 6-4PP damaged DNA. Photorepair assays in vitro clearly show that Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, México
| | - Alberto Flores-Martínez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato, Guanajuato, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato, Guanajuato, México
- * E-mail:
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Medina-Castellanos E, Esquivel-Naranjo EU, Heil M, Herrera-Estrella A. Extracellular ATP activates MAPK and ROS signaling during injury response in the fungus Trichoderma atroviride. Front Plant Sci 2014; 5:659. [PMID: 25484887 PMCID: PMC4240048 DOI: 10.3389/fpls.2014.00659] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/04/2014] [Indexed: 05/17/2023]
Abstract
The response to mechanical damage is crucial for the survival of multicellular organisms, enabling their adaptation to hostile environments. Trichoderma atroviride, a filamentous fungus of great importance in the biological control of plant diseases, responds to mechanical damage by activating regenerative processes and asexual reproduction (conidiation). During this response, reactive oxygen species (ROS) are produced by the NADPH oxidase complex. To understand the underlying early signaling events, we evaluated molecules such as extracellular ATP (eATP) and Ca(2+) that are known to trigger wound-induced responses in plants and animals. Concretely, we investigated the activation of mitogen-activated protein kinase (MAPK) pathways by eATP, Ca(2+), and ROS. Indeed, application of exogenous ATP and Ca(2+) triggered conidiation. Furthermore, eATP promoted the Nox1-dependent production of ROS and activated a MAPK pathway. Mutants in the MAPK-encoding genes tmk1 and tmk3 were affected in wound-induced conidiation, and phosphorylation of both Tmk1 and Tmk3 was triggered by eATP. We conclude that in this fungus, eATP acts as a damage-associated molecular pattern (DAMP). Our data indicate the existence of an eATP receptor and suggest that in fungi, eATP triggers pathways that converge to regulate asexual reproduction genes that are required for injury-induced conidiation. By contrast, Ca(2+) is more likely to act as a downstream second messenger. The early steps of mechanical damage response in T. atroviride share conserved elements with those known from plants and animals.
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Affiliation(s)
| | | | - Martin Heil
- Departamento de Ingeniería Genética, CINVESTAV-IrapuatoIrapuato, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodeversidad, CINVESTAV-IrapuatoIrapuato, México
- *Correspondence: Alfredo Herrera-Estrella, Laboratorio Nacional de Genómica para la Biodeversidad, CINVESTAV-Irapuato, Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato 36821, Guanajuato, México e-mail:
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Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM, Abreu-Goodger C, Herrera-Estrella A. The RNAi machinery regulates growth and development in the filamentous fungusTrichoderma atroviride. Mol Microbiol 2013; 89:96-112. [DOI: 10.1111/mmi.12261] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Nohemi Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Edgardo U. Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - J. Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
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Abstract
Trichoderma species are widely used in agriculture and industry as biopesticides and sources of enzymes, respectively. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Many strains produce elicitors and induce resistance in plants through colonization of roots. Seven species have now been sequenced. Comparison of a primarily saprophytic species with two mycoparasitic species has provided striking contrasts and has established that mycoparasitism is an ancestral trait of this genus. Among the interesting outcomes of genome comparison is the discovery of a vast repertoire of secondary metabolism pathways and of numerous small cysteine-rich secreted proteins. Genomics has also facilitated investigation of sexual crossing in Trichoderma reesei, suggesting the possibility of strain improvement through hybridization.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India.
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Rendón-Anaya M, Delaye L, Possani LD, Herrera-Estrella A. Global transcriptome analysis of the scorpion Centruroides noxius: new toxin families and evolutionary insights from an ancestral scorpion species. PLoS One 2012; 7:e43331. [PMID: 22912855 PMCID: PMC3422302 DOI: 10.1371/journal.pone.0043331] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 07/19/2012] [Indexed: 02/05/2023] Open
Abstract
Scorpion venoms have been studied for decades, leading to the identification of hundreds of different toxins with medical and pharmacological implications. However, little emphasis has been given to the description of these arthropods from cellular and evolutionary perspectives. In this report, we describe a transcriptomic analysis of the Mexican scorpion Centruroides noxius Hoffmann, performed with a pyrosequencing platform. Three independent sequencing experiments were carried out, each including three different cDNA libraries constructed from RNA extracted from the whole body of the scorpion after telson removal, and from the venom gland before and after venom extraction. Over three million reads were obtained and assembled in almost 19000 isogroups. Within the telson-specific sequences, 72 isogroups (0.4% of total unique transcripts) were found to be similar to toxins previously reported in other scorpion species, spiders and sea anemones. The annotation pipeline also revealed the presence of important elements of the small non-coding RNA processing machinery, as well as microRNA candidates. A phylogenomic analysis of concatenated essential genes evidenced differential evolution rates in this species, particularly in ribosomal proteins and proteasome components. Additionally, statistical comparison of transcript abundance before and after venom extraction showed that 3% and 2% of the assembled isogroups had higher expression levels in the active and replenishing gland, respectively. Thus, our sequencing and annotation strategies provide a general view of the cellular and molecular processes that take place in these arthropods, allowed the discovery of new pharmacological and biotechnological targets and uncovered several regulatory and metabolic responses behind the assembly of the scorpion venom. The results obtained in this report represent the first high-throughput study that thoroughly describes the universe of genes that are expressed in the scorpion Centruroides noxius Hoffmann, a highly relevant organism from medical and evolutionary perspectives.
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Affiliation(s)
- Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
| | - Lourival D. Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
- * E-mail: (AH-E); (LDP)
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
- * E-mail: (AH-E); (LDP)
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