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Torres de Oliveira C, Alexandrino de Assis M, Lourenço Franco Cairo JP, Damasio A, Guimarães Pereira GA, Mazutti MA, de Oliveira D. Functional characterization and structural insights of three cutinases from the ascomycete Fusarium verticillioides. Protein Expr Purif 2024; 216:106415. [PMID: 38104791 DOI: 10.1016/j.pep.2023.106415] [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: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
Cutinases are serine esterases that belong to the α/β hydrolases superfamily. The natural substrates for these enzymes are cutin and suberin, components of the plant cuticle, the first barrier in the defense system against pathogen invasion. It is well-reported that plant pathogens produce cutinases to facilitate infection. Fusarium verticillioides, one important corn pathogens, is an ascomycete upon which its cutinases are poorly explored. Consequently, the objective of this study was to perform the biochemical characterization of three precursor cutinases (FvCut1, FvCut2, and FvCut3) from F. verticillioides and to obtain structural insights about them. The cutinases were produced in Escherichia coli and purified. FvCut1, FvCut2, and FvCut3 presented optimal temperatures of 20, 40, and 35 °C, and optimal pH of 9, 7, and 8, respectively. Some chemicals stimulated the enzymatic activity. The kinetic parameters revealed that FvCut1 has higher catalytic efficiency (Kcat/Km) in the p-nitrophenyl-butyrate (p-NPB) substrate. Nevertheless, the enzymes were not able to hydrolyze polyethylene terephthalate (PET). Furthermore, the three-dimensional models of these enzymes showed structural differences among them, mainly FvCut1, which presented a narrower opening cleft to access the catalytic site. Therefore, our study contributes to exploring the diversity of fungal cutinases and their potential biotechnological applications.
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Affiliation(s)
- Caroline Torres de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil
| | - Michelle Alexandrino de Assis
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, UNICAMP, Campinas, Brazil
| | | | - Marcio Antonio Mazutti
- Department of Chemical Engineering, Technology Center, Federal University of Santa Maria, UFSM, Santa Maria, Brazil
| | - Débora de Oliveira
- Department of Chemical and Food Engineering, Technology Center, Federal University of Santa Catarina, UFSC, Florianópolis, Brazil.
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Vargas BDO, dos Santos JR, Pereira GAG, de Mello FDSB. An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae. PeerJ 2023; 11:e16340. [PMID: 38047029 PMCID: PMC10691383 DOI: 10.7717/peerj.16340] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 12/05/2023] Open
Abstract
Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
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Affiliation(s)
- Beatriz de Oliveira Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jade Ribeiro dos Santos
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
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3
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Bastos TSB, de Paula AGP, Dos Santos Luz RB, Garnique AMB, Belo MAA, Eto SF, Fernandes DC, Ferraris FK, de Pontes LG, França TT, Barcellos LJG, Veras FP, Bermejo P, Guidelli G, Maneira C, da Silveira Bezerra de Mello F, Teixeira G, Pereira GAG, Fernandes BHV, Sanches PRS, Braz HLB, Jorge RJB, Malafaia G, Cilli EM, Olivier DDS, do Amaral MS, Medeiros RJ, Condino-Neto A, Carvalho LR, Machado-Santelli GM, Charlie-Silva I, Galindo-Villegas J, Braga TT. Author Correction: A novel insight on SARS-CoV-2 S-derived fragments in the control of the host immunity. Sci Rep 2023; 13:12012. [PMID: 37491374 PMCID: PMC10368618 DOI: 10.1038/s41598-023-39134-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Affiliation(s)
| | | | | | - Anali M B Garnique
- Department of Cell Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Butantan Institute, São Paulo, Brazil
- Center of Innovation and Development, Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | | | - Fausto Klabund Ferraris
- Department of Pharmacology and Toxicology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Leticia Gomes de Pontes
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Tábata Takahashi França
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Leonardo José Gil Barcellos
- Laboratory of Fish Physiology, Graduate Program of Bioexperimentation, University of Passo Fundo, Santa Maria, Brazil
- Graduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Flavio P Veras
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Pamela Bermejo
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | - Giovanna Guidelli
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | - Carla Maneira
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | | | - Gleidson Teixeira
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | | | - Bianca H Ventura Fernandes
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Paulo R S Sanches
- Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Helyson Lucas Bezerra Braz
- Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Roberta Jeane Bezerra Jorge
- Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Guilherme Malafaia
- Biological Research Laboratory, Goiano Federal Institute, Urutai Campus, Urutaí, GO, Brazil
| | - Eduardo M Cilli
- Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | | | - Marcos Serrou do Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Renata J Medeiros
- Laboratory of Physiology, INCQS/Fiocruz Zebrafish Facility, Department of Pharmacology and Toxicology, National Institute for Quality Control in Health, Rio de Janeiro, Brazil
| | - Antonio Condino-Neto
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Luciani R Carvalho
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Glaucia M Machado-Santelli
- Laboratory of Cellular and Molecular Biology, Department of Cell and Developmental Biology, Institute of Biomedical Science, University of Sao Paulo, University of São Paulo, São Paulo, Brazil
| | - Ives Charlie-Silva
- Department of Pharmacology, University of São Paulo-ICB/USP, São Paulo, Brazil.
| | - Jorge Galindo-Villegas
- Department of Genomics, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Tárcio Teodoro Braga
- Department of Pathology, Federal University of Parana, Curitiba, Brazil.
- Graduate Program in Biosciences and Biotechnology, Instituto Carlos Chagas, Fiocruz-Parana, Brazil.
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Bastos TSB, de Paula AGP, Dos Santos Luz RB, Garnique AMB, Belo MAA, Eto SF, Fernandes DC, Ferraris FK, de Pontes LG, França TT, Barcellos LJG, Veras FP, Bermejo P, Guidelli G, Maneira C, da Silveira Bezerra de Mello F, Teixeira G, Pereira GAG, Fernandes BHV, Sanches PRS, Braz HLB, Jorge RJB, Malafaia G, Cilli EM, Olivier DDS, do Amaral MS, Medeiros RJ, Condino-Neto A, Carvalho LR, Machado-Santelli GM, Charlie-Silva I, Galindo-Villegas J, Braga TT. A novel insight on SARS-CoV-2 S-derived fragments in the control of the host immunity. Sci Rep 2023; 13:8060. [PMID: 37198208 PMCID: PMC10191404 DOI: 10.1038/s41598-023-29588-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/07/2023] [Indexed: 05/19/2023] Open
Abstract
Despite all efforts to combat the pandemic of COVID-19, we are still living with high numbers of infected persons, an overburdened health care system, and the lack of an effective and definitive treatment. Understanding the pathophysiology of the disease is crucial for the development of new technologies and therapies for the best clinical management of patients. Since the manipulation of the whole virus requires a structure with an adequate level of biosafety, the development of alternative technologies, such as the synthesis of peptides from viral proteins, is a possible solution to circumvent this problem. In addition, the use and validation of animal models is of extreme importance to screen new drugs and to compress the organism's response to the disease. Peptides derived from recombinant S protein from SARS-CoV-2 were synthesized and validated by in silico, in vitro and in vivo methodologies. Macrophages and neutrophils were challenged with the peptides and the production of inflammatory mediators and activation profile were evaluated. These peptides were also inoculated into the swim bladder of transgenic zebrafish larvae at 6 days post fertilization (dpf) to mimic the inflammatory process triggered by the virus, which was evaluated by confocal microscopy. In addition, toxicity and oxidative stress assays were also developed. In silico and molecular dynamics assays revealed that the peptides bind to the ACE2 receptor stably and interact with receptors and adhesion molecules, such as MHC and TCR, from humans and zebrafish. Macrophages stimulated with one of the peptides showed increased production of NO, TNF-α and CXCL2. Inoculation of the peptides in zebrafish larvae triggered an inflammatory process marked by macrophage recruitment and increased mortality, as well as histopathological changes, similarly to what is observed in individuals with COVID-19. The use of peptides is a valuable alternative for the study of host immune response in the context of COVID-19. The use of zebrafish as an animal model also proved to be appropriate and effective in evaluating the inflammatory process, comparable to humans.
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Affiliation(s)
| | | | | | - Anali M B Garnique
- Department of Cell Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Butantan Institute, São Paulo, Brazil
- Center of Innovation and Development, Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | | | - Fausto Klabund Ferraris
- Department of Pharmacology and Toxicology, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro, Brazil
| | - Leticia Gomes de Pontes
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Tábata Takahashi França
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Leonardo José Gil Barcellos
- Laboratory of Fish Physiology, Graduate Program of Bioexperimentation, University of Passo Fundo, Santa Maria, Brazil
- Graduate Program of Pharmacology, Federal University of Santa Maria, Santa Maria, Brazil
| | - Flavio P Veras
- Center of Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, São Paulo, Brazil
| | - Pamela Bermejo
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | - Giovanna Guidelli
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | - Carla Maneira
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | | | - Gleidson Teixeira
- Laboratório de Genômica e bioEnergia (LGE), Institute of Biology - Unicamp, Campinas, Brazil
| | | | - Bianca H Ventura Fernandes
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Paulo R S Sanches
- Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Helyson Lucas Bezerra Braz
- Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Roberta Jeane Bezerra Jorge
- Department of Physiology and Pharmacology, School of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Guilherme Malafaia
- Biological Research Laboratory, Goiano Federal Institute, Urutai Campus, Urutaí, GO, Brazil
| | - Eduardo M Cilli
- Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | | | - Marcos Serrou do Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79070-900, Brazil
| | - Renata J Medeiros
- Laboratory of Physiology, INCQS/Fiocruz Zebrafish Facility, Department of Pharmacology and Toxicology, National Institute for Quality Control in Health, Rio de Janeiro, Brazil
| | - Antonio Condino-Neto
- Laboratory of Human Immunology, Department Immunology, Institute Biomedical Sciences, University São Paulo, São Paulo, Brazil
| | - Luciani R Carvalho
- Laboratório de Controle Genético e Sanitário, Diretoria Técnica de Apoio ao Ensino e Pesquisa, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Glaucia M Machado-Santelli
- Laboratory of Cellular and Molecular Biology, Department of Cell and Developmental Biology, Institute of Biomedical Science, University of Sao Paulo, University of São Paulo, São Paulo, Brazil
| | - Ives Charlie-Silva
- Department of Pharmacology, University of São Paulo-ICB/USP, São Paulo, Brazil.
| | - Jorge Galindo-Villegas
- Department of Genomics, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
| | - Tárcio Teodoro Braga
- Department of Pathology, Federal University of Parana, Curitiba, Brazil.
- Graduate Program in Biosciences and Biotechnology, Instituto Carlos Chagas, Fiocruz-Parana, Brazil.
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Fiamenghi MB, Bueno JGR, Camargo AP, Borelli G, Carazzolle MF, Pereira GAG, dos Santos LV, José J. Machine learning and comparative genomics approaches for the discovery of xylose transporters in yeast. Biotechnol Biofuels 2022; 15:57. [PMID: 35596177 PMCID: PMC9123741 DOI: 10.1186/s13068-022-02153-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/05/2022] [Indexed: 11/15/2022]
Abstract
Background The need to mitigate and substitute the use of fossil fuels as the main energy matrix has led to the study and development of biofuels as an alternative. Second-generation (2G) ethanol arises as one biofuel with great potential, due to not only maintaining food security, but also as a product from economically interesting crops such as energy-cane. One of the main challenges of 2G ethanol is the inefficient uptake of pentose sugars by industrial yeast Saccharomyces cerevisiae, the main organism used for ethanol production. Understanding the main drivers for xylose assimilation and identify novel and efficient transporters is a key step to make the 2G process economically viable. Results By implementing a strategy of searching for present motifs that may be responsible for xylose transport and past adaptations of sugar transporters in xylose fermenting species, we obtained a classifying model which was successfully used to select four different candidate transporters for evaluation in the S. cerevisiae hxt-null strain, EBY.VW4000, harbouring the xylose consumption pathway. Yeast cells expressing the transporters SpX, SpH and SpG showed a superior uptake performance in xylose compared to traditional literature control Gxf1. Conclusions Modelling xylose transport with the small data available for yeast and bacteria proved a challenge that was overcome through different statistical strategies. Through this strategy, we present four novel xylose transporters which expands the repertoire of candidates targeting yeast genetic engineering for industrial fermentation. The repeated use of the model for characterizing new transporters will be useful both into finding the best candidates for industrial utilization and to increase the model’s predictive capabilities. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02153-7.
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Quintanilha-Peixoto G, Marone MP, Raya FT, José J, Oliveira A, Fonseca PLC, Tomé LMR, Bortolini DE, Kato RB, Araújo DS, De-Paula RB, Cuesta-Astroz Y, Duarte EAA, Badotti F, de Carvalho Azevedo VA, Brenig B, Soares ACF, Carazzolle MF, Pereira GAG, Aguiar ERGR, Góes-Neto A. Phylogenomics and gene selection in Aspergillus welwitschiae: Possible implications in the pathogenicity in Agave sisalana. Genomics 2022; 114:110517. [PMID: 36306958 DOI: 10.1016/j.ygeno.2022.110517] [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: 07/12/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
Abstract
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodium‑calcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
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Affiliation(s)
| | - Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Juliana José
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriele Oliveira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Dener Eduardo Bortolini
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, United States
| | - Ruth B De-Paula
- Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Yesid Cuesta-Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Medellín, Colombia
| | - Elizabeth A A Duarte
- Centro Universitário Maria Milza, Cruz das Almas, Brazil; Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Federal Center of Technological Education of Minas Gerais, Belo Horizonte, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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de Mello FDSB, Coradini ALV, Carazzolle MF, Maneira C, Furlan M, Pereira GAG, Teixeira GS. Genetic mapping of a bioethanol yeast strain reveals new targets for hydroxymethylfurfural- and thermotolerance. Microbiol Res 2022; 263:127138. [DOI: 10.1016/j.micres.2022.127138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 10/16/2022]
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de Mello FDSB, Maneira C, Suarez FUL, Nagamatsu S, Vargas B, Vieira C, Secches T, Coradini ALV, Silvello MADC, Goldbeck R, Pereira GAG, Teixeira GS. Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw. J Genet Eng Biotechnol 2022; 20:80. [PMID: 35612634 PMCID: PMC9133290 DOI: 10.1186/s43141-022-00359-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/02/2022] [Indexed: 12/15/2022]
Abstract
Background Sugarcane hemicellulosic material is a compelling source of usually neglected xylose that could figure as feedstock to produce chemical building blocks of high economic value, such as xylitol. In this context, Saccharomyces cerevisiae strains typically used in the Brazilian bioethanol industry are a robust chassis for genetic engineering, given their robustness towards harsh operational conditions and outstanding fermentation performance. Nevertheless, there are no reports on the use of these strains for xylitol production using sugarcane hydrolysate. Results Potential single-guided RNA off-targets were analyzed in two preeminent industrial strains (PE-2 and SA-1), providing a database of 5′-NGG 20 nucleotide sequences and guidelines for the fast and cost-effective CRISPR editing of such strains. After genomic integration of a NADPH-preferring xylose reductase (XR), FMYX (SA-1 hoΔ::xyl1) and CENPKX (CEN.PK-122 hoΔ::xyl1) were tested in varying cultivation conditions for xylitol productivity to infer influence of the genetic background. Near-theoretical yields were achieved for all strains; however, the industrial consistently outperformed the laboratory strain. Batch fermentation of raw sugarcane straw hydrolysate with remaining solid particles represented a challenge for xylose metabolization, and 3.65 ± 0.16 g/L xylitol titer was achieved by FMYX. Finally, quantification of NADPH — cofactor implied in XR activity — revealed that FMYX has 33% more available cofactors than CENPKX. Conclusions Although widely used in several S. cerevisiae strains, this is the first report of CRISPR-Cas9 editing major yeast of the Brazilian bioethanol industry. Fermentative assays of xylose consumption revealed that NADPH availability is closely related to mutant strains’ performance. We also pioneer the use of sugarcane straw as a substrate for xylitol production. Finally, we demonstrate how industrial background SA-1 is a compelling chassis for the second-generation industry, given its inhibitor tolerance and better redox environment that may favor production of reduced sugars. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00359-8.
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Affiliation(s)
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Frank Uriel Lizarazo Suarez
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Basic Sciences, University of Pamplona, Pamplona, Colombia
| | - Sheila Nagamatsu
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Beatriz Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla Vieira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thais Secches
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Alessando L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Rosana Goldbeck
- School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
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Marone MP, Campanari MFZ, Raya FT, Pereira GAG, Carazzolle MF. Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions. PeerJ 2022; 10:e13252. [PMID: 35529479 PMCID: PMC9070324 DOI: 10.7717/peerj.13252] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves' fungi as biotechnological tools.
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Affiliation(s)
- Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Fabio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil,Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil
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Corrêa TLR, Román EKB, da Silva Cassoli J, dos Santos LV, Pereira GAG. Secretome analysis of Trichoderma reesei RUT-C30 and Penicillium oxalicum reveals their synergic potential to deconstruct sugarcane and energy cane biomasses. Microbiol Res 2022; 260:127017. [DOI: 10.1016/j.micres.2022.127017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/18/2022] [Accepted: 03/29/2022] [Indexed: 11/28/2022]
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11
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Quintanilha-Peixoto G, Fonseca PLC, Raya FT, Marone MP, Bortolini DE, Mieczkowski P, Olmo RP, Carazzolle MF, Voigt CA, Soares ACF, Pereira GAG, Góes-Neto A, Aguiar ERGR. The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses. Microorganisms 2021; 9:microorganisms9081704. [PMID: 34442783 PMCID: PMC8400513 DOI: 10.3390/microorganisms9081704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/29/2022] Open
Abstract
Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.
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Affiliation(s)
- Gabriel Quintanilha-Peixoto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Paula Luize Camargos Fonseca
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Fábio Trigo Raya
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Marina Pupke Marone
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Dener Eduardo Bortolini
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Roenick Proveti Olmo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- CNRS UPR9022, INSERM U1257, Université de Strasbourg, 67084 Strasbourg, France
| | - Marcelo Falsarella Carazzolle
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | | | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Brazil;
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
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12
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Maneira C, Bermejo PM, Pereira GAG, de Mello FDSB. Exploring G protein-coupled receptors and yeast surface display strategies for viral detection in baker's yeast: SARS-CoV-2 as a case study. FEMS Yeast Res 2021; 21:6104486. [PMID: 33469649 PMCID: PMC7928939 DOI: 10.1093/femsyr/foab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
Viral infections pose intense burdens to healthcare systems and global economies. The correct diagnosis of viral diseases represents a crucial step towards effective treatments and control. Biosensors have been successfully implemented as accessible and accurate detection tests for some of the most important viruses. While most biosensors are based on physical or chemical interactions of cell-free components, the complexity of living microorganisms holds a poorly explored potential for viral detection in the face of the advances of synthetic biology. Indeed, cell-based biosensors have been praised for their versatility and economic attractiveness, however, yeast platforms for viral disease diagnostics are still limited to indirect antibody recognition. Here we propose a novel strategy for viral detection in Saccharomyces cerevisiae, which combines the transductive properties of G Protein-Coupled Receptors (GPCRs) with the Yeast Surface Display (YSD) of specific enzymes enrolled in the viral recognition process. The GPCR/YSD complex might allow for active virus detection through a modulated signal activated by a GPCR agonist, whose concentration correlates to the viral titer. Additionally, we explore this methodology in a case study for the detection of highly pathogenic coronaviruses that share the same cell receptor upon infection (i.e. the Angiotensin-Converting Enzyme 2, ACE2), as a conceptual example of the potential of the GPCR/YSD strategy for the diagnosis of COVID-19.
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Affiliation(s)
- Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, 13083-862, Campinas, Brazil
| | - Pamela Magalí Bermejo
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, 13083-862, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, 13083-862, Campinas, Brazil
| | - Fellipe da Silveira Bezerra de Mello
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, 13083-862, Campinas, Brazil
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Nagamatsu ST, Coutouné N, José J, Fiamenghi MB, Pereira GAG, Oliveira JVDC, Carazzolle MF. Ethanol production process driving changes on industrial strains. FEMS Yeast Res 2021; 21:6070656. [PMID: 33417685 DOI: 10.1093/femsyr/foaa071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Ethanol production has key differences between the two largest producing countries of this biofuel, Brazil and the USA, such as feedstock source, sugar concentration and ethanol titers in industrial fermentation. Therefore, it is highly probable that these specificities have led to genome adaptation of the Saccharomyces cerevisiae strains employed in each process to tolerate different environments. In order to identify particular adaptations, in this work, we have compared the genomes of industrial yeast strains widely used to produce ethanol from sugarcane, corn and sweet sorghum, and also two laboratory strains as reference. The genes were predicted and then 4524 single-copy orthologous were selected to build the phylogenetic tree. We found that the geographic location and industrial process were shown as the main evolutionary drivers: for sugarcane fermentation, positive selection was identified for metal homeostasis and stress response genes, whereas genes involved in membrane modeling have been connected with corn fermentation. In addition, the corn specialized strain Ethanol Red showed an increased number of copies of MAL31, a gene encoding a maltose transporter. In summary, our work can help to guide new strain chassis selection for engineering strategies, to produce more robust strains for biofuel production and other industrial applications.
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Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Natalia Coutouné
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Mateus Bernabe Fiamenghi
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
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14
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Borelli G, Fiamenghi MB, dos Santos LV, Carazzolle MF, Pereira GAG, José J. Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry. Genome Biol Evol 2019; 11:1923-1938. [PMID: 31070742 PMCID: PMC6637916 DOI: 10.1093/gbe/evz036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar's metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts' xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters' clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
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Affiliation(s)
- Guilherme Borelli
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Mateus Bernabe Fiamenghi
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Juliana José
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
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15
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Moretti-Almeida G, Thomazella DPT, Pereira GAG, Monteiro G. Heterologous expression of an alternative oxidase from Moniliophthora perniciosa in Saccharomyces cerevisiae: Antioxidant function and in vivo platform for the study of new drugs against witches' broom disease. Fungal Genet Biol 2019; 126:50-55. [PMID: 30794952 DOI: 10.1016/j.fgb.2019.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 07/31/2018] [Revised: 01/22/2019] [Accepted: 02/17/2019] [Indexed: 11/24/2022]
Abstract
The fungus Moniliophthora perniciosa is the causal agent of witches' broom disease (WBD), one of the most devastating diseases of cacao, the chocolate tree. Many strategies to control WBD have been tested so far, including the use of agrochemicals such as the strobilurins. Strobilurins are fungicides of the QoI family, and they are used in the control of a wide array of fungal diseases in many different crops, including cereals, field crops, fruits, tree nuts, and vegetables. These drugs act by specifically inhibiting fungal respiration at the Qo site of complex III, which is a component of the main mitochondrial respiratory chain. However, M. perniciosa is resistant to this family of chemicals. It has been postulated that this resistant phenotype is, at least in part, a result of the strong ability of this fungus to counteract the oxidative stress generated by the impairment of the main mitochondrial respiratory chain, through the activation of an alternative oxidase (Mp-AOX). To test this hypothesis, we expressed functional mitochondria-localized Mp-AOX in the model yeast Saccharomyces cerevisiae. We demonstrated that heterologous expression of Mp-AOX strongly inhibits hydrogen peroxide production by mitochondria. It also diminishes the total cell amount of oxidized glutathione (GSSG), resulting in a fifty-fold higher GSH/GSSG ratio in cells expressing Mp-AOX than in wild type cells. In addition, Mp-AOX activity decreases yeast growth rate and leads to low biomass production. Therefore, we propose the use of this heterologous expression system to direct the development of new inhibitors of fungal AOX by comparing the differences in optical density of Mp-AOX-expressing cells in the presence and absence of potential AOX inhibitors. Together, our results confirm the antioxidant role of Mp-AOX and provide an in vivo platform to be used in the screening of new fungicides based on Mp-AOX inhibition.
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Affiliation(s)
- G Moretti-Almeida
- Laboratório de Biologia Molecular e Biotecnologia Industrial de Microrganismos, Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - D P T Thomazella
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - G A G Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil
| | - G Monteiro
- Laboratório de Biologia Molecular e Biotecnologia Industrial de Microrganismos, Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil.
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16
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Bazzo BR, de Carvalho LM, Carazzolle MF, Pereira GAG, Colombo CA. Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species. BMC Plant Biol 2018; 18:276. [PMID: 30419831 PMCID: PMC6233587 DOI: 10.1186/s12870-018-1509-9] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/29/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The macaúba palm is a novel feedstock for oil production suitable for multiple uses, including as biodiesel and in the food and cosmetic industries. As an efficient alternative, the macaúba palm has limited genomic resources, particularly expressed sequence tag (EST) markers. We report a comprehensive set of validated EST-simple sequence repeat (SSR) markers by using transcriptome sequencing, its application in genetic diversity analysis and cross transferability in other palm trees with environmental and economic importance. RESULTS In this study, a total of 418 EST-SSRs were identified to be unique for one transcript and region; 232 EST-SSRs were selected, with trinucleotide repeats being the most frequent motif, representing 380 (90.9%), followed by composited (4.5%), di- (3.6%), and hexanucleotides (3.6%). A total of 145 EST-SSRs (62.5%) were validated for consistent amplification in seventeen macaúba palm samples, and 100 were determined to be polymorphic with PIC values ranging from 0.25 to 0.77. Genetic diversity analysis was performed with the 20 most informative EST-SSR markers showing a distinct separation of the different groups of macaúba palm. Additionally, these 145 markers were transferred in six other palm species resulting in transferability rates of 99% (144) in Acrocomia intumescens, 98% (143) in Acrocomia totai, 80.7% (117 EST-EST) in African oil palm (Elaeis guineensis) and peach palm (Bactris gasipaes) samples, 70% (102) in the juçara palm (Euterpe edulis) and 71.7% (104) in the hat palm (Sabal causiarum). Analysis of genetic distance showed a high separation in accordance with geographic location, establishing distinct groups by genera. CONCLUSIONS The EST markers identified in our study are a valuable resource and provide a genomic tool for genetic mapping and further genetic studies, as well as evaluation of co-location between QTLs and functionally associated markers.
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Affiliation(s)
- Bárbara Regina Bazzo
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, Campinas, Brazil
| | - Lucas Miguel de Carvalho
- Institute of Biology, Laboratory of Genomic and Expression, State University of Campinas, Campinas, Brazil
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Fiorin GL, Sanchéz-Vallet A, Thomazella DPDT, do Prado PFV, do Nascimento LC, Figueira AVDO, Thomma BPHJ, Pereira GAG, Teixeira PJPL. Suppression of Plant Immunity by Fungal Chitinase-like Effectors. Curr Biol 2018; 28:3023-3030.e5. [PMID: 30220500 DOI: 10.1016/j.cub.2018.07.055] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/03/2018] [Accepted: 07/19/2018] [Indexed: 10/28/2022]
Abstract
Crop diseases caused by fungi constitute one of the most important problems in agriculture, posing a serious threat to food security [1]. To establish infection, phytopathogens interfere with plant immune responses [2, 3]. However, strategies to promote virulence employed by fungal pathogens, especially non-model organisms, remain elusive [4], mainly because fungi are more complex and difficult to study when compared to the better-characterized bacterial pathogens. Equally incomplete is our understanding of the birth of microbial virulence effectors. Here, we show that the cacao pathogen Moniliophthora perniciosa evolved an enzymatically inactive chitinase (MpChi) that functions as a putative pathogenicity factor. MpChi is among the most highly expressed fungal genes during the biotrophic interaction with cacao and encodes a chitinase with mutations that abolish its enzymatic activity. Despite the lack of chitinolytic activity, MpChi retains substrate binding specificity and prevents chitin-triggered immunity by sequestering immunogenic chitin fragments. Remarkably, its sister species M. roreri encodes a second non-orthologous catalytically impaired chitinase with equivalent function. Thus, a class of conserved enzymes independently evolved as putative virulence factors in these fungi. In addition to unveiling a strategy of host immune suppression by fungal pathogens, our results demonstrate that the neofunctionalization of enzymes may be an evolutionary pathway for the rise of new virulence factors in fungi. We anticipate that analogous strategies are likely employed by other pathogens.
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Affiliation(s)
- Gabriel Lorencini Fiorin
- Graduate Program in Genetics and Molecular Biology, Instituto de Biologia, Universidade de Estadual de Campinas, Campinas 13083-970, Brazil; Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Andrea Sanchéz-Vallet
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 Wageningen, the Netherlands; Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | | | - Paula Favoretti Vital do Prado
- Graduate Program in Genetics and Molecular Biology, Instituto de Biologia, Universidade de Estadual de Campinas, Campinas 13083-970, Brazil; Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil; Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas 13083-970, Brazil
| | - Antonio Vargas de Oliveira Figueira
- Laboratório de Melhoramento de Plantas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Campus "Luiz de Queiroz," Piracicaba 13400-970, Brazil
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 Wageningen, the Netherlands
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13083-970, Brazil.
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Nascimento LC, Salazar MM, Lepikson-Neto J, Camargo ELO, Parreiras LS, Pereira GAG, Carazzolle MF. EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. Database (Oxford) 2018; 2017:4564812. [PMID: 29220468 PMCID: PMC5737058 DOI: 10.1093/database/bax079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/29/2017] [Indexed: 12/05/2022]
Abstract
Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL:http://www.lge.ibi.unicamp.br/eucalyptusdb
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Affiliation(s)
- Leandro Costa Nascimento
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Laboratório Central de Tecnologias de Alto Desempenho (LaCTAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Marcela Mendes Salazar
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Jorge Lepikson-Neto
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Eduardo Leal Oliveira Camargo
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Lucas Salera Parreiras
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão (LGE), Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brasil.,Centro Nacional de Processamento de Alto Desempenho em São Paulo (CENAPAD), Universidade Estadual de Campinas, Campinas, SP, Brasil
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19
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Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG. Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). BMC Genomics 2018; 19:58. [PMID: 29343217 PMCID: PMC5773145 DOI: 10.1186/s12864-018-4440-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 08/24/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. RESULTS We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. CONCLUSION Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity.
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Affiliation(s)
- Eddy Patricia Lopez Molano
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Odalys García Cabrera
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Juliana Jose
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Marcelo Falsarella Carazzolle
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo José Pereira Lima Teixeira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Present Address: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Javier Correa Alvarez
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellın, Colombia
| | - Ricardo Augusto Tiburcio
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Paulo Massanari Tokimatu Filho
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Gustavo Machado Alvares de Lima
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Victório Carvalho Guido
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Gonçalo Amarante Guimarães Pereira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.
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20
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Temer B, dos Santos LV, Negri VA, Galhardo JP, Magalhães PHM, José J, Marschalk C, Corrêa TLR, Carazzolle MF, Pereira GAG. Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae. BMC Biotechnol 2017; 17:71. [PMID: 28888227 PMCID: PMC5591498 DOI: 10.1186/s12896-017-0389-7] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Second-generation ethanol production is a clean bioenergy source with potential to mitigate fossil fuel emissions. The engineering of Saccharomyces cerevisiae for xylose utilization is an essential step towards the production of this biofuel. Though xylose isomerase (XI) is the key enzyme for xylose conversion, almost half of the XI genes are not functional when expressed in S. cerevisiae. To date, protein misfolding is the most plausible hypothesis to explain this phenomenon. RESULTS This study demonstrated that XI from the bacterium Propionibacterium acidipropionici becomes functional in S. cerevisiae when co-expressed with GroEL-GroES chaperonin complex from Escherichia coli. The developed strain BTY34, harboring the chaperonin complex, is able to efficiently convert xylose to ethanol with a yield of 0.44 g ethanol/g xylose. Furthermore, the BTY34 strain presents a xylose consumption rate similar to those observed for strains carrying the widely used XI from the fungus Orpinomyces sp. In addition, the tetrameric XI structure from P. acidipropionici showed an elevated number of hydrophobic amino acid residues on the surface of protein when compared to XI commonly expressed in S. cerevisiae. CONCLUSIONS Based on our results, we elaborate an extensive discussion concerning the uncertainties that surround heterologous expression of xylose isomerases in S. cerevisiae. Probably, a correct folding promoted by GroEL-GroES could solve some issues regarding a limited or absent XI activity in S. cerevisiae. The strains developed in this work have promising industrial characteristics, and the designed strategy could be an interesting approach to overcome the non-functionality of bacterial protein expression in yeasts.
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Affiliation(s)
- Beatriz Temer
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Leandro Vieira dos Santos
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
- CTBE – Brazilian Bioethanol Science and Technology Laboratory, Campinas, SP Brazil
| | - Victor Augusti Negri
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Juliana Pimentel Galhardo
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Pedro Henrique Mello Magalhães
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Juliana José
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Cidnei Marschalk
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratory of Genomics and Expression, Department of Genetics and Evolution, Institute of Biology, UNICAMP, Campinas, São Paulo, 13083-970 Brazil
- CTBE – Brazilian Bioethanol Science and Technology Laboratory, Campinas, SP Brazil
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21
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Dos Santos LV, Carazzolle MF, Nagamatsu ST, Sampaio NMV, Almeida LD, Pirolla RAS, Borelli G, Corrêa TLR, Argueso JL, Pereira GAG. Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. Sci Rep 2016; 6:38676. [PMID: 28000736 PMCID: PMC5175268 DOI: 10.1038/srep38676] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/11/2016] [Indexed: 11/21/2022] Open
Abstract
The development of biocatalysts capable of fermenting xylose, a five-carbon sugar abundant in lignocellulosic biomass, is a key step to achieve a viable production of second-generation ethanol. In this work, a robust industrial strain of Saccharomyces cerevisiae was modified by the addition of essential genes for pentose metabolism. Subsequently, taken through cycles of adaptive evolution with selection for optimal xylose utilization, strains could efficiently convert xylose to ethanol with a yield of about 0.46 g ethanol/g xylose. Though evolved independently, two strains carried shared mutations: amplification of the xylose isomerase gene and inactivation of ISU1, a gene encoding a scaffold protein involved in the assembly of iron-sulfur clusters. In addition, one of evolved strains carried a mutation in SSK2, a member of MAPKKK signaling pathway. In validation experiments, mutating ISU1 or SSK2 improved the ability to metabolize xylose of yeast cells without adaptive evolution, suggesting that these genes are key players in a regulatory network for xylose fermentation. Furthermore, addition of iron ion to the growth media improved xylose fermentation even by non-evolved cells. Our results provide promising new targets for metabolic engineering of C5-yeasts and point to iron as a potential new additive for improvement of second-generation ethanol production.
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Affiliation(s)
- Leandro Vieira Dos Santos
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Sheila Tiemi Nagamatsu
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Nádia Maria Vieira Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | | | | | - Guilherme Borelli
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins-CO, 80523-1618, USA
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, UNICAMP, Campinas, São Paulo 13083-970, Brazil.,GranBio/BioCelere, Campinas, Brazil
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22
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Corrêa TLR, dos Santos LV, Pereira GAG. AA9 and AA10: from enigmatic to essential enzymes. Appl Microbiol Biotechnol 2016; 100:9-16. [PMID: 26476647 DOI: 10.1007/s00253-015-7040-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field.
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Mofatto LS, Carneiro FDA, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GAG, Andrade AC, Marraccini P. Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. BMC Plant Biol 2016; 16:94. [PMID: 27095276 PMCID: PMC4837521 DOI: 10.1186/s12870-016-0777-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 10/14/2015] [Accepted: 04/13/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee.
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Affiliation(s)
- Luciana Souto Mofatto
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Fernanda de Araújo Carneiro
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Natalia Gomes Vieira
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Karoline Estefani Duarte
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Ramon Oliveira Vidal
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Jean Carlos Alekcevetch
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Michelle Guitton Cotta
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | | | | | | | | | | | - David Pot
- />CIRAD UMR AGAP, F-34398 Montpellier, France
| | - Gustavo Costa Rodrigues
- />Embrapa Informática Agropecuária, UNICAMP, Av. André Tosello n° 209, CP 6041, 13083-886 Campinas, SP Brazil
| | - Marcelo Falsarella Carazzolle
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Gonçalo Amarante Guimarães Pereira
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Alan Carvalho Andrade
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
- />present address: Embrapa Café, INOVACAFÉ, Campus UFLA, 37200-000 Lavras, MG Brazil
| | - Pierre Marraccini
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
- />CIRAD UMR AGAP, F-34398 Montpellier, France
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dos Santos LV, de Barros Grassi MC, Gallardo JCM, Pirolla RAS, Calderón LL, de Carvalho-Netto OV, Parreiras LS, Camargo ELO, Drezza AL, Missawa SK, Teixeira GS, Lunardi I, Bressiani J, Pereira GAG. Second-Generation Ethanol: The Need is Becoming a Reality. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1089/ind.2015.0017] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
| | | | | | | | - Luige Llerena Calderón
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | | | - Lucas Salera Parreiras
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | | | | | - Sílvia Kazue Missawa
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
| | - Gleidson Silva Teixeira
- GranBio/BioCelere, Campinas, Brazil
- Laboratório de Genômica e Expressão, UNICAMP, Campinas, Brazil
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25
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Affiliation(s)
| | | | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
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26
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Franco SDF, Baroni RM, Carazzolle MF, Teixeira PJPL, Reis O, Pereira GAG, Mondego JMC. Genomic analyses and expression evaluation of thaumatin-like gene family in the cacao fungal pathogen Moniliophthora perniciosa. Biochem Biophys Res Commun 2015; 466:629-36. [PMID: 26367180 DOI: 10.1016/j.bbrc.2015.09.054] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Abstract
Thaumatin-like proteins (TLPs) are found in diverse eukaryotes. Plant TLPs, known as Pathogenicity Related Protein (PR-5), are considered fungal inhibitors. However, genes encoding TLPs are frequently found in fungal genomes. In this work, we have identified that Moniliophthora perniciosa, a basidiomycete pathogen that causes the Witches' Broom Disease (WBD) of cacao, presents thirteen putative TLPs from which four are expressed during WBD progression. One of them is similar to small TLPs, which are present in phytopathogenic basidiomycete, such as wheat stem rust fungus Puccinia graminis. Fungi genomes annotation and phylogenetic data revealed a larger number of TLPs in basidiomycetes when comparing with ascomycetes, suggesting that these proteins could be involved in specific traits of mushroom-forming species. Based on the present data, we discuss the contribution of TLPs in the combat against fungal competitors and hypothesize a role of these proteins in M. perniciosa pathogenicity.
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Affiliation(s)
- Sulamita de Freitas Franco
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil
| | - Renata Moro Baroni
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil; Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, SP, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil
| | - Paulo José Pereira Lima Teixeira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil
| | - Osvaldo Reis
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, UNICAMP, Campinas, SP, Brazil.
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Barau J, Grandis A, Carvalho VMDA, Teixeira GS, Zaparoli GHA, do Rio MCS, Rincones J, Buckeridge MS, Pereira GAG. Apoplastic and intracellular plant sugars regulate developmental transitions in witches' broom disease of cacao. J Exp Bot 2015; 66:1325-37. [PMID: 25540440 PMCID: PMC4339597 DOI: 10.1093/jxb/eru485] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 05/21/2023]
Abstract
Witches' broom disease (WBD) of cacao differs from other typical hemibiotrophic plant diseases by its unusually long biotrophic phase. Plant carbon sources have been proposed to regulate WBD developmental transitions; however, nothing is known about their availability at the plant-fungus interface, the apoplastic fluid of cacao. Data are provided supporting a role for the dynamics of soluble carbon in the apoplastic fluid in prompting the end of the biotrophic phase of infection. Carbon depletion and the consequent fungal sensing of starvation were identified as key signalling factors at the apoplast. MpNEP2, a fungal effector of host necrosis, was found to be up-regulated in an autophagic-like response to carbon starvation in vitro. In addition, the in vivo artificial manipulation of carbon availability in the apoplastic fluid considerably modulated both its expression and plant necrosis rate. Strikingly, infected cacao tissues accumulated intracellular hexoses, and showed stunted photosynthesis and the up-regulation of senescence markers immediately prior to the transition to the necrotrophic phase. These opposite findings of carbon depletion and accumulation in different host cell compartments are discussed within the frame of WBD development. A model is suggested to explain phase transition as a synergic outcome of fungal-related factors released upon sensing of extracellular carbon starvation, and an early senescence of infected tissues probably triggered by intracellular sugar accumulation.
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Affiliation(s)
- Joan Barau
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Adriana Grandis
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo-USP, CP 11461, Rua do Matão 277, São Paulo-SP, CEP 05508-090, Brazil
| | - Vinicius Miessler de Andrade Carvalho
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Gleidson Silva Teixeira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Gustavo Henrique Alcalá Zaparoli
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Maria Carolina Scatolin do Rio
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Johana Rincones
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia Ecológica de Plantas, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo-USP, CP 11461, Rua do Matão 277, São Paulo-SP, CEP 05508-090, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-UNICAMP, CP 6109, Campinas-SP, CEP 13083-970, Brazil
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Teixeira PJPL, Thomazella DPDT, Reis O, do Prado PFV, do Rio MCS, Fiorin GL, José J, Costa GGL, Negri VA, Mondego JMC, Mieczkowski P, Pereira GAG. High-resolution transcript profiling of the atypical biotrophic interaction between Theobroma cacao and the fungal pathogen Moniliophthora perniciosa. Plant Cell 2014; 26:4245-69. [PMID: 25371547 PMCID: PMC4277218 DOI: 10.1105/tpc.114.130807] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 09/01/2014] [Accepted: 10/15/2014] [Indexed: 05/18/2023]
Abstract
Witches' broom disease (WBD), caused by the hemibiotrophic fungus Moniliophthora perniciosa, is one of the most devastating diseases of Theobroma cacao, the chocolate tree. In contrast to other hemibiotrophic interactions, the WBD biotrophic stage lasts for months and is responsible for the most distinctive symptoms of the disease, which comprise drastic morphological changes in the infected shoots. Here, we used the dual RNA-seq approach to simultaneously assess the transcriptomes of cacao and M. perniciosa during their peculiar biotrophic interaction. Infection with M. perniciosa triggers massive metabolic reprogramming in the diseased tissues. Although apparently vigorous, the infected shoots are energetically expensive structures characterized by the induction of ineffective defense responses and by a clear carbon deprivation signature. Remarkably, the infection culminates in the establishment of a senescence process in the host, which signals the end of the WBD biotrophic stage. We analyzed the pathogen's transcriptome in unprecedented detail and thereby characterized the fungal nutritional and infection strategies during WBD and identified putative virulence effectors. Interestingly, M. perniciosa biotrophic mycelia develop as long-term parasites that orchestrate changes in plant metabolism to increase the availability of soluble nutrients before plant death. Collectively, our results provide unique insight into an intriguing tropical disease and advance our understanding of the development of (hemi)biotrophic plant-pathogen interactions.
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Affiliation(s)
- Paulo José Pereira Lima Teixeira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Daniela Paula de Toledo Thomazella
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Osvaldo Reis
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Paula Favoretti Vital do Prado
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Maria Carolina Scatolin do Rio
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Gabriel Lorencini Fiorin
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Juliana José
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Gustavo Gilson Lacerda Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Victor Augusti Negri
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
| | - Jorge Maurício Costa Mondego
- Centro de Pesquisa e Desenvolvimento em Recursos Genéticos Vegetais, Instituto Agronômico, Campinas SP 13001-970, Brazil
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas SP 13083-970, Brazil
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de Oliveira Ceita G, Vilas-Boas LA, Castilho MS, Carazzolle MF, Pirovani CP, Selbach-Schnadelbach A, Gramacho KP, Ramos PIP, Barbosa LV, Pereira GAG, Góes-Neto A. Analysis of the ergosterol biosynthesis pathway cloning, molecular characterization and phylogeny of lanosterol 14 α-demethylase (ERG11) gene of Moniliophthora perniciosa. Genet Mol Biol 2014; 37:683-93. [PMID: 25505843 PMCID: PMC4261968 DOI: 10.1590/s1415-47572014005000017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 04/11/2014] [Accepted: 06/04/2014] [Indexed: 11/22/2022] Open
Abstract
The phytopathogenic fungus Moniliophthora perniciosa (Stahel) Aime & Philips-Mora, causal agent of witches' broom disease of cocoa, causes countless damage to cocoa production in Brazil. Molecular studies have attempted to identify genes that play important roles in fungal survival and virulence. In this study, sequences deposited in the M. perniciosa Genome Sequencing Project database were analyzed to identify potential biological targets. For the first time, the ergosterol biosynthetic pathway in M. perniciosa was studied and the lanosterol 14α-demethylase gene (ERG11) that encodes the main enzyme of this pathway and is a target for fungicides was cloned, characterized molecularly and its phylogeny analyzed. ERG11 genomic DNA and cDNA were characterized and sequence analysis of the ERG11 protein identified highly conserved domains typical of this enzyme, such as SRS1, SRS4, EXXR and the heme-binding region (HBR). Comparison of the protein sequences and phylogenetic analysis revealed that the M. perniciosa enzyme was most closely related to that of Coprinopsis cinerea.
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Affiliation(s)
- Geruza de Oliveira Ceita
- Laboratório de Pesquisa em Microbiologia,
Departamento de Ciências Biológicas,
Universidade Estadual de Feira de Santana,
Feira de Santana,
BA,
Brazil
- Laboratório de Biologia Molecular,
Instituto de Biologia,
Departamento de Biologia Geral,
Universidade Federal da Bahia,
Salvador,
BA,
Brazil
| | - Laurival Antônio Vilas-Boas
- Centro de Ciências Biológicas,
Departamento de Biologia Geral,
Universidade Estadual de Londrina,
Londrina,
PR,
Brazil
| | - Marcelo Santos Castilho
- Laboratório de Bioinformática e Modelagem Molecular,
Departamento do Medicamento,
Faculdade de Farmácia,
Universidade Federal da Bahia,
Salvador,
BA,
Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Proteômica,
Departamento de Genética e Evolução,
Universidade Estadual de Campinas,
Campinas,
SP,
Brazil
| | - Carlos Priminho Pirovani
- Centro de Biotecnologia e Genética,
Departamento de Ciências Biológicas,
Universidade Estadual de Santa Cruz,
Ilhéus,
BA,
Brazil
| | - Alessandra Selbach-Schnadelbach
- Laboratório de Biologia Molecular,
Instituto de Biologia,
Departamento de Biologia Geral,
Universidade Federal da Bahia,
Salvador,
BA,
Brazil
| | - Karina Peres Gramacho
- Laboratório de Fitopatologia Molecular,
Centro de Pesquisas do Cacau,
Ilhéus,
BA,
Brazil
| | - Pablo Ivan Pereira Ramos
- Laboratório de Biologia Molecular,
Instituto de Biologia,
Departamento de Biologia Geral,
Universidade Federal da Bahia,
Salvador,
BA,
Brazil
| | - Luciana Veiga Barbosa
- Laboratório de Biologia Molecular,
Instituto de Biologia,
Departamento de Biologia Geral,
Universidade Federal da Bahia,
Salvador,
BA,
Brazil
| | | | - Aristóteles Góes-Neto
- Laboratório de Pesquisa em Microbiologia,
Departamento de Ciências Biológicas,
Universidade Estadual de Feira de Santana,
Feira de Santana,
BA,
Brazil
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Temer B, Santos LV, Calderón LA, Guimarães Pereira GA. Expression of a bacterial xylose isomerase in an industrial strain of Saccharomyces cerevisiae. BMC Proc 2014. [PMCID: PMC4210710 DOI: 10.1186/1753-6561-8-s4-p222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Camargo ELO, Nascimento LC, Soler M, Salazar MM, Lepikson-Neto J, Marques WL, Alves A, Teixeira PJPL, Mieczkowski P, Carazzolle MF, Martinez Y, Deckmann AC, Rodrigues JC, Grima-Pettenati J, Pereira GAG. Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. BMC Plant Biol 2014; 14:256. [PMID: 25260963 PMCID: PMC4189757 DOI: 10.1186/s12870-014-0256-9] [Citation(s) in RCA: 30] [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: 06/11/2014] [Accepted: 09/20/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND Nitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns. RESULTS Histological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants. CONCLUSIONS This work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.
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Affiliation(s)
- Eduardo Leal Oliveira Camargo
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Leandro Costa Nascimento
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Marçal Soler
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Marcela Mendes Salazar
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Jorge Lepikson-Neto
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Wesley Leoricy Marques
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Ana Alves
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Paulo José Pereira Lima Teixeira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | | | - Marcelo Falsarella Carazzolle
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - Yves Martinez
- />Fédération de Recherche “Agrobiosciences, Interactions et Biodiversité”, 24 Chemin de borde rouge, BP 42617, 31326 Castanet-Tolosan, France
| | - Ana Carolina Deckmann
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
| | - José Carlos Rodrigues
- />Tropical Research Institute of Portugal (IICT), Forestry and Forest Products Group, Tapada da Ajuda, Lisboa, Portugal
- />Centro de Estudos Florestais, Tapada da Ajuda, Lisboa, Portugal
| | - Jacqueline Grima-Pettenati
- />Laboratoire de Recherche en Sciences Végétales, UMR 5546: CNRS - Université de Toulouse III (UPS), Auzeville, BP 42617, F-31326 Castanet-Tolosan, France
| | - Gonçalo Amarante Guimarães Pereira
- />Universidade Estadual de Campinas; UNICAMP; Instituto de Biologia; Departamento de Genética, Evolução e Bioagentes; Laboratório de Genômica e Expressão, Campinas, Brazil
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Carazzolle MF, de Carvalho LM, Slepicka HH, Vidal RO, Pereira GAG, Kobarg J, Vaz Meirelles G. IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PLoS One 2014; 9:e100385. [PMID: 24949626 PMCID: PMC4065059 DOI: 10.1371/journal.pone.0100385] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. RESULTS We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. CONCLUSIONS We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.
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Affiliation(s)
- Marcelo Falsarella Carazzolle
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Unicamp, Campinas, São Paulo, Brazil
| | - Lucas Miguel de Carvalho
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Hugo Henrique Slepicka
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Unicamp, Campinas, São Paulo, Brazil
| | | | - Jörg Kobarg
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Gabriela Vaz Meirelles
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
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Teixeira PJPL, Costa GGL, Fiorin GL, Pereira GAG, Mondego JMC. Novel receptor-like kinases in cacao contain PR-1 extracellular domains. Mol Plant Pathol 2013; 14:602-9. [PMID: 23573899 PMCID: PMC6638629 DOI: 10.1111/mpp.12028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Members of the pathogenesis-related protein 1 (PR-1) family are well-known markers of plant defence responses, forming part of the arsenal of the secreted proteins produced on pathogen recognition. Here, we report the identification of two cacao (Theobroma cacao L.) PR-1s that are fused to transmembrane regions and serine/threonine kinase domains, in a manner characteristic of receptor-like kinases (RLKs). These proteins (TcPR-1f and TcPR-1g) were named PR-1 receptor kinases (PR-1RKs). Phylogenetic analysis of RLKs and PR-1 proteins from cacao indicated that PR-1RKs originated from a fusion between sequences encoding PR-1 and the kinase domain of a LecRLK (Lectin Receptor-Like Kinase). Retrotransposition marks surround TcPR-1f, suggesting that retrotransposition was involved in the origin of PR-1RKs. Genes with a similar domain architecture to cacao PR-1RKs were found in rice (Oryza sativa), barrel medic (Medicago truncatula) and a nonphototrophic bacterium (Herpetosiphon aurantiacus). However, their kinase domains differed from those found in LecRLKs, indicating the occurrence of convergent evolution. TcPR-1g expression was up-regulated in the biotrophic stage of witches' broom disease, suggesting a role for PR-1RKs during cacao defence responses. We hypothesize that PR-1RKs transduce a defence signal by interacting with a PR-1 ligand.
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Affiliation(s)
- Paulo José Pereira Lima Teixeira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas-Uicamp, CP 6109, Campinas, SP 13083-970, Brazil
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Real F, Vidal RO, Carazzolle MF, Mondego JMC, Costa GGL, Herai RH, Würtele M, de Carvalho LM, Carmona e Ferreira R, Mortara RA, Barbiéri CL, Mieczkowski P, da Silveira JF, Briones MRDS, Pereira GAG, Bahia D. The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. DNA Res 2013; 20:567-81. [PMID: 23857904 PMCID: PMC3859324 DOI: 10.1093/dnares/dst031] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [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] [Indexed: 01/09/2023] Open
Abstract
We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.
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Affiliation(s)
- Fernando Real
- 1Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo - EPM/UNIFESP, Rua Botucatu 862, 6 andar, 04023-062 São Paulo, Brazil
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Salazar MM, Nascimento LC, Camargo ELO, Gonçalves DC, Lepikson Neto J, Marques WL, Teixeira PJPL, Mieczkowski P, Mondego JMC, Carazzolle MF, Deckmann AC, Pereira GAG. Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. BMC Genomics 2013; 14:201. [PMID: 23521840 PMCID: PMC3618336 DOI: 10.1186/1471-2164-14-201] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 10/17/2012] [Accepted: 03/08/2013] [Indexed: 12/02/2022] Open
Abstract
Background Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. grandis grows rapidly and is adapted to tropical/subtropical climates; and E. urophylla, though less productive, is considered a source of genes related to robustness. Wood, or secondary xylem, results from cambium vascular differentiation and is mostly composed of cellulose, lignin and hemicelluloses. In this study, the xylem transcriptomes of the three Eucalyptus species were investigated in order to provide insights on the particularities presented by each of these species. Results Data analysis showed that (1) most Eucalyptus genes are expressed in xylem; (2) most genes expressed in species-specific way constitutes genes with unknown functions and are interesting targets for future studies; (3) relevant differences were observed in the phenylpropanoid pathway: E. grandis xylem presents higher expression of genes involved in lignin formation whereas E. urophylla seems to deviates the pathway towards flavonoid formation; (4) stress-related genes are considerably more expressed in E. urophylla, suggesting that these genes may contribute to its robustness. Conclusions The comparison of these three transcriptomes indicates the molecular signatures underlying some of their distinct wood characteristics. This information may contribute to the understanding of xylogenesis, thus increasing the potential of genetic engineering approaches aiming at the improvement of Eucalyptus forest plantations productivity.
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Affiliation(s)
- Marcela Mendes Salazar
- Laboratório de Genômica e Expressão, Departamento de Genética Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo CEP: 13083-970, Campinas, Brasil
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Pereira JF, Almeida APMM, Cota J, Pamphile JA, Ferreira da Silva G, de Araújo EF, Gramacho KP, Brommonschenkel SH, Pereira GAG, de Queiroz MV. Boto, a class II transposon in Moniliophthora perniciosa, is the first representative of the PIF/Harbinger superfamily in a phytopathogenic fungus. Microbiology (Reading) 2013; 159:112-125. [DOI: 10.1099/mic.0.062901-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Jorge Fernando Pereira
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | - Júnio Cota
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - João Alencar Pamphile
- Universidade Estadual de Maringá, Departamento de Biologia Celular e Genética, CEP 87020-900, Maringá, PR, Brazil
| | - Gilvan Ferreira da Silva
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | - Elza Fernandes de Araújo
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
| | | | | | | | - Marisa Vieira de Queiroz
- Universidade Federal de Viçosa, Departamento de Microbiologia, CEP 36571-000, Viçosa, MG, Brazil
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Vidal RO, do Nascimento LC, Mondego JMC, Pereira GAG, Carazzolle MF. Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 2012; 35:331-4. [PMID: 22802718 PMCID: PMC3392885 DOI: 10.1590/s1415-47572012000200014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [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] [Indexed: 12/30/2022] Open
Abstract
The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both cultivars. Our method identified more than 6,000 SNPs in tolerant and sensitive Brazilian cultivars in those drought stress related genes. Among these SNPs, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (MYB, WRKY) related to tolerance to abiotic stress.
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Affiliation(s)
- Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, SP, Brazil
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do Nascimento LC, Costa GGL, Binneck E, Pereira GAG, Carazzolle MF. A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. Genet Mol Biol 2012; 35:203-11. [PMID: 22802706 PMCID: PMC3392873 DOI: 10.1590/s1415-47572012000200002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [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] [Indexed: 12/22/2022] Open
Abstract
The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive cDNA libraries), as well as web interfaces to access information about soybean gene annotation and expression.
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Affiliation(s)
- Leandro Costa do Nascimento
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Gustavo Gilson Lacerda Costa
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuária, Londrina, PR, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Nascimento LC, Neto JL, Salaza MM, Camargo ELO, Marques WL, Gonçalves DC, Vidal RO, Pereira GAG, Carazzolle MF. An integrated database of Eucalyptusspp. genome project. BMC Proc 2011. [PMCID: PMC3240020 DOI: 10.1186/1753-6561-5-s7-p170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Zaparoli G, Barsottini MRDO, de Oliveira JF, Dyszy F, Teixeira PJPL, Barau JG, Garcia O, Costa-Filho AJ, Ambrosio ALB, Pereira GAG, Dias SMG. The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity. Biochemistry 2011; 50:9901-10. [PMID: 21999603 DOI: 10.1021/bi201253b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The necrosis- and ethylene-inducing peptide 1 (NEP1)-like proteins (NLPs) are proteins secreted from bacteria, fungi and oomycetes, triggering immune responses and cell death in dicotyledonous plants. Genomic-scale studies of Moniliophthora perniciosa, the fungus that causes the Witches' Broom disease in cacao, which is a serious economic concern for South and Central American crops, have identified five members of this family (termed MpNEP1-5). Here, we show by RNA-seq that MpNEP2 is virtually the only NLP expressed during the fungus infection. The quantitative real-time polymerase chain reaction results revealed that MpNEP2 has an expression pattern that positively correlates with the necrotic symptoms, with MpNEP2 reaching its highest level of expression at the advanced necrotic stage. To improve our understanding of MpNEP2's molecular mechanism of action, we determined the crystallographic structure of MpNEP2 at 1.8 Å resolution, unveiling some key structural features. The implications of a cation coordination found in the crystal structure were explored, and we show that MpNEP2, in contrast to another previously described member of the NLP family, NLP(Pya) from Pythium aphanidermatum, does not depend on an ion to accomplish its necrosis- and electrolyte leakage-promoting activities. Results of site-directed mutagenesis experiments confirmed the importance of a negatively charged cavity and an unforeseen hydrophobic β-hairpin loop for MpNEP2 activity, thus offering a platform for compound design with implications for disease control. Electron paramagnetic resonance and fluorescence assays with MpNEP2 performed in the presence of lipid vesicles of different compositions showed no sign of interaction between the protein and the lipids, implying that MpNEP2 likely requires other anchoring elements from the membrane to promote cytolysis or send death signals.
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Affiliation(s)
- Gustavo Zaparoli
- Departamento de Genética e Evolução, IB/UNICAMP, CP 6109, 13083-970 Campinas, SP, Brazil
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Salazar MM, Nascimento LC, Camargo ELO, Vidal RO, Lepikson-Neto J, Goncalves DC, Marques WL, Teixeira PJSL, Pereira GAG. Comparative transcriptome analysis of tree Eucalyptusspecies using RNAseq technology: analysis of genes interfering in wood quality aspects. BMC Proc 2011. [PMCID: PMC3240025 DOI: 10.1186/1753-6561-5-s7-p175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Pirovani CP, da Silva Santiago A, dos Santos LS, Micheli F, Margis R, da Silva Gesteira A, Alvim FC, Pereira GAG, de Mattos Cascardo JC. Theobroma cacao cystatins impair Moniliophthora perniciosa mycelial growth and are involved in postponing cell death symptoms. Planta 2010; 232:1485-1497. [PMID: 20859638 DOI: 10.1007/s00425-010-1272-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 09/06/2010] [Indexed: 05/29/2023]
Abstract
Three cystatin open reading frames named TcCys1, TcCys2 and TcCys3 were identified in cDNA libraries from compatible interactions between Theobroma cacao (cacao) and Moniliophthora perniciosa. In addition, an ORF named TcCys4 was identified in the cDNA library of the incompatible interaction. The cDNAs encoded conceptual proteins with 209, 127, 124, and 205 amino acid residues, with a deduced molecular weight of 24.3, 14.1, 14.3 and 22.8 kDa, respectively. His-tagged recombinant proteins were purified from Escherichia coli expression, and showed inhibitory activities against M. perniciosa. The four recombinant cystatins exhibited K(i) values against papain in the range of 152-221 nM. Recombinant TcCYS3 and TcCYS4 immobilized in CNBr-Sepharose were efficient to capture M. perniciosa proteases from culture media. Polyclonal antibodies raised against the recombinant TcCYS4 detected that the endogenous protein was more abundant in young cacao tissues, when compared with mature tissues. A ~85 kDa cacao multicystatin induced by M. perniciosa inoculation, MpNEP (necrosis and ethylene-inducing protein) and M. perniciosa culture supernatant infiltration were detected by anti-TcCYS4 antibodies in cacao young tissues. A direct role of the cacao cystatins in the defense against this phytopathogen was proposed, as well as its involvement in the development of symptoms of programmed cell death.
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Affiliation(s)
- Carlos Priminho Pirovani
- UESC, DCB, Laboratório de Proteômica, Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, BA, 45650-000, Brazil
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Vidal RO, Mondego JMC, Pot D, Ambrósio AB, Andrade AC, Pereira LFP, Colombo CA, Vieira LGE, Carazzolle MF, Pereira GAG. A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica. Plant Physiol 2010; 154:1053-66. [PMID: 20864545 PMCID: PMC2971587 DOI: 10.1104/pp.110.162438] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
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Deckmann AC, Theizen TH, Medrano FJ, Franchini KG, Pereira GAG. Immediate response of myocardium to pressure overload includes transient regulation of genes associated with mitochondrial bioenergetics and calcium availability. Genet Mol Biol 2010; 33:12-6. [PMID: 21637598 PMCID: PMC3036092 DOI: 10.1590/s1415-47572010005000004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/12/2008] [Accepted: 08/17/2009] [Indexed: 12/24/2022] Open
Abstract
Ventricular hypertrophy is one of the major myocardial responses to pressure overload (PO). Most studies on early myocardial response focus on the days or even weeks after induction of hypertrophic stimuli. Since mechanotransduction pathways are immediately activated in hearts undergoing increased work load, it is reasonable to infer that the myocardial gene program may be regulated in the first few hours. In the present study, we monitored the expression of some genes previously described in the context of myocardial hypertrophic growth by using the Northern blot technique, to estimate the mRNA content of selected genes in rat myocardium for the periods 1, 3, 6, 12 and 48 h after PO stimuli. Results revealed an immediate switch in the expression of genes encoding alpha and beta isoforms of myosin heavy chain, and up-regulation of the cardiac isoform of alpha actin. We also detected transitory gene regulation as the increase in mitochondrial cytochrome c oxidase 1 gene expression, parallel to down-regulation of genes encoding sarco(endo)plasmic reticulum Ca+2 ATPase and sodium-calcium exchanger. Taken together, these results indicate that initial myocardial responses to increased work load include alterations in the contractile properties of sarcomeres and transitory adjustment of mitochondrial bioenergetics and calcium availability.
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Affiliation(s)
- Ana Carolina Deckmann
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP Brazil
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Pirovani CP, Carvalho HAS, Machado RCR, Gomes DS, Alvim FC, Pomella AWV, Gramacho KP, Cascardo JCDM, Pereira GAG, Micheli F. Protein extraction for proteome analysis from cacao leaves and meristems, organs infected by Moniliophthora perniciosa, the causal agent of the witches' broom disease. Electrophoresis 2008; 29:2391-401. [PMID: 18435495 DOI: 10.1002/elps.200700743] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Preparation of high-quality proteins from cacao vegetative organs is difficult due to very high endogenous levels of polysaccharides and polyphenols. In order to establish a routine procedure for the application of proteomic and biochemical analysis to cacao tissues, three new protocols were developed; one for apoplastic washing fluid (AWF) extraction, and two for protein extraction--under denaturing and nondenaturing conditions. The first described method allows a quick and easy collection of AWF--using infiltration-centrifugation procedure--that is representative of its composition in intact leaves according to the smaller symplastic contamination detected by the use of the hexose phosphate isomerase marker. Protein extraction under denaturing conditions for 2-DE was remarkably improved by the combination of chemically and physically modified processes including phenol, SDS dense buffer and sonication steps. With this protocol, high-quality proteins from cacao leaves and meristems were isolated, and for the first time well-resolved 1-DE and 2-DE protein patterns of cacao vegetative organs are shown. It also appears that sonication associated with polysaccharide precipitation using tert-butanol was a crucial step for the nondenaturing protein extraction and subsequent enzymatic activity detection. It is expected that the protocols described here could help to develop high-level proteomic and biochemical studies in cacao also being applicable to other recalcitrant plant tissues.
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Affiliation(s)
- Carlos Priminho Pirovani
- UESC, DCB, Laboratório de Genômica e Expressão Gênica, Rodovia Ilhéus-Itabuna, Ilhéus-BA, Brasil
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de Souza Dantas D, Ramos Dos Santos C, Guimarães Pereira GA, Medrano FJ. Biochemical and structural characterization of the hypoxanthine-guanine-xanthine phosphoribosyltransferase from Pyrococcus horikoshii. Biochim Biophys Acta 2008; 1784:953-60. [PMID: 18405676 DOI: 10.1016/j.bbapap.2008.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/06/2008] [Accepted: 03/07/2008] [Indexed: 11/15/2022]
Abstract
The 6-oxopurine phosphoribosyltransferase (HPRT, EC 2.4.2.8) from the hyperthermophile Pyrococcus horikoshii was expressed in Escherichia coli and purified. Steady-state kinetic studies indicated that the enzyme is able to use hypoxanthine, guanine and xanthine. The first two substrates showed similar catalytic efficiencies, and xanthine presented a much lower value (around 20 times lower), but the catalytic constant was comparable to that of hypoxanthine. The enzyme was not able to bind to GMP-agarose, but was able to bind the other reverse reaction substrate, inorganic pyrophosphate, with low affinity (K(d) of 4.7+/-0.1 mM). Dynamic light scattering and analytical gel filtration suggested that the enzyme exists as a homohexamer in solution.
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Affiliation(s)
- Deyse de Souza Dantas
- Laboratorio de Genômica e Expressão, Departamento de Genética e Evolução, IB-UNICAMP, Caixa Postal 6109, CEP 13083-970, Campinas, Brazil
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Lopes FR, Carazzolle MF, Pereira GAG, Colombo CA, Carareto CMA. Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants. Mol Genet Genomics 2008; 279:385-401. [PMID: 18231813 DOI: 10.1007/s00438-008-0319-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Accepted: 01/02/2008] [Indexed: 11/28/2022]
Abstract
Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and Populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.
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Affiliation(s)
- Fabrício Ramon Lopes
- Laboratory of Molecular Evolution, Department of Biology, UNESP, São Paulo State University, 15054-000, São José do Rio Preto, São Paulo, Brazil
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Rogério F, Teixeira SA, Júnior HJ, Maria CCJ, Vieira AS, de Rezende ACS, Pereira GAG, Muscará MN, Langone F. mRNA and protein expression and activities of nitric oxide synthases in the lumbar spinal cord of neonatal rats after sciatic nerve transection and melatonin administration. Neurosci Lett 2006; 407:182-7. [PMID: 16978780 DOI: 10.1016/j.neulet.2006.08.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 08/15/2006] [Accepted: 08/16/2006] [Indexed: 11/27/2022]
Abstract
Sciatic axotomy in 2-day-old rats (P2) causes lumbar motoneuron loss, which could be associated with nitric oxide (NO) production. NO may be produced by three isoforms of synthase (NOS): neuronal (nNOS), endothelial (eNOS) and inducible (iNOS). We investigated NOS expression and NO synthesis in the lumbar enlargement of rats after sciatic nerve transection at P2 and treatment with the antioxidant melatonin (sc; 1 mg/kg). At time points ranging from P2 to P7, expression of each isoform was assessed by RT-PCR and immunohistochemistry; catalytic rates of calcium-dependent (nNOS, eNOS) and independent (iNOS) NOS were measured by the conversion of [3H]L-arginine to [3H]L-citrulline. All NOS isoforms were expressed and active in unlesioned animals. nNOS and iNOS were detected in some small cells in the parenchyma. Only endothelial cells were positive for eNOS. No NOS isoform was detected in motoneurons. Axotomy did not change these immunohistochemical findings, nNOS and iNOS mRNA expression and calcium-independent activity at all survival times. However, sciatic nerve transection reduced eNOS mRNA levels at P7 and increased calcium-dependent activity at 1 and 6 h. Melatonin did not alter NOS expression. Despite having no action on NOS activity in unlesioned controls the neurohormone enhanced calcium-dependent activity at 1 and 72 h and reduced calcium-independent catalysis at 72 h in lesioned rats. These results suggest that NOS isoforms are constitutive in the neonatal lumbar enlargement and are not overexpressed after sciatic axotomy. Changes in NO synthesis induced by axotomy and melatonin administration in the current model are discussed considering some beneficial and deleterious effects that NO may have.
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Affiliation(s)
- Fábio Rogério
- Department of Physiology and Biophysics, State University of Campinas, UNICAMP, 13083-970 Campinas, SP, Brazil
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Rogério F, Jordão H, Vieira AS, Maria CCJ, Santos de Rezende AC, Pereira GAG, Langone F. Bax and Bcl-2 expression and TUNEL labeling in lumbar enlargement of neonatal rats after sciatic axotomy and melatonin treatment. Brain Res 2006; 1112:80-90. [PMID: 16890920 DOI: 10.1016/j.brainres.2006.07.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 07/05/2006] [Accepted: 07/06/2006] [Indexed: 02/01/2023]
Abstract
Peripheral axotomy in neonatal rats induces neuronal death. We studied the anti-apoptotic protein Bcl-2 and cell death promoter Bax in spinal cord of neonatal rats after sciatic transection and treatment with melatonin, a neuroprotective substance. Pups were unilaterally axotomized at P2 and received melatonin (1 mg/kg; sc) or vehicle 1 h prior to lesion, immediately after, at 1 h, 2 h and then once daily. Rats were sacrificed at 3 h, 6 h, 24 h, 72 h and 5 days postaxotomy. Intact animals were used as controls. Lumbar enlargement was processed for Nissl staining, immunohistochemistry and RT-PCR for Bax or Bcl-2 and TUNEL reaction. Motoneurons (MN) of lesioned (L) and normal (N) sides were counted, and MN survival ratio (MSR=L/N) was calculated. Bax and Bcl-2 showed cytoplasmic immunoreactivity (IR). Bax IR was noticeable in small cells but less evident in MN. In unlesioned pups, some Bax-positive small cells (B+) and TUNEL-positive nuclei (T+) were mainly seen in the dorsal horn. In lesioned animals given vehicle, Bax mRNA levels and numbers of B+ and T+ were increased in comparison with intact controls at 24 h postaxotomy. The basal IR for Bax in MN was not changed by axotomy. Bcl-2 IR was noted in all cells and, like Bcl-2 mRNA, was unaltered after lesion. Melatonin reduced MN loss at 24 h, 72 h and 5 days and T+ at 24 h after lesion but did not interfere with Bax or Bcl-2 expression. These results suggest that (1) sciatic transection at P2 increases Bax mRNA and the amount of B+ and T+ in the lumbar enlargement, (2) Bax IR in immature MN is not altered by axotomy and (3) melatonin protects MN and dorsal horn cells through a mechanism independent of Bax and Bcl-2.
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Affiliation(s)
- Fábio Rogério
- Department of Physiology and Biophysics, State University of Campinas, UNICAMP, 13083-970, Campinas, SP, Brazil
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Vieira LGE, Andrade AC, Colombo CA, Moraes AHDA, Metha Â, Oliveira ACD, Labate CA, Marino CL, Monteiro-Vitorello CDB, Monte DDC, Giglioti É, Kimura ET, Romano E, Kuramae EE, Lemos EGM, Almeida ERPD, Jorge ÉC, Albuquerque ÉVS, Silva FRD, Vinecky F, Sawazaki HE, Dorry HFA, Carrer H, Abreu IN, Batista JAN, Teixeira JB, Kitajima JP, Xavier KG, Lima LMD, Camargo LEAD, Pereira LFP, Coutinho LL, Lemos MVF, Romano MR, Machado MA, Costa MMDC, Sá MFGD, Goldman MHS, Ferro MIT, Tinoco MLP, Oliveira MC, Van Sluys MA, Shimizu MM, Maluf MP, Eira MTSD, Guerreiro Filho O, Arruda P, Mazzafera P, Mariani PDSC, Oliveira RLD, Harakava R, Balbao SF, Tsai SM, Mauro SMZD, Santos SN, Siqueira WJ, Costa GGL, Formighieri EF, Carazzolle MF, Pereira GAG. Brazilian coffee genome project: an EST-based genomic resource. ACTA ACUST UNITED AC 2006. [DOI: 10.1590/s1677-04202006000100008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Coffee is one of the most valuable agricultural commodities and ranks second on international trade exchanges. The genus Coffea belongs to the Rubiaceae family which includes other important plants. The genus contains about 100 species but commercial production is based only on two species, Coffea arabica and Coffea canephora that represent about 70 % and 30 % of the total coffee market, respectively. The Brazilian Coffee Genome Project was designed with the objective of making modern genomics resources available to the coffee scientific community, working on different aspects of the coffee production chain. We have single-pass sequenced a total of 214,964 randomly picked clones from 37 cDNA libraries of C. arabica, C. canephora and C. racemosa, representing specific stages of cells and plant development that after trimming resulted in 130,792, 12,381 and 10,566 sequences for each species, respectively. The ESTs clustered into 17,982 clusters and 32,155 singletons. Blast analysis of these sequences revealed that 22 % had no significant matches to sequences in the National Center for Biotechnology Information database (of known or unknown function). The generated coffee EST database resulted in the identification of close to 33,000 different unigenes. Annotated sequencing results have been stored in an online database at <A HREF="http://www.lge.ibi.unicamp.br/cafe">http://www.lge.ibi.unicamp.br/cafe</A>. Resources developed in this project provide genetic and genomic tools that may hold the key to the sustainability, competitiveness and future viability of the coffee industry in local and international markets.
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Affiliation(s)
| | | | | | | | - Ângela Metha
- Embrapa Recursos Genéticos e Biotecnologia, Brazil
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