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Villalobos-Escobedo JM, Martínez-Hernández JP, Pelagio-Flores R, González-De la Rosa PM, Carreras-Villaseñor N, Abreu-Goodger C, Herrera-Estrella AH. Trichoderma atroviride hyphal regeneration and conidiation depend on cell-signaling processes regulated by a microRNA-like RNA. Microb Genom 2022; 8. [PMID: 36239595 DOI: 10.1099/mgen.0.000869] [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] [Indexed: 11/18/2022] Open
Abstract
The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring regulation by small RNAs for adequate healing of the wounded area. We have previously reported that the response to injury of the filamentous fungus Trichoderma atroviride involves molecular mechanisms closely resembling those of plants and animals that lead to the formation of new hyphae (regeneration) and the development of asexual reproduction structures (conidiophores). However, the involvement of microRNAs in this process has not been investigated in fungi. In this work, we explore the participation of microRNA-like RNAs (milRNAs) molecules by sequencing messenger and small RNAs during the injury response of the WT strain and RNAi mutants. We found that Dcr2 appears to play an important role in hyphal regeneration and is required to produce the majority of sRNAs in T. atroviride. We also determined that the three main milRNAs produced via Dcr2 are induced during the damage-triggered developmental process. Importantly, elimination of a single milRNA phenocopied the main defects observed in the dcr2 mutant. Our results demonstrate the essential role of milRNAs in hyphal regeneration and asexual development by post-transcriptionally regulating cellular signalling processes involving phosphorylation events. These observations allow us to conclude that fungi, like plants and animals, in response to damage activate fine-tuning regulatory mechanisms.
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Affiliation(s)
- José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - J Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - Ramón Pelagio-Flores
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58030 Morelia, Michoacán, Mexico
| | - Pablo M González-De la Rosa
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Nohemí Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C. C.P. 91070 Xalapa, Veracruz, Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Alfredo H Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
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Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol 2016; 26:1577-1584. [PMID: 27238284 DOI: 10.1016/j.cub.2016.04.038] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 02/03/2023]
Abstract
Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.
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Affiliation(s)
- Luis M Corrochano
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Polaino
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - M Isabel Álvarez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Javier Avalos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gertraud Burger
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - Lola P Camino
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - David Cánovas
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Enrique Cerdá-Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Angel Domínguez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Arturo P Eslava
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Fabian Glaser
- Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Gabriel Gutiérrez
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enrique A Iturriaga
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - B Franz Lang
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Wenjun Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Sergio López-García
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Eva M Luque
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Ana T Marcos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA
| | - Humberto R Medina
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | | | - Atsushi Miyazaki
- Department of Biological Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki 986-8580, Japan
| | - Elisa Muñoz-Torres
- Departamento de Biología Celular y Patología, Facultad de Medicina, Universidad de Salamanca, Avenida Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José A Oguiza
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - María Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | - Lucila Ortiz-Castellanos
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Antonio G Pisabarro
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Julio Rodríguez-Romero
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Rosa Ruiz-Vázquez
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mahdi Shahriari
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Ekaterina Shelest
- Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Fátima Silva-Franco
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Khajamohiddin Syed
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Víctor G Tagua
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Nicholas J Talbot
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Michael R Thon
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Hope Tice
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jagjit S Yadav
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Edward L Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611-8525, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | | | - Alexander Idnurm
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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