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Ji S, Liu B, Han J, Kong N, Yang Y, Wang Y, Liu Z. Decrypting biocontrol functions and application modes by genomes data of three Trichoderma Strains/Species. Fungal Genet Biol 2024; 172:103889. [PMID: 38513939 DOI: 10.1016/j.fgb.2024.103889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Trichoderma is an excellent biocontrol agent, but most Trichoderma genomes remained at the scaffold level, which greatly limits the research of biocontrol mechanism. Here, we reported the chromosome-level genome of Trichoderma harzianum CGMCC20739 (Tha739), T. asperellum CGMCC11653 (Tas653) and T. atroviride CGMCC40488 (Tat488), they were assembled into 7 chromosomes, genome size were 40 Mb (10,611 genes), 37.3 Mb (10,102 genes) and 36.3 Mb (9,896 genes), respectively. The positive selected genes of three strains were associated to response to stimulus, signaling transduction, immune system and localization. Furthermore, the number of transcription factors in Tha739, Tas653 and Tat488 strains had significant difference, which may contribute to the differential biocontrol function and stress tolerance. The genes related to signal transduction and gene clusters related to antimicrobial compounds in Tha739 were more than those in Tas653 and Tat488, which showed Tha739 may keenly sense other fungi and quickly secret antimicrobial compounds to inhibit other fungi. Tha739 also contained more genes associated to detoxification, antioxidant and nutrition utilization, indicating it had higher stress-tolerance to hostile environments. And the substrate for synthesizing IAA in Tha739 was mainly 3-indole acetonitrile and indole acetaldehyde, but in Tat488, it was indole-3-acetamide, moreover, Tha739 secreted more phosphatase and phytase and was more related to soil phosphorus metabolism, Tat488 secreted more urease and was more related to soil nitrogen metabolism. These candidate genes related to biocontrol function and stress-tolerance laid foundations for construction of functional strains. All above proved the difference in biocontrol function of Tha739, Tas653 and Tat488 strains, however, the defects in individual strains could be compensated for through Trichoderma-biome during the commercial application process of biocontrol Trichoderma strains.
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Affiliation(s)
- Shida Ji
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; College of Horticulture, ShenYang Agricultural University, Shenyang 110866, China
| | - Bin Liu
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Jing Han
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Ning Kong
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Yongfeng Yang
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China
| | - Yucheng Wang
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
| | - Zhihua Liu
- College of Forestry, ShenYang Agricultural University, Shenyang 110866, China; School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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Martinossi-Allibert I, Ament-Velásquez SL, Saupe SJ, Johannesson H. To self or not to self? Absence of mate choice despite costly outcrossing in the fungus Podospora anserina. J Evol Biol 2023; 36:238-250. [PMID: 36263943 PMCID: PMC10092876 DOI: 10.1111/jeb.14108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Fungi have a large potential for flexibility in their mode of sexual reproduction, resulting in mating systems ranging from haploid selfing to outcrossing. However, we know little about which mating strategies are used in nature, and why, even in well-studied model organisms. Here, we explored the fitness consequences of alternative mating strategies in the ascomycete fungus Podospora anserina. We measured and compared fitness proxies of nine genotypes in either diploid selfing or outcrossing events, over two generations, and with or without environmental stress. We showed that fitness was consistently lower in outcrossing events, irrespective of the environment. The cost of outcrossing was partly attributed to non-self recognition genes with pleiotropic effects on fertility. We then predicted that when presented with options to either self or outcross, individuals would perform mate choice in favour of the reproductive strategy that yields higher fitness. Contrary to our prediction, individuals did not seem to avoid outcrossing when a choice was offered, in spite of the fitness cost incurred. Our results suggest that, although functionally diploid, P. anserina does not benefit from outcrossing in most cases. We outline different explanations for the apparent lack of mate choice in face of high fitness costs associated with outcrossing, including a new perspective on the pleiotropic effect of non-self recognition genes.
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Affiliation(s)
- Ivain Martinossi-Allibert
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux CEDEX, France.,Department of Biology, Realfagbygget, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Sven J Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux CEDEX, France
| | - Hanna Johannesson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome. BMC Genomics 2019; 20:87. [PMID: 30683046 PMCID: PMC6347839 DOI: 10.1186/s12864-019-5426-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Background Brain sexual differentiation is sculpted by precise coordination of steroid hormones during development. Programming of several brain regions in males depends upon aromatase conversion of testosterone to estrogen. However, it is not clear the direct contribution that Y chromosome associated genes, especially sex-determining region Y (Sry), might exert on brain sexual differentiation in therian mammals. Two species of spiny rats: Amami spiny rat (Tokudaia osimensis) and Tokunoshima spiny rat (T. tokunoshimensis) lack a Y chromosome/Sry, and these individuals possess an XO chromosome system in both sexes. Both Tokudaia species are highly endangered. To assess the neural transcriptome profile in male and female Amami spiny rats, RNA was isolated from brain samples of adult male and female spiny rats that had died accidentally and used for RNAseq analyses. Results RNAseq analyses confirmed that several genes and individual transcripts were differentially expressed between males and females. In males, seminal vesicle secretory protein 5 (Svs5) and cytochrome P450 1B1 (Cyp1b1) genes were significantly elevated compared to females, whereas serine (or cysteine) peptidase inhibitor, clade A, member 3 N (Serpina3n) was upregulated in females. Many individual transcripts elevated in males included those encoding for zinc finger proteins, e.g. zinc finger protein X-linked (Zfx). Conclusions This method successfully identified several genes and transcripts that showed expression differences in the brain of adult male and female Amami spiny rat. The functional significance of these findings, especially differential expression of transcripts encoding zinc finger proteins, in this unusual rodent species remains to be determined. Electronic supplementary material The online version of this article (10.1186/s12864-019-5426-6) contains supplementary material, which is available to authorized users.
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Boni AC, Ambrósio DL, Cupertino FB, Montenegro-Montero A, Virgilio S, Freitas FZ, Corrocher FA, Gonçalves RD, Yang A, Weirauch MT, Hughes TR, Larrondo LF, Bertolini MC. Neurospora crassa developmental control mediated by the FLB-3 transcription factor. Fungal Biol 2018; 122:570-582. [PMID: 29801802 DOI: 10.1016/j.funbio.2018.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/16/2018] [Accepted: 01/22/2018] [Indexed: 10/17/2022]
Abstract
Here, we report that the Neurospora crassa FLB-3 protein, the ortholog of the Aspergillus nidulans FlbC transcription factor, is required for developmental control. Deletion of flb-3 leads to changes in hyphae morphology and affects sexual and asexual development. We identified, as putative FLB-3 targets, the N. crassa aba-1, wet-1 and vos-1 genes, orthologs of the ones involved in A. nidulans asexual development and that work downstream of FlbC (abaA, wetA and vosA). In N. crassa, these three genes require FLB-3 for proper expression; however, they appear not to be required for normal development, as demonstrated by gene expression analyses during vegetative growth and asexual development. Moreover, mutant strains in the three genes conidiate well and produce viable conidia. We also determined FLB-3 DNA-binding preferences via protein-binding microarrays (PBMs) and demonstrated by chromatin immunoprecipitation (ChIP) that FLB-3 binds the aba-1, wet-1 and vos-1 promoters. Our data support an important role for FLB-3 in N. crassa development and highlight differences between the regulatory pathways controlled by this transcription factor in different fungal species.
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Affiliation(s)
- Ana Carolina Boni
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Daniela Luz Ambrósio
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Fernanda Barbosa Cupertino
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Alejandro Montenegro-Montero
- Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Stela Virgilio
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Fernanda Zanolli Freitas
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Flávia Adolfo Corrocher
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Rodrigo Duarte Gonçalves
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil
| | - Ally Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Canadian Institutes for Advanced Research, Toronto, ON, Canada
| | - Luis F Larrondo
- Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Maria Célia Bertolini
- Departamento de Bioquímica e Tecnologia Química, Instituto de Química, UNESP, Universidade Estadual Paulista, 14800-060, Araraquara, SP, Brazil.
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Yao G, Li Z, Wu R, Qin Y, Liu G, Qu Y. Penicillium oxalicum PoFlbC regulates fungal asexual development and is important for cellulase gene expression. Fungal Genet Biol 2016; 86:91-102. [DOI: 10.1016/j.fgb.2015.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 12/25/2022]
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Xiang L, Li Y, Zhu Y, Luo H, Li C, Xu X, Sun C, Song J, Shi L, He L, Sun W, Chen S. Transcriptome analysis of the Ophiocordyceps sinensis fruiting body reveals putative genes involved in fruiting body development and cordycepin biosynthesis. Genomics 2014; 103:154-9. [PMID: 24440419 DOI: 10.1016/j.ygeno.2014.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 11/09/2013] [Accepted: 01/07/2014] [Indexed: 12/20/2022]
Abstract
Ophiocordyceps sinensis is a highly valuable and popular medicinal fungus used as a tonic and roborant for thousands of years in traditional Asian medicine. However, unsustainable harvesting practices have endangered this species and very little is known about its developmental programming, its biochemistry and genetics. To begin to address this, the transcriptome of the medicinal O. sinensis fruiting body was analyzed by high-throughput. In this O. sinensis 454-EST dataset, four mating type genes and 121 genes that may be involved in fruiting body development, especially in signal transduction and transcription regulation, were discovered. Moreover, a model was developed for the synthesis of the primary medicinal compound, cordycepin, and the putative biosynthetic enzymes identified. This transcriptome dataset provides a significant new resource for gene discovery in O. sinensis and dissection of its valuable biosynthetic and developmental pathways.
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Affiliation(s)
- Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Yingjie Zhu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Hongmei Luo
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Chunfang Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Xiaolan Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Chao Sun
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Linchun Shi
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Liu He
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100094, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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Reverberi M, Fabbri AA, Fanelli C. Ochratoxin A and Related Mycotoxins. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1191-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nieuwenhuis BPS, Aanen DK. Sexual selection in fungi. J Evol Biol 2013; 25:2397-411. [PMID: 23163326 DOI: 10.1111/jeb.12017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/07/2012] [Accepted: 09/07/2012] [Indexed: 12/14/2022]
Abstract
The significance of sexual selection, the component of natural selection associated with variation in mating success, is well established for the evolution of animals and plants, but not for the evolution of fungi. Even though fungi do not have separate sexes, most filamentous fungi mate in a hermaphroditic fashion, with distinct sex roles, that is, investment in large gametes (female role) and fertilization by other small gametes (male role). Fungi compete to fertilize, analogous to 'male-male' competition, whereas they can be selective when being fertilized, analogous to female choice. Mating types, which determine genetic compatibility among fungal gametes, are important for sexual selection in two respects. First, genes at the mating-type loci regulate different aspects of mating and thus can be subject to sexual selection. Second, for sexual selection, not only the two sexes (or sex roles) but also the mating types can form the classes, the members of which compete for access to members of the other class. This is significant if mating-type gene products are costly, thus signalling genetic quality according to Zahavi's handicap principle. We propose that sexual selection explains various fungal characteristics such as the observed high redundancy of pheromones at the B mating-type locus of Agaricomycotina, the occurrence of multiple types of spores in Ascomycotina or the strong pheromone signalling in yeasts. Furthermore, we argue that fungi are good model systems to experimentally study fundamental aspects of sexual selection, due to their fast generation times and high diversity of life cycles and mating systems.
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Affiliation(s)
- B P S Nieuwenhuis
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
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Bidard F, Coppin E, Silar P. The transcriptional response to the inactivation of the PaMpk1 and PaMpk2 MAP kinase pathways in Podospora anserina. Fungal Genet Biol 2012; 49:643-52. [PMID: 22721649 DOI: 10.1016/j.fgb.2012.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/29/2012] [Accepted: 06/01/2012] [Indexed: 10/28/2022]
Abstract
Transcription pattern during mycelium growth of Podospora anserina was assayed by microarray analysis in wild type and in mutants affected in the MAP kinase genes PaMpk1 and PaMpk2 and in the NADPH oxidase gene PaNox1. 15% of the genes have their expression modified by a factor two or more as growth proceeds in wild type. The genes whose expression is modified during growth in P. anserina are either not conserved or differently regulated in Neurospora crassa and Aspergillus niger, two fungi for which transcriptome data during growth are available. The P. anserina mutants display a similar alteration of their transcriptome profile, with nearly 1000 genes affected similarly in the three mutants, accounting for their similar growth phenotypes. Yet, each mutant has its specific set of modified transcripts, in line with particular phenotypes exhibited by each mutant. Again, there is limited conservation during evolution of the genes regulated at the transcription level by MAP kinases, as indicated by the comparison the P. anserina data, with those of Aspergillus fumigatus and N. crassa, two fungi for which gene expression data are available for mutants of the MAPK pathways. Among the genes regulated in wild type and affected in the mutants, those involved in carbohydrate and secondary metabolisms appear prominent. The vast majority of the genes differentially expressed are of unknown function. Availability of their transcription profile at various stages of development should help to decipher their role in fungal physiology and development.
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Affiliation(s)
- Frédérique Bidard
- Univ Paris Sud, Institut de Génétique et Microbiologie, UMR8621 Orsay, France
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Bourdais A, Bidard F, Zickler D, Berteaux-Lecellier V, Silar P, Espagne E. Wood utilization is dependent on catalase activities in the filamentous fungus Podospora anserina. PLoS One 2012; 7:e29820. [PMID: 22558065 PMCID: PMC3338752 DOI: 10.1371/journal.pone.0029820] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/06/2011] [Indexed: 01/24/2023] Open
Abstract
Catalases are enzymes that play critical roles in protecting cells against the toxic effects of hydrogen peroxide. They are implicated in various physiological and pathological conditions but some of their functions remain unclear. In order to decipher the role(s) of catalases during the life cycle of Podospora anserina, we analyzed the role of the four monofunctional catalases and one bifunctional catalase-peroxidase genes present in its genome. The five genes were deleted and the phenotypes of each single and all multiple mutants were investigated. Intriguingly, although the genes are differently expressed during the life cycle, catalase activity is dispensable during both vegetative growth and sexual reproduction in laboratory conditions. Catalases are also not essential for cellulose or fatty acid assimilation. In contrast, they are strictly required for efficient utilization of more complex biomass like wood shavings by allowing growth in the presence of lignin. The secreted CATB and cytosolic CAT2 are the major catalases implicated in peroxide resistance, while CAT2 is the major player during complex biomass assimilation. Our results suggest that P. anserina produces external H2O2 to assimilate complex biomass and that catalases are necessary to protect the cells during this process. In addition, the phenotypes of strains lacking only one catalase gene suggest that a decrease of catalase activity improves the capacity of the fungus to degrade complex biomass.
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Affiliation(s)
- Anne Bourdais
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Institut Génétique et Développement de Rennes, CNRS, UMR 6061, Rennes, France
- UEB Université Rennes 1, IFR 140, Faculté de Médecine, Rennes, France
| | - Frederique Bidard
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Denise Zickler
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Veronique Berteaux-Lecellier
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Laboratoire d’Excellence « CORAIL », USR 3278 CNRS-EPHE, CRIOBE, BP 1013, Moorea, French Polynesia
| | - Philippe Silar
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- CNRS, Orsay, France
- Univ Paris Diderot, Sorbonne Paris Cité, UFR des Sciences du Vivant, Paris, France
| | - Eric Espagne
- Institut de Génétique et Microbiologie, Univ Paris-Sud, UMR 8621, Orsay, France
- * E-mail:
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Gonçalves RD, Cupertino FB, Freitas FZ, Luchessi AD, Bertolini MC. A genome-wide screen for Neurospora crassa transcription factors regulating glycogen metabolism. Mol Cell Proteomics 2011; 10:M111.007963. [PMID: 21768394 DOI: 10.1074/mcp.m111.007963] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transcription factors play a key role in transcription regulation as they recognize and directly bind to defined sites in promoter regions of target genes, and thus modulate differential expression. The overall process is extremely dynamic, as they have to move through the nucleus and transiently bind to chromatin in order to regulate gene transcription. To identify transcription factors that affect glycogen accumulation in Neurospora crassa, we performed a systematic screen of a deletion strains set generated by the Neurospora Knockout Project and available at the Fungal Genetics Stock Center. In a wild-type strain of N. crassa, glycogen content reaches a maximal level at the end of the exponential growth phase, but upon heat stress the glycogen content rapidly drops. The gene encoding glycogen synthase (gsn) is transcriptionally down-regulated when the mycelium is exposed to the same stress condition. We identified 17 deleted strains having glycogen accumulation profiles different from that of the wild-type strain under both normal growth and heat stress conditions. Most of the transcription factors identified were annotated as hypothetical protein, however some of them, such as the PacC, XlnR, and NIT2 proteins, were biochemically well-characterized either in N. crassa or in other fungi. The identification of some of the transcription factors was coincident with the presence of DNA-binding motifs specific for the transcription factors in the gsn 5'-flanking region, and some of these DNA-binding motifs were demonstrated to be functional by Electrophoretic Mobility Shift Assay (EMSA) experiments. Strains knocked-out in these transcription factors presented impairment in the regulation of gsn expression, suggesting that the transcription factors regulate glycogen accumulation by directly regulating gsn gene expression. Five selected mutant strains showed defects in cell cycle progression, and two transcription factors were light-regulated. The results indicate that there are connections linking different cellular processes, such as metabolism control, biological clock, and cell cycle progression.
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Affiliation(s)
- Rodrigo Duarte Gonçalves
- Instituto de Química, UNESP, Departamento de Bioquímica e Tecnologia Química, 14800-900, Araraquara, SP, Brazil
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Kwon NJ, Garzia A, Espeso EA, Ugalde U, Yu JH. FlbC is a putative nuclear C2H2 transcription factor regulating development in Aspergillus nidulans. Mol Microbiol 2011; 77:1203-19. [PMID: 20624219 DOI: 10.1111/j.1365-2958.2010.07282.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Asexual development (conidiation) in Aspergillus is governed by multiple regulators. Here, we characterize the upstream developmental activator FlbC in Aspergillus nidulans. flbC mRNA is detectable throughout the life cycle, at relatively high levels during vegetative growth, early asexual and late sexual developmental phases. The deletion of flbC causes a delay/reduction in conidiation, brlA and vosA expression, and conidial germination. While overexpression of flbC (OEflbC) does not elaborate conidiophores, it inhibits hyphal growth and activates expression of brlA, abaA and vosA, but not wetA. FlbC is conserved in filamentous Ascomycetes containing two C(2) H(2) zinc fingers at the C-terminus and a putative activation domain at the N-terminus. FlbC localizes in the nuclei of both hyphae and developmental cells. Localization and expression of FlbC are not affected by the absence of FlbB or FlbE, and vice versa. Importantly, overexpression of flbC causes growth inhibition and activation of abaA and vosA in the absence of brlA and abaA respectively. In vitro DNA-binding assay reveals that FlbC binds to the brlA, abaA and vosA, but not the wetA, promoters. In summary, FlbC is a putative nuclear transcription factor necessary for proper activation of conidiation, and its balanced activity is crucial for governing growth and development in A. nidulans.
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Affiliation(s)
- Nak-Jung Kwon
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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Wiemann P, Brown DW, Kleigrewe K, Bok JW, Keller NP, Humpf HU, Tudzynski B. FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence. Mol Microbiol 2010; 77:972-94. [PMID: 20572938 DOI: 10.1111/j.1365-2958.2010.07263.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Besides industrially produced gibberellins (GAs), Fusarium fujikuroi is able to produce additional secondary metabolites such as the pigments bikaverin and neurosporaxanthin and the mycotoxins fumonisins and fusarin C. The global regulation of these biosynthetic pathways is only poorly understood. Recently, the velvet complex containing VeA and several other regulatory proteins was shown to be involved in global regulation of secondary metabolism and differentiation in Aspergillus nidulans. Here, we report on the characterization of two components of the F. fujikuroi velvet-like complex, FfVel1 and FfLae1. The gene encoding this first reported LaeA orthologue outside the class of Eurotiomycetidae is upregulated in ΔFfvel1 microarray-studies and FfLae1 interacts with FfVel1 in the nucleus. Deletion of Ffvel1 and Fflae1 revealed for the first time that velvet can simultaneously act as positive (GAs, fumonisins and fusarin C) and negative (bikaverin) regulator of secondary metabolism, and that both components affect conidiation and virulence of F. fujikuroi. Furthermore, the velvet-like protein FfVel2 revealed similar functions regarding conidiation, secondary metabolism and virulence as FfVel1. Cross-genus complementation studies of velvet complex component mutants between Fusarium, Aspergillus and Penicillium support an ancient origin for this complex, which has undergone a divergence in specific functions mediating development and secondary metabolism.
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Affiliation(s)
- Philipp Wiemann
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Daren W Brown
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Karin Kleigrewe
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Jin Woo Bok
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Nancy P Keller
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Hans-Ulrich Humpf
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Bettina Tudzynski
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
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Zheng Y, Kief J, Auffarth K, Farfsing JW, Mahlert M, Nieto F, Basse CW. The Ustilago maydis Cys2His2-type zinc finger transcription factor Mzr1 regulates fungal gene expression during the biotrophic growth stage. Mol Microbiol 2008; 68:1450-70. [PMID: 18410495 DOI: 10.1111/j.1365-2958.2008.06244.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The smut fungus Ustilago maydis establishes a biotrophic relationship with its host plant maize to progress through sexual development. Here, we report the identification and characterization of the Cys(2)His(2)-type zinc finger protein Mzr1 that functions as a transcriptional activator during host colonization. Expression of the U. maydis mig2 cluster genes is tightly linked to this phase. Upon conditional overexpression, Mzr1 confers induction of a subset of mig2 genes during vegetative growth and this requires the same promoter elements that confer inducible expression in planta. Furthermore, expression of the mig2-4 and mig2-5 genes during biotrophic growth is strongly reduced in cells deleted in mzr1. DNA-array analysis led to the identification of additional Mzr1-induced genes. Some of these genes show a mig2-like plant-specific expression pattern and Mzr1 is responsible for their high-level expression during pathogenesis. Mzr1 function requires the b-dependently regulated Cys(2)His(2)-type cell cycle regulator Biz1, indicating that two stage-specific regulators mediate gene expression during host colonization. In spite of a role as transcriptional activator during biotrophic growth, mzr1 is not essential for pathogenesis; however, conditional overexpression interfered with proliferation during vegetative growth and mating ability, caused a cell separation defect, and triggered filamentous growth. We discuss the implications of these findings.
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Affiliation(s)
- Yan Zheng
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
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15
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Coppin E, de Renty C, Debuchy R. The function of the coding sequences for the putative pheromone precursors in Podospora anserina is restricted to fertilization. EUKARYOTIC CELL 2005; 4:407-20. [PMID: 15701803 PMCID: PMC549327 DOI: 10.1128/ec.4.2.407-420.2005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We cloned the pheromone precursor genes of Podospora anserina in order to elucidate their role in the biology of this fungus. The mfp gene encodes a 24-amino-acid polypeptide finished by the CAAX motif, characteristic of fungal lipopeptide pheromone precursors similar to the a-factor precursor of Saccharomyces cerevisiae. The mfm gene encodes a 221-amino-acid polypeptide, which is related to the S. cerevisiae alpha-factor precursor and contains two 13-residue repeats assumed to correspond to the mature pheromone. We deleted the mfp and mfm coding sequence by gene replacement. The mutations specifically affect male fertility, without impairing female fertility and vegetative growth. The male defect is mating type specific: the mat+ Deltamfp and mat- Deltamfm mutants produce male cells inactive in fertilization whereas the mat- Deltamfp and mat+ Deltamfm mutants show normal male fertility. Genetic data indicate that both mfp and mfm are transcribed at a low level in mat+ and mat- vegetative hyphae. Northern-blot analysis shows that their transcription is induced by the mating types in microconidia (mfp by mat+ and mfm by mat-). We managed to cross Deltamfp Deltamfm strains of opposite mating type, by complementation and transient expression of the pheromone precursor gene to trigger fertilization. These crosses were fertile, demonstrating that once fertilization occurs, the pheromone precursor genes are unnecessary for the completion of the sexual cycle. Finally, we show that the constitutively transcribed gpd::mfm and gpd::mfp constructs are repressed at a posttranscriptional level by the noncognate mating type.
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Affiliation(s)
- Evelyne Coppin
- Institut de Génétique et Microbiologie, UMR 8621 CNRS, Université Paris-Sud, Orsay, France.
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16
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Silar P, Barreau C, Debuchy R, Kicka S, Turcq B, Sainsard-Chanet A, Sellem CH, Billault A, Cattolico L, Duprat S, Weissenbach J. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing. Fungal Genet Biol 2003; 39:250-63. [PMID: 12892638 DOI: 10.1016/s1087-1845(03)00025-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.
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MESH Headings
- Amino Acid Sequence
- Centromere/chemistry
- Centromere/genetics
- Chromosomes, Artificial, Bacterial
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- DNA, Intergenic/analysis
- Gene Rearrangement
- Genes, Fungal
- Genes, rRNA
- Genome, Fungal
- Genomic Library
- Introns
- Molecular Sequence Data
- Physical Chromosome Mapping
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Sordariales/genetics
- Synteny
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Affiliation(s)
- Philippe Silar
- Institut de Génétique et Microbiologie, UMR CNRS 8621, Bât. 400, Université de Paris Sud, 91405 Orsay Cedex, France.
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