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Wang Z, Wang YW, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend JP. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLoS Genet 2023; 19:e1011019. [PMID: 37934795 PMCID: PMC10684091 DOI: 10.1371/journal.pgen.1011019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
Lineage-specific genes (LSGs) have long been postulated to play roles in the establishment of genetic barriers to intercrossing and speciation. In the genome of Neurospora crassa, most of the 670 Neurospora LSGs that are aggregated adjacent to the telomeres are clustered with 61% of the HET-domain genes, some of which regulate self-recognition and define vegetative incompatibility groups. In contrast, the LSG-encoding proteins possess few to no domains that would help to identify potential functional roles. Possible functional roles of LSGs were further assessed by performing transcriptomic profiling in genetic mutants and in response to environmental alterations, as well as examining gene knockouts for phenotypes. Among the 342 LSGs that are dynamically expressed during both asexual and sexual phases, 64% were detectable on unusual carbon sources such as furfural, a wildfire-produced chemical that is a strong inducer of sexual development, and the structurally-related furan 5-hydroxymethyl furfural (HMF). Expression of a significant portion of the LSGs was sensitive to light and temperature, factors that also regulate the switch from asexual to sexual reproduction. Furthermore, expression of the LSGs was significantly affected in the knockouts of adv-1 and pp-1 that regulate hyphal communication, and expression of more than one quarter of the LSGs was affected by perturbation of the mating locus. These observations encouraged further investigation of the roles of clustered lineage-specific and HET-domain genes in ecology and reproduction regulation in Neurospora, especially the regulation of the switch from the asexual growth to sexual reproduction, in response to dramatic environmental conditions changes.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Takao Kasuga
- College of Biological Sciences, University of California, Davis, California, United States of America
| | | | - Yang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yaning Wang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anita Sil
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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Schalamun M, Beier S, Hinterdobler W, Wanko N, Schinnerl J, Brecker L, Engl DE, Schmoll M. MAPkinases regulate secondary metabolism, sexual development and light dependent cellulase regulation in Trichoderma reesei. Sci Rep 2023; 13:1912. [PMID: 36732590 PMCID: PMC9894936 DOI: 10.1038/s41598-023-28938-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is a prolific producer of plant cell wall degrading enzymes, which are regulated in response to diverse environmental signals for optimal adaptation, but also produces a wide array of secondary metabolites. Available carbon source and light are the strongest cues currently known to impact secreted enzyme levels and an interplay with regulation of secondary metabolism became increasingly obvious in recent years. While cellulase regulation is already known to be modulated by different mitogen activated protein kinase (MAPK) pathways, the relevance of the light signal, which is transmitted by this pathway in other fungi as well, is still unknown in T. reesei as are interconnections to secondary metabolism and chemical communication under mating conditions. Here we show that MAPkinases differentially influence cellulase regulation in light and darkness and that the Hog1 homologue TMK3, but not TMK1 or TMK2 are required for the chemotropic response to glucose in T. reesei. Additionally, MAPkinases regulate production of specific secondary metabolites including trichodimerol and bisorbibutenolid, a bioactive compound with cytostatic effect on cancer cells and deterrent effect on larvae, under conditions facilitating mating, which reflects a defect in chemical communication. Strains lacking either of the MAPkinases become female sterile, indicating the conservation of the role of MAPkinases in sexual fertility also in T. reesei. In summary, our findings substantiate the previously detected interconnection of cellulase regulation with regulation of secondary metabolism as well as the involvement of MAPkinases in light dependent gene regulation of cellulase and secondary metabolite genes in fungi.
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Affiliation(s)
- Miriam Schalamun
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Sabrina Beier
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Wolfgang Hinterdobler
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
- MyPilz GmbH, Wienerbergstrasse 55/13-15, 1120, Vienna, Austria
| | - Nicole Wanko
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Dorothea Elisa Engl
- Department of Organic Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Strasse 24, 3430, Tulln, Austria.
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
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Wu T, Chen J, Jiao C, Hu H, Wu Q, Xie Y. Identification of Long Non-Coding RNAs and Their Target Genes from Mycelium and Primordium in Model Mushroom Schizophyllum commune. MYCOBIOLOGY 2022; 50:357-365. [PMID: 36404904 PMCID: PMC9645281 DOI: 10.1080/12298093.2022.2116819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.
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Affiliation(s)
- Tuheng Wu
- Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Jian Chen
- Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Chunwei Jiao
- Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
| | - Huiping Hu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yizhen Xie
- Guangdong Yuewei Edible Fungi Technology Co., Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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