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Inoue S, Thanh Nguyen D, Hamada K, Okuma R, Okada C, Okada M, Abe I, Sengoku T, Goto Y, Suga H. De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2024:e202409973. [PMID: 38837490 DOI: 10.1002/anie.202409973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
Prenylation of peptides is widely observed in the secondary metabolites of diverse organisms, granting peptides unique chemical properties distinct from proteinogenic amino acids. Discovery of prenylated peptide agents has largely relied on isolation or genome mining of naturally occurring molecules. To devise a platform technology for de novo discovery of artificial prenylated peptides targeting a protein of choice, here we have integrated the thioether-macrocyclic peptide (teMP) library construction/selection technology, so-called RaPID (Random nonstandard Peptides Integrated Discovery) system, with a Trp-C3-prenyltransferase KgpF involved in the biosynthesis of a prenylated natural product. This unique enzyme exhibited remarkably broad substrate tolerance, capable of modifying various Trp-containing teMPs to install a prenylated residue with tricyclic constrained structure. We constructed a vast library of prenylated teMPs and subjected it to in vitro selection against a phosphoglycerate mutase. This selection platform has led to the identification of a pseudo-natural prenylated teMP inhibiting the target enzyme with an IC50 of 30 nM. Importantly, the prenylation was essential for the inhibitory activity, enhanced serum stability, and cellular uptake of the peptide, highlighting the benefits of peptide prenylation. This work showcases the de novo discovery platform for pseudo-natural prenylated peptides, which is readily applicable to other drug targets.
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Affiliation(s)
- Sumika Inoue
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Dinh Thanh Nguyen
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Rika Okuma
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Masahiro Okada
- Department of Material and Life Chemistry, Kanagawa University, Kanagawa-ku, 221-8686, Yokohama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, 606-8502, Kyoto, Japan
- Toyota Riken Rising Fellow, Toyota Physical and Chemical Research Institute, Sakyo, 606-8502, Kyoto, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
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2
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Zhang YD, Ji XB, Zong J, Dai XF, Klosterman SJ, Subbarao KV, Zhang DD, Chen JY. Functional analysis of the mating type genes in Verticillium dahliae. BMC Biol 2024; 22:108. [PMID: 38714997 PMCID: PMC11077750 DOI: 10.1186/s12915-024-01900-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Populations of the plant pathogenic fungus Verticillium dahliae display a complex and rich genetic diversity, yet the existence of sexual reproduction in the fungus remains contested. As pivotal genes, MAT genes play a crucial role in regulating cell differentiation, morphological development, and mating of compatible cells. However, the functions of the two mating type genes in V. dahliae, VdMAT1-1-1, and VdMAT1-2-1, remain poorly understood. RESULTS In this study, we confirmed that the MAT loci in V. dahliae are highly conserved, including both VdMAT1-1-1 and VdMAT1-2-1 which share high collinearity. The conserved core transcription factor encoded by the two MAT loci may facilitate the regulation of pheromone precursor and pheromone receptor genes by directly binding to their promoter regions. Additionally, peptide activity assays demonstrated that the signal peptide of the pheromone VdPpg1 possessed secretory activity, while VdPpg2, lacked a predicted signal peptide. Chemotactic growth assays revealed that V. dahliae senses and grows towards the pheromones FO-a and FO-α of Fusarium oxysporum, as well as towards VdPpg2 of V. dahliae, but not in response to VdPpg1. The findings herein also revealed that VdMAT1-1-1 and VdMAT1-2-1 regulate vegetative growth, carbon source utilization, and resistance to stressors in V. dahliae, while negatively regulating virulence. CONCLUSIONS These findings underscore the potential roles of VdMAT1-1-1 and VdMAT1-2-1 in sexual reproduction and confirm their involvement in various asexual processes of V. dahliae, offering novel insights into the functions of mating type genes in this species.
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Affiliation(s)
- Ya-Duo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Bin Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Juan Zong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o United States Agricultural Research Station, Salinas, CA, USA.
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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3
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Srikant S, Gaudet R, Murray AW. Extending the reach of homology by using successive computational filters to find yeast pheromone genes. Curr Biol 2023; 33:4098-4110.e3. [PMID: 37699395 PMCID: PMC10592104 DOI: 10.1016/j.cub.2023.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 07/04/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.
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Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, Oxford Street, Cambridge, MA 02138, USA.
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Yao L, Kong Y, Yang W, Tian H, Meng X, Zhao X, Zhang R, Sun G, Rollins JA, Liang X. Two Putative Pheromone Receptors, but Not Their Cognate Pheromones, Regulate Female Fertility in the Atypical Mating Fungus Colletotrichum fructicola. PHYTOPATHOLOGY 2023; 113:1934-1945. [PMID: 37141175 DOI: 10.1094/phyto-11-22-0436-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Colletotrichum fungi are a group of damaging phytopathogens with atypical mating type loci (harboring only MAT1-2-1 but not MAT1-1-1) and complex sexual behaviors. Sex pheromones and their cognate G-protein-coupled receptors are conserved regulators of fungal mating. These genes, however, lose function frequently among Colletotrichum species, indicating a possibility that pheromone signaling is dispensable for Colletotrichum sexual reproduction. We have identified two putative pheromone-receptor pairs (PPG1:PRE2, PPG2:PRE1) in C. fructicola, a species that exhibits plus-to-minus mating type switching and plus-minus-mediated mating line development. Here, we report the generation and characterization of gene-deletion mutants for all four genes in both plus and minus strain backgrounds. Single-gene deletion of pre1 or pre2 had no effect on sexual development, whereas their double deletion caused self-sterility in both the plus and minus strains. Moreover, double deletion of pre1 and pre2 caused female sterility in plus-minus outcrossing. Double deletion of pre1 and pre2, however, did not inhibit perithecial differentiation or plus-minus-mediated enhancement of perithecial differentiation. Contrary to the results with pre1 and pre2, double deletion of ppg1 and ppg2 had no effect on sexual compatibility, development, or fecundity. We concluded that pre1 and pre2 coordinately regulate C. fructicola mating by recognizing novel signal molecule(s) distinct from canonical Ascomycota pheromones. The contrasting importance between pheromone receptors and their cognate pheromones highlights the complicated nature of sex regulation in Colletotrichum fungi.
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Affiliation(s)
- Liqiang Yao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Kong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Wenrui Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Huanhuan Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xiangchen Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xuemei Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Jeffrey A Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, China
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Schalamun M, Molin EM, Schmoll M. RGS4 impacts carbohydrate and siderophore metabolism in Trichoderma reesei. BMC Genomics 2023; 24:372. [PMID: 37400774 PMCID: PMC10316542 DOI: 10.1186/s12864-023-09467-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Adaptation to complex, rapidly changing environments is crucial for evolutionary success of fungi. The heterotrimeric G-protein pathway belongs to the most important signaling cascades applied for this task. In Trichoderma reesei, enzyme production, growth and secondary metabolism are among the physiological traits influenced by the G-protein pathway in a light dependent manner. RESULTS Here, we investigated the function of the SNX/H-type regulator of G-protein signaling (RGS) protein RGS4 of T. reesei. We show that RGS4 is involved in regulation of cellulase production, growth, asexual development and oxidative stress response in darkness as well as in osmotic stress response in the presence of sodium chloride, particularly in light. Transcriptome analysis revealed regulation of several ribosomal genes, six genes mutated in RutC30 as well as several genes encoding transcription factors and transporters. Importantly, RGS4 positively regulates the siderophore cluster responsible for fusarinine C biosynthesis in light. The respective deletion mutant shows altered growth on nutrient sources related to siderophore production such as ornithine or proline in a BIOLOG phenotype microarray assay. Additionally, growth on storage carbohydrates as well as several intermediates of the D-galactose and D-arabinose catabolic pathway is decreased, predominantly in light. CONCLUSIONS We conclude that RGS4 mainly operates in light and targets plant cell wall degradation, siderophore production and storage compound metabolism in T. reesei.
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Affiliation(s)
- Miriam Schalamun
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Konrad Lorenz Strasse 24, Tulln, 3430 Austria
| | - Eva Maria Molin
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Konrad Lorenz Strasse 24, Tulln, 3430 Austria
| | - Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Konrad Lorenz Strasse 24, Tulln, 3430 Austria
- Division of Terrestrial Ecosystem Research, Centre of Microbiology and Ecosystem Science, University of Vienna, Djerassiplatz 1, Vienna, 1030 Austria
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6
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Wilson AM, Wingfield MJ, Wingfield BD. Structure and number of mating pheromone genes is closely linked to sexual reproductive strategy in Huntiella. BMC Genomics 2023; 24:261. [PMID: 37179314 PMCID: PMC10182648 DOI: 10.1186/s12864-023-09355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Huntiella resides in the Ceratocystidaceae, a family of fungi that accommodates important plant pathogens and insect-associated saprotrophs. Species in the genus have either heterothallic or unisexual (a form of homothallism) mating systems, providing an opportunity to investigate the genetic mechanisms that enable transitions between reproductive strategies in related species. Two newly sequenced Huntiella genomes are introduced in this study and comparative genomics and transcriptomics tools are used to investigate the differences between heterothallism and unisexuality across the genus. RESULTS Heterothallic species harbored up to seven copies of the a-factor pheromone, each of which possessed numerous mature peptide repeats. In comparison, unisexual Huntiella species had only two or three copies of this gene, each with fewer repeats. Similarly, while the heterothallic species expressed up to 12 copies of the mature α-factor pheromone, unisexual species had up to six copies. These significant differences imply that unisexual Huntiella species do not rely on a mating partner recognition system in the same way that heterothallic fungi do. CONCLUSION While it is suspected that mating type-independent pheromone expression is the mechanism allowing for unisexual reproduction in Huntiella species, our results suggest that the transition to unisexuality may also have been associated with changes in the genes governing the pheromone pathway. While these results are specifically related to Huntiella, they provide clues leading to a better understanding of sexual reproduction and the fluidity of mating strategies in fungi more broadly.
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Affiliation(s)
- Andi M Wilson
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa.
| | - Michael J Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
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7
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Schmoll M, Hinterdobler W. Tools for adapting to a complex habitat: G-protein coupled receptors in Trichoderma. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:65-97. [PMID: 36357080 DOI: 10.1016/bs.pmbts.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sensing the environment and interpretation of the received signals are crucial competences of living organisms in order to properly adapt to their habitat, succeed in competition and to reproduce. G-protein coupled receptors (GPCRs) are members of a large family of sensors for extracellular signals and represent the starting point of complex signaling cascades regulating a plethora of intracellular physiological processes and output pathways in fungi. In Trichoderma spp. current research involves a wide range of topics from enzyme production, light response and secondary metabolism to sexual and asexual development as well as biocontrol, all of which require delicate balancing of resources in response to the environmental challenges or biotechnological needs at hand, which are crucially impacted by the surroundings of the fungi and their intercellular signaling cascades triggering a precisely tailored response. In this review we summarize recent findings on sensing by GPCRs in Trichoderma, including the function of pheromone receptors, glucose sensing by CSG1 and CSG2, regulation of secondary metabolism by GPR8 and impacts on mycoparasitism by GPR1. Additionally, we provide an overview on structural determinants, posttranslational modifications and interactions for regulation, activation and signal termination of GPCRs in order to inspire future in depth analyses of their function and to understand previous regulatory outcomes of natural and biotechnological processes modulated or enabled by GPCRs.
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Affiliation(s)
- Monika Schmoll
- Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria.
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8
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Peris D, Lu DS, Kinneberg VB, Methlie IS, Dahl MS, James TY, Kauserud H, Skrede I. Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection. PLoS Genet 2022; 18:e1010097. [PMID: 35358178 PMCID: PMC8970355 DOI: 10.1371/journal.pgen.1010097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/14/2022] [Indexed: 11/19/2022] Open
Abstract
Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.
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Affiliation(s)
- David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Health, Valencian International University (VIU), Valencia, Spain
| | - Dabao Sun Lu
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ine-Susanne Methlie
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Malin Stapnes Dahl
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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9
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Harting R, Starke J, Kusch H, Pöggeler S, Maurus I, Schlüter R, Landesfeind M, Bulla I, Nowrousian M, de Jonge R, Stahlhut G, Hoff KJ, Aßhauer KP, Thürmer A, Stanke M, Daniel R, Morgenstern B, Thomma BPHJ, Kronstad JW, Braus‐Stromeyer SA, Braus GH. A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum. MOLECULAR PLANT PATHOLOGY 2021; 22:939-953. [PMID: 33955130 PMCID: PMC8295516 DOI: 10.1111/mpp.13071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/30/2021] [Indexed: 05/04/2023]
Abstract
Amphidiploid fungal Verticillium longisporum strains Vl43 and Vl32 colonize the plant host Brassica napus but differ in their ability to cause disease symptoms. These strains represent two V. longisporum lineages derived from different hybridization events of haploid parental Verticillium strains. Vl32 and Vl43 carry same-sex mating-type genes derived from both parental lineages. Vl32 and Vl43 similarly colonize and penetrate plant roots, but asymptomatic Vl32 proliferation in planta is lower than virulent Vl43. The highly conserved Vl43 and Vl32 genomes include less than 1% unique genes, and the karyotypes of 15 or 16 chromosomes display changed genetic synteny due to substantial genomic reshuffling. A 20 kb Vl43 lineage-specific (LS) region apparently originating from the Verticillium dahliae-related ancestor is specific for symptomatic Vl43 and encodes seven genes, including two putative transcription factors. Either partial or complete deletion of this LS region in Vl43 did not reduce virulence but led to induction of even more severe disease symptoms in rapeseed. This suggests that the LS insertion in the genome of symptomatic V. longisporum Vl43 mediates virulence-reducing functions, limits damage on the host plant, and therefore tames Vl43 from being even more virulent.
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Affiliation(s)
- Rebekka Harting
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Jessica Starke
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Harald Kusch
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Stefanie Pöggeler
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Isabel Maurus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Rabea Schlüter
- Imaging Center of the Department of BiologyUniversity of GreifswaldGreifswaldGermany
| | - Manuel Landesfeind
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Ingo Bulla
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
| | - Minou Nowrousian
- Department of Molecular and Cellular BotanyRuhr‐Universität BochumBochumGermany
| | - Ronnie de Jonge
- Plant–Microbe Interactions, Department of Biology, Science4LifeUtrecht UniversityUtrechtNetherlands
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Gertrud Stahlhut
- Department of Genetics of Eukaryotic MicroorganismsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Katharina J. Hoff
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Kathrin P. Aßhauer
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Andrea Thürmer
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Mario Stanke
- Institute for Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
- Center for Functional Genomics of MicrobesUniversity of GreifswaldGreifswaldGermany
| | - Rolf Daniel
- Department of Genomic and Applied MicrobiologyInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Burkhard Morgenstern
- Department of BioinformaticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | | | - James W. Kronstad
- Michael Smith Laboratories, Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCCanada
| | - Susanna A. Braus‐Stromeyer
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and GeneticsInstitute of Microbiology and Genetics and Göttingen Center for Molecular BiosciencesUniversity of GöttingenGöttingenGermany
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Hinterdobler W, Li G, Spiegel K, Basyouni-Khamis S, Gorfer M, Schmoll M. Trichoderma reesei Isolated From Austrian Soil With High Potential for Biotechnological Application. Front Microbiol 2021; 12:552301. [PMID: 33584603 PMCID: PMC7876326 DOI: 10.3389/fmicb.2021.552301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/12/2021] [Indexed: 11/24/2022] Open
Abstract
Fungi of the genus Trichoderma are of high importance for biotechnological applications, in biocontrol and for production of homologous and heterologous proteins. However, sexual crossing under laboratory conditions has so far only been achieved with the species Trichoderma reesei, which was so far only isolated from tropical regions. Our isolation efforts aimed at the collection of Trichoderma strains from Austrian soils surprisingly also yielded 12 strains of the species T. reesei, which was previously not known to occur in Europe. Their identity was confirmed with tef1- and rpb2-sequencing and phylogenetic analysis. They could clearly be distinguished from tropical strains including the common laboratory wildtypes by UP-PCR and genetic variations adjacent to the mating type locus. The strains readily mated with reference strains derived from CBS999.97. Secreted cellulase and xylanase levels of these isolates were up to six-fold higher than those of QM6a indicating a high potential for strain improvement. The strains showed different responses to injury in terms of induction of sporulation, but a correlation to alterations in the nox1-gene sequence was not detected. Several synonymous SNPs were found in the sequence of the regulator gene noxR of the soil isolates compared to QM6a. Only in one strain, non-synonymous SNPs were found which impact a PEST sequence of NoxR, suggesting altered protein stability. The availability of sexually fertile strains from middle Europe naturally producing decent amounts of plant cell wall degrading enzymes opens up novel perspectives for non-GMO strain improvement and biological pretreatment of plant biomass for bioethanol production. Moreover, the varied response of these strains to injury in terms of sporulation, which is independent of Nox1 and NoxR suggests that additional regulators impact this phenomenon in T. reesei.
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Affiliation(s)
- Wolfgang Hinterdobler
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Guofen Li
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Katharina Spiegel
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Samira Basyouni-Khamis
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria.,Department of Sustainable Agricultural Systems, Institute of Agricultural Engineering, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Markus Gorfer
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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11
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Vasieva O, Goryanin I. Is there a Function for a Sex Pheromone Precursor? J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2019-0016/jib-2019-0016.xml. [PMID: 31301673 PMCID: PMC7074142 DOI: 10.1515/jib-2019-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/07/2019] [Indexed: 12/29/2022] Open
Abstract
Functional coupling and comparative genomics analysis have been applied to study functional associations of orthologs of enterococcal cAD1 sex pheromone (P13268) known to be responsible for biofilm formation, conjugative plasmid transfer and spreading of bacterial antibiotics resistance. cAD1 peptide pheromone is released from the membrane lipoprotein with the peptide precursor encoded by a gene cad (tr|C2JQE7). Our analysis of genomic neighbourhood of cad and motifs of the encoded polypeptide and its orthologs suggests a close functional association between cAD1 and ApbE protein (Q82Z24), a FMN insertion and trafficking facilitator. The cad and apbE orthologs were coupled in the genomes and ApbE-specific motifs for FMN covalent attachment were identified in cad-encoded protein sequence and its orthologs. These findings suggest a potential role of FMN-based reductase function of the cAD1 lipoprotein precursor in its processing and release of the active sex pheromone peptide. They may lead to a new approach in prevention of antibiotic resistance spread via targeting sex pheromone processing chaperones or by suppression of the FMN availability and covalent binding. This methods can be also applied to a controlled evolution of bacterial pathogenicity in microbial fuel cells, as the findings suggest the crosstalk between bacterial pathogenicity and bacterial electro-activity.
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Affiliation(s)
- O Vasieva
- University of Liverpool, Crown street, Liverpool, UK.,Ingenet ltd, 3d floor, 207 Regent street, London, UK
| | - I Goryanin
- University of Edinburgh, Edinburgh, UK.,Okinawa Institute Science and Technology, Okinawa, Japan.,Tianjin Institute of Industrial Biotechnology, Tianjin, China
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12
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Autocrine pheromone signalling regulates community behaviour in the fungal pathogen Fusarium oxysporum. Nat Microbiol 2019; 4:1443-1449. [PMID: 31133754 DOI: 10.1038/s41564-019-0456-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 04/12/2019] [Indexed: 11/09/2022]
Abstract
Autocrine self-signalling via secreted peptides and cognate receptors regulates cell development in eukaryotes and is conserved from protozoans to mammals1,2. In contrast, secreted peptides from higher fungi have been traditionally associated with paracrine non-self-signalling during sexual reproduction3. For example, cells of the model fungus Saccharomyces cerevisiae fall into two distinct mating types (MAT), which produce either a- or α-pheromone and the cognate receptors Ste2 or Ste3, respectively4. Inappropriate autocrine pheromone signalling (APS) during mating is prevented by downregulation of the self-pheromone receptor4,5 and by a-type cell-specific cleavage of α-pheromone through the protease Bar1 (refs. 6-8). While APS can be artificially induced by manipulation of the pheromone secrete-and-sense circuit7,9-11, its natural occurrence in ascomycete fungi has not been described. Here, we show that Fusarium oxysporum-a devastating plant pathogen that lacks a known sexual cycle12-co-expresses both pheromone-receptor pairs, resulting in autocrine regulation of developmental programmes other than mating. We found that unisexual populations of MAT1-1 cells (α-type idiomorphs13) secrete and sense both a- and α-pheromone, and that their perception requires the cognate receptors and conserved elements of the cell wall integrity mitogen-activated protein kinase cascade. We further show that F. oxysporum uses APS to regulate spore germination in a cell-density-dependent manner, whereby the α-Ste2 interaction leads to repression of conidial germination while the a-Ste3 interaction relieves repression. Our results reveal the existence of a regulatory function for peptide pheromones in the quorum-sensing-mediated control of fungal development.
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13
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It's All in the Genes: The Regulatory Pathways of Sexual Reproduction in Filamentous Ascomycetes. Genes (Basel) 2019; 10:genes10050330. [PMID: 31052334 PMCID: PMC6562746 DOI: 10.3390/genes10050330] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/17/2019] [Accepted: 04/24/2019] [Indexed: 12/23/2022] Open
Abstract
Sexual reproduction in filamentous ascomycete fungi results in the production of highly specialized sexual tissues, which arise from relatively simple, vegetative mycelia. This conversion takes place after the recognition of and response to a variety of exogenous and endogenous cues, and relies on very strictly regulated gene, protein, and metabolite pathways. This makes studying sexual development in fungi an interesting tool in which to study gene-gene, gene-protein, and protein-metabolite interactions. This review provides an overview of some of the most important genes involved in this process; from those involved in the conversion of mycelia into sexually-competent tissue, to those involved in the development of the ascomata, the asci, and ultimately, the ascospores.
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14
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Dattenböck C, Tisch D, Schuster A, Monroy AA, Hinterdobler W, Schmoll M. Gene regulation associated with sexual development and female fertility in different isolates of Trichoderma reesei. Fungal Biol Biotechnol 2018; 5:9. [PMID: 29785273 PMCID: PMC5952832 DOI: 10.1186/s40694-018-0055-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/12/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Trichoderma reesei is one of the most frequently used filamentous fungi in industry for production of homologous and heterologous proteins. The ability to use sexual crossing in this fungus was discovered several years ago and opens up new perspectives for industrial strain improvement and investigation of gene regulation. RESULTS Here we investigated the female sterile strain QM6a in comparison to the fertile isolate CBS999.97 and backcrossed derivatives of QM6a, which have regained fertility (FF1 and FF2 strains) in both mating types under conditions of sexual development. We found considerable differences in gene regulation between strains with the CBS999.97 genetic background and the QM6a background. Regulation patterns of QM6a largely clustered with the backcrossed FF1 and FF2 strains. Differential regulation between QM6a and FF1/FF2 as well as clustering of QM6a patterns with those of CBS999.97 strains was also observed. Consistent mating type dependent regulation was limited to mating type genes and those involved in pheromone response, but included also nta1 encoding a putative N-terminal amidase previously not associated with development. Comparison of female sterile QM6a with female fertile strains showed differential expression in genes encoding several transcription factors, metabolic genes and genes involved in secondary metabolism. CONCLUSIONS Evaluation of the functions of genes specifically regulated under conditions of sexual development and of genes with highest levels of transcripts under these conditions indicated a relevance of secondary metabolism for sexual development in T. reesei. Among others, the biosynthetic genes of the recently characterized SOR cluster are in this gene group. However, these genes are not essential for sexual development, but rather have a function in protection and defence against competitors during reproduction.
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Affiliation(s)
- Christoph Dattenböck
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Doris Tisch
- Institute of Chemical Engineering, Research Area Molecular Biotechnology, TU Wien, 1060 Vienna, Austria
| | - Andre Schuster
- Institute of Chemical Engineering, Research Area Molecular Biotechnology, TU Wien, 1060 Vienna, Austria
| | - Alberto Alonso Monroy
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Wolfgang Hinterdobler
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430 Tulln, Austria
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15
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Hennig S, Wenzel M, Haas C, Hoffmann A, Weber J, Rödel G, Ostermann K. New approaches in bioprocess-control: Consortium guidance by synthetic cell-cell communication based on fungal pheromones. Eng Life Sci 2018; 18:387-400. [PMID: 32624919 DOI: 10.1002/elsc.201700181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 01/02/2023] Open
Abstract
Bioconversions in industrial processes are currently dominated by single-strain approaches. With the growing complexity of tasks to be carried out, microbial consortia become increasingly advantageous and eventually may outperform single-strain fermentations. Consortium approaches benefit from the combined metabolic capabilities of highly specialized strains and species, and the inherent division of labor reduces the metabolic burden for each strain while increasing product yields and reaction specificities. However, consortium-based designs still suffer from a lack of available tools to control the behavior and performance of the individual subpopulations and of the entire consortium. Here, we propose to implement novel control elements for microbial consortia based on artificial cell-cell communication via fungal mating pheromones. Coupling to the desired output is mediated by pheromone-responsive gene expression, thereby creating pheromone-dependent communication channels between different subpopulations of the consortia. We highlight the benefits of artificial communication to specifically target individual subpopulations of microbial consortia and to control e.g. their metabolic profile or proliferation rate in a predefined and customized manner. Due to the steadily increasing knowledge of sexual cycles of industrially relevant fungi, a growing number of strains and species can be integrated into pheromone-controlled sensor-actor systems, exploiting their unique metabolic properties for microbial consortia approaches.
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Affiliation(s)
- Stefan Hennig
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Mandy Wenzel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Christiane Haas
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Andreas Hoffmann
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany
| | - Jost Weber
- Institute of Natural Materials Technology Technische Universität Dresden Dresden Germany.,Evolva Biotec A/S Lersø Parkallé 42 Copenhagen Denmark
| | - Gerhard Rödel
- Institute of Genetics Technische Universität Dresden Dresden Germany
| | - Kai Ostermann
- Institute of Genetics Technische Universität Dresden Dresden Germany
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16
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Wallen RM, Perlin MH. An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi. Front Microbiol 2018; 9:503. [PMID: 29619017 PMCID: PMC5871698 DOI: 10.3389/fmicb.2018.00503] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/05/2018] [Indexed: 12/11/2022] Open
Abstract
Sexual reproduction likely evolved as protection from environmental stresses, specifically, to repair DNA damage, often via homologous recombination. In higher eukaryotes, meiosis and the production of gametes with allelic combinations different from parental type provides the side effect of increased genetic variation. In fungi it appears that while the maintenance of meiosis is paramount for success, outcrossing is not a driving force. In the subkingdom Dikarya, fungal members are characterized by existence of a dikaryon for extended stages within the life cycle. Such fungi possess functional or, in some cases, relictual, loci that govern sexual reproduction between members of their own species. All mating systems identified so far in the Dikarya employ a pheromone/receptor system for haploid organisms to recognize a compatible mating partner, although the paradigm in the Ascomycota, e.g., Saccharomyces cerevisiae, is that genes for the pheromone precursor and receptor are not found in the mating-type locus but rather are regulated by its products. Similarly, the mating systems in the Ascomycota are bipolar, with two non-allelic idiomorphs expressed in cells of opposite mating type. In contrast, for the Basidiomycota, both bipolar and tetrapolar mating systems have been well characterized; further, at least one locus directly encodes the pheromone precursor and the receptor for the pheromone of a different mating type, while a separate locus encodes proteins that may regulate the first locus and/or additional genes required for downstream events. Heterozygosity at both of two unlinked loci is required for cells to productively mate in tetrapolar systems, whereas in bipolar systems the two loci are tightly linked. Finally, a trade-off exists in wild fungal populations between sexual reproduction and the associated costs, with adverse conditions leading to mating. For fungal mammal pathogens, the products of sexual reproduction can be targets for the host immune system. The opposite appears true for phytopathogenic fungi, where mating and pathogenicity are inextricably linked. Here, we explore, compare, and contrast different strategies used among the Dikarya, both saprophytic and pathogenic fungi, and highlight differences between pathogens of mammals and pathogens of plants, providing context for selective pressures acting on this interesting group of fungi.
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Affiliation(s)
| | - Michael H. Perlin
- Department of Biology, University of Louisville, Louisville, KY, United States
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17
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The mating type locus protein MAT1-2-1 of Trichoderma reesei interacts with Xyr1 and regulates cellulase gene expression in response to light. Sci Rep 2017; 7:17346. [PMID: 29229981 PMCID: PMC5725425 DOI: 10.1038/s41598-017-17439-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Cellulase production in the model cellulolytic fungus Trichoderma reesei is subject to a variety of environmental and physiological conditions involving an intricate regulatory network with multiple transcription factors. Here, we identified the mating type locus protein MAT1-2-1 as an interacting partner for the key transcriptional activator Xyr1 of T. reesei cellulase genes. Yeast two-hybrid and GST pulldown analyses revealed that MAT1-2-1 directly interacted with the putative transcription activation domain (AD, 767~940 aa) and the middle homology region (MHR2, 314~632 aa) of Xyr1. Disruption of the mat1-2-1 gene compromised the induced expression of cellulase genes with Avicel in response to light or with lactose. Chromatin immunoprecipitation (ChIP) demonstrated that MAT1-2-1 was recruited to the cbh1 (cellobiohydrolase 1-encoding) gene promoter in a Xyr1-dependent manner. These results strongly support an important role of MAT1-2-1 as a physiological cofactor of Xyr1, and suggest that MAT1-2-1 represents another regulatory node that integrates the light response with carbon source signaling to fine tune cellulase gene transcription.
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18
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Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels. Appl Environ Microbiol 2017; 83:AEM.01578-17. [PMID: 28916559 PMCID: PMC5666144 DOI: 10.1128/aem.01578-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/31/2017] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Trichoderma reesei is found predominantly in the tropics but also in more temperate regions, such as Europe, and is widely known as a producer of large amounts of plant cell wall-degrading enzymes. We sequenced the genome of the sexually competent isolate CBS999.97, which is phenotypically different from the female sterile strain QM6a but can cross sexually with QM6a. Transcriptome data for growth on cellulose showed that entire carbohydrate-active enzyme (CAZyme) families are consistently differentially regulated between these strains. We evaluated backcrossed strains of both mating types, which acquired female fertility from CBS999.97 but maintained a mostly QM6a genetic background, and we could thereby distinguish between the effects of strain background and female fertility or mating type. We found clear regulatory differences associated with female fertility and female sterility, including regulation of CAZyme and transporter genes. Analysis of carbon source utilization, transcriptomes, and secondary metabolites in these strains revealed that only a few changes in gene regulation are consistently correlated with different mating types. Different strain backgrounds (QM6a versus CBS999.97) resulted in the most significant alterations in the transcriptomes and in carbon source utilization, with decreased growth of CBS999.97 on several amino acids (for example proline or alanine), which further correlated with the downregulation of genes involved in the respective pathways. In combination, our findings support a role of fertility-associated processes in physiology and gene regulation and are of high relevance for the use of sexual crossing in combining the characteristics of two compatible strains or quantitative trait locus (QTL) analysis.IMPORTANCETrichoderma reesei is a filamentous fungus with a high potential for secretion of plant cell wall-degrading enzymes. We sequenced the genome of the fully fertile field isolate CBS999.97 and analyzed its gene regulation characteristics in comparison with the commonly used laboratory wild-type strain QM6a, which is not female fertile. Additionally, we also evaluated fully fertile strains with genotypes very close to that of QM6a in order to distinguish between strain-specific and fertility-specific characteristics. We found that QM6a and CBS999.97 clearly differ in their growth patterns on different carbon sources, CAZyme gene regulation, and secondary metabolism. Importantly, we found altered regulation of 90 genes associated with female fertility, including CAZyme genes and transporter genes, but only minor mating type-dependent differences. Hence, when using sexual crossing in research and for strain improvement, it is important to consider female fertile and female sterile strains for comparison with QM6a and to achieve optimal performance.
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19
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Light, stress, sex and carbon - The photoreceptor ENVOY as a central checkpoint in the physiology of Trichoderma reesei. Fungal Biol 2017; 122:479-486. [PMID: 29801792 DOI: 10.1016/j.funbio.2017.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/11/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Abstract
Trichoderma reesei represents one of the most prolific producers of homologous and heterologous proteins. Discovery of the photoreceptor ENV1 as a regulator of cellulase gene expression initiated analysis of light response pathways and their physiological relevance for T. reesei. The function of ENV1 in regulation of plant cell wall degrading enzymes is conserved in Neurospora crassa. ENV1 emerged as a central checkpoint for integration of nutrient sensing, light response and development. This photoreceptor exerts its function by influencing transcript abundance and feedback cycles of the alpha subunits of the heterotrimeric G-protein pathway and impacts regulation of the beta and gamma subunits via mutual regulation with the phosducin PhLP1. The output of regulation by ENV1 is in part mediated by the cAMP pathway and likely aimed at cellulose recognition. Lack of ENV1 causes deregulation of the pheromone system and female sterility in light. A regulatory interconnection with VEL1 and influence on other regulators of secondary metabolism like YPR2 as well as polyketide synthase encoding genes indicates a function in secondary metabolism. The function of ENV1 in integrating light response with signaling of osmotic and oxidative stress is evolutionary conserved in Hypocreales and distinct from other sordariomycetes including N. crassa.
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20
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Bazafkan H, Beier S, Stappler E, Böhmdorfer S, Oberlerchner JT, Sulyok M, Schmoll M. SUB1 has photoreceptor dependent and independent functions in sexual development and secondary metabolism in Trichoderma reesei. Mol Microbiol 2017; 106:742-759. [PMID: 28925526 DOI: 10.1111/mmi.13842] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2017] [Indexed: 12/17/2022]
Abstract
Light dependent processes are involved in the regulation of growth, development and enzyme production in Trichoderma reesei. The photoreceptors BLR1, BLR2 and ENV1 exert crucial functions in these processes. We analyzed the involvement of the transcription factor SUB1 in sexual development as well as secondary metabolism and its position in the light signaling cascade. SUB1 influences growth and in contrast to its homologue in N. crassa, SUB1 is not essential for fruiting body formation and male fertility in T. reesei, but required for female fertility. Accordingly, SUB1 is involved in the regulation of the pheromone system of T. reesei. Female sterility of mutants lacking env1 is rescued in triple mutants of blr1, blr2 and env1, but not in double mutants of these genes. Confrontation of strains lacking sub1 results in growth arrest prior to contact of the potential mating partners. This effect is at least in part due to altered secondary metabolite production. Additionally, together with BLR1 and BLR2, SUB1 is essential for spore pigmentation and transcription of pks4, and secondary metabolism is regulated by SUB1 in a light- and nutrient dependent manner. Our results hence indicate rewiring of several pathways targeted by SUB1 in T. reesei.
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Affiliation(s)
- Hoda Bazafkan
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Strasse 24, 3430 Tulln, Austria
| | - Sabrina Beier
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Strasse 24, 3430 Tulln, Austria
| | - Eva Stappler
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Strasse 24, 3430 Tulln, Austria
| | - Stefan Böhmdorfer
- Department of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Josua T Oberlerchner
- Department of Chemistry, Division of Chemistry of Renewable Resources, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Straße 20, 3430 Tulln, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Strasse 24, 3430 Tulln, Austria
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21
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Bazafkan H, Dattenböck C, Stappler E, Beier S, Schmoll M. Interrelationships of VEL1 and ENV1 in light response and development in Trichoderma reesei. PLoS One 2017; 12:e0175946. [PMID: 28423024 PMCID: PMC5397039 DOI: 10.1371/journal.pone.0175946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 04/03/2017] [Indexed: 12/25/2022] Open
Abstract
Sexual development is regulated by a complex regulatory mechanism in fungi. For Trichoderma reesei, the light response pathway was shown to impact sexual development, particularly through the photoreceptor ENVOY. Moreover, T. reesei communicates chemically with a potential mating partner in its vicinity, a response which is mediated by the velvet family protein VEL1 and its impact on secondary metabolism. We therefore studied the regulatory interactions of ENV1 and VEL1 with a focus on sexual development. Although individual mutants in both genes are female sterile under standard crossing conditions (light—dark cycles), an altered light regime enabled sexual development, which we found to be due to conditional female sterility of Δenv1, but not Δvel1. Phenotypes of growth and asexual sporulation as well as regulation of the peptide pheromone precursors of double mutants suggested that ENV1 and VEL1 balance positive and negative regulators of these functions. Additionally, VEL1 contributed to the strong deregulation of the pheromone system observed in env1 mutants. Female sterility of Δvel1 was rescued by deletion of env1 in darkness in MAT1-1, indicating a block of sexual development by ENV1 in darkness that is balanced by VEL1 in the wild-type. We conclude that ENV1 and VEL1 exert complementing functions in development of T. reesei. Our results further showed that the different developmental phenotypes of vel1/veA mutants in T. reesei and Aspergillus nidulans are not due to the presence or function of ENV1 in the VELVET regulatory pathway in T. reesei.
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Affiliation(s)
- Hoda Bazafkan
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Christoph Dattenböck
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Eva Stappler
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Sabrina Beier
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
| | - Monika Schmoll
- AIT Austrian Institute of Technology GmbH, Department Health and Environment, Bioresources, Tulln, Austria
- * E-mail:
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22
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Li WC, Huang CH, Chen CL, Chuang YC, Tung SY, Wang TF. Trichoderma reesei complete genome sequence, repeat-induced point mutation, and partitioning of CAZyme gene clusters. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:170. [PMID: 28690679 PMCID: PMC5496416 DOI: 10.1186/s13068-017-0825-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/22/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Trichoderma reesei (Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis, and plant-fungal interactions. The genomes of QM6a and its high enzyme-producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute. While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture, and genetic modification or engineering. RESULTS We integrated Pacific Biosciences and Illumina sequencing platforms for the highest-quality genome assembly yet achieved, revealing seven telomere-to-telomere chromosomes (34,922,528 bp; 10877 genes) with 1630 newly predicted genes and >1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres, and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis that T. reesei has evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression in T. reesei. CONCLUSION Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus' soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications.
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Affiliation(s)
- Wan-Chen Li
- Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Life Sciences, National Defense Medical Center, Taipei, 115 Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Chien-Hao Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Genome Sciences, National Yang-Ming University, Taipei, 112 Taiwan
| | - Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yu-Chien Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Shu-Yun Tung
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Ting-Fang Wang
- Taiwan International Graduate Program in Molecular and Cellular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
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Assessing the relevance of light for fungi: Implications and insights into the network of signal transmission. ADVANCES IN APPLIED MICROBIOLOGY 2016; 76:27-78. [PMID: 21924971 DOI: 10.1016/b978-0-12-387048-3.00002-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Light represents an important environmental cue, which provides information enabling fungi to prepare and react to the different ambient conditions between day and night. This adaptation requires both anticipation of the changing conditions, which is accomplished by daily rhythmicity of gene expression brought about by the circadian clock, and reaction to sudden illumination. Besides perception of the light signal, also integration of this signal with other environmental cues, most importantly nutrient availability, necessitates light-dependent regulation of signal transduction pathways and metabolic pathways. An influence of light and/or the circadian clock is known for the cAMP pathway, heterotrimeric G-protein signaling, mitogen-activated protein kinases, two-component phosphorelays, and Ca(2+) signaling. Moreover, also the target of rapamycin signaling pathway and reactive oxygen species as signal transducing elements are assumed to be connected to the light-response pathway. The interplay of the light-response pathway with signaling cascades results in light-dependent regulation of primary and secondary metabolism, morphology, development, biocontrol activity, and virulence. The frequent use of fungi in biotechnology as well as analysis of fungi in the artificial environment of a laboratory therefore requires careful consideration of still operative evolutionary heritage of these organisms. This review summarizes the diverse effects of light on fungi and the mechanisms they apply to deal both with the information content and with the harmful properties of light. Additionally, the implications of the reaction of fungi to light in a laboratory environment for experimental work and industrial applications are discussed.
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Comparative transcriptome analysis of fruiting body and sporulating mycelia of Villosiclava virens reveals genes with putative functions in sexual reproduction. Curr Genet 2016; 62:575-84. [DOI: 10.1007/s00294-015-0563-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/23/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
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Druzhinina IS, Kubicek CP. Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:69-147. [PMID: 27261782 DOI: 10.1016/bs.aambs.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The filamentous fungus Trichoderma reesei (Hypocreales, Ascomycota) has properties of an efficient cell factory for protein production that is exploited by the enzyme industry, particularly with respect to cellulase and hemicellulase formation. Under conditions of industrial fermentations it yields more than 100g secreted protein L(-1). Consequently, T. reesei has been intensively studied in the 20th century. Most of these investigations focused on the biochemical characteristics of its cellulases and hemicellulases, on the improvement of their properties by protein engineering, and on enhanced enzyme production by recombinant strategies. However, as the fungus is rare in nature, its ecology remained unknown. The breakthrough in the understanding of the fundamental biology of T. reesei only happened during 2000s-2010s. In this review, we compile the current knowledge on T. reesei ecology, physiology, and genomics to present a holistic view on the natural behavior of the organism. This is not only critical for science-driven further improvement of the biotechnological applications of this fungus, but also renders T. reesei as an attractive model of filamentous fungi with superior saprotrophic abilities.
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Affiliation(s)
- I S Druzhinina
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - C P Kubicek
- Institute of Chemical Engineering, TU Wien, Vienna, Austria
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Bazafkan H, Dattenböck C, Böhmdorfer S, Tisch D, Stappler E, Schmoll M. Mating type-dependent partner sensing as mediated by VEL1 in Trichoderma reesei. Mol Microbiol 2015; 96:1103-18. [PMID: 25757597 PMCID: PMC4949666 DOI: 10.1111/mmi.12993] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2015] [Indexed: 12/21/2022]
Abstract
Sexual development in the filamentous model ascomycete Trichoderma reesei (syn. Hypocrea jecorina) was described only a few years ago. In this study, we show a novel role for VELVET in fungi, which links light response, development and secondary metabolism. Vel1 is required for mating in darkness, normal growth and conidiation. In light, vel1 was dispensable for male fertility but essential for female fertility in both mating types. VEL1 impacted regulation of the pheromone system (hpr1, hpr2, hpp1, ppg1) in a mating type‐dependent manner and depending on the mating partner of a given strain. These partner effects only occurred for hpp1 and hpr2, the pheromone precursor and receptor genes associated with the MAT1‐2 mating type and for the mating type gene mat1‐2‐1. Analysis of secondary metabolite patterns secreted by wild type and mutants under asexual and sexual conditions revealed that even in the wild type, the patterns change upon encounter of a mating partner, with again distinct differences for wild type and vel1 mutants. Hence, T. reesei applies a language of pheromones and secondary metabolites to communicate with mating partners and that this communication is at least in part mediated by VEL1.
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Affiliation(s)
- Hoda Bazafkan
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Christoph Dattenböck
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Stefan Böhmdorfer
- University of Natural Resources and Life Sciences Vienna, Department of Chemistry, Division of Chemistry of Renewable Resources, Konrad-Lorenz-Straße 24, Tulln, 3430, Austria
| | - Doris Tisch
- Research Area Molecular Biotechnology, Vienna University of Technology, Gumpendorfer Straße 1a, Wien, 1060, Austria
| | - Eva Stappler
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
| | - Monika Schmoll
- Department Health and Environment, AIT Austrian Institute of Technology GmbH, Bioresources, Konrad-Lorenz Strasse 24, Tulln, 3430, Austria
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Biogenesis of the Saccharomyces cerevisiae pheromone a-factor, from yeast mating to human disease. Microbiol Mol Biol Rev 2013; 76:626-51. [PMID: 22933563 DOI: 10.1128/mmbr.00010-12] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The mating pheromone a-factor secreted by Saccharomyces cerevisiae is a farnesylated and carboxylmethylated peptide and is unusually hydrophobic compared to other extracellular signaling molecules. Mature a-factor is derived from a precursor with a C-terminal CAAX motif that directs a series of posttranslational reactions, including prenylation, endoproteolysis, and carboxylmethylation. Historically, a-factor has served as a valuable model for the discovery and functional analysis of CAAX-processing enzymes. In this review, we discuss the three modules comprising the a-factor biogenesis pathway: (i) the C-terminal CAAX-processing steps carried out by Ram1/Ram2, Ste24 or Rce1, and Ste14; (ii) two sequential N-terminal cleavage steps, mediated by Ste24 and Axl1; and (iii) export by a nonclassical mechanism, mediated by the ATP binding cassette (ABC) transporter Ste6. The small size and hydrophobicity of a-factor present both challenges and advantages for biochemical analysis, as discussed here. The enzymes involved in a-factor biogenesis are conserved from yeasts to mammals. Notably, studies of the zinc metalloprotease Ste24 in S. cerevisiae led to the discovery of its mammalian homolog ZMPSTE24, which cleaves the prenylated C-terminal tail of the nuclear scaffold protein lamin A. Mutations that alter ZMPSTE24 processing of lamin A in humans cause the premature-aging disease progeria and related progeroid disorders. Intriguingly, recent evidence suggests that the entire a-factor pathway, including all three biogenesis modules, may be used to produce a prenylated, secreted signaling molecule involved in germ cell migration in Drosophila. Thus, additional prenylated signaling molecules resembling a-factor, with as-yet-unknown roles in metazoan biology, may await discovery.
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Mukherjee PK, Horwitz BA, Herrera-Estrella A, Schmoll M, Kenerley CM. Trichoderma research in the genome era. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:105-29. [PMID: 23915132 DOI: 10.1146/annurev-phyto-082712-102353] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Trichoderma species are widely used in agriculture and industry as biopesticides and sources of enzymes, respectively. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Many strains produce elicitors and induce resistance in plants through colonization of roots. Seven species have now been sequenced. Comparison of a primarily saprophytic species with two mycoparasitic species has provided striking contrasts and has established that mycoparasitism is an ancestral trait of this genus. Among the interesting outcomes of genome comparison is the discovery of a vast repertoire of secondary metabolism pathways and of numerous small cysteine-rich secreted proteins. Genomics has also facilitated investigation of sexual crossing in Trichoderma reesei, suggesting the possibility of strain improvement through hybridization.
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Affiliation(s)
- Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Center, Trombay, Mumbai 400085, India.
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Chen CL, Kuo HC, Tung SY, Hsu PWC, Wang CL, Seibel C, Schmoll M, Chen RS, Wang TF. Blue light acts as a double-edged sword in regulating sexual development of Hypocrea jecorina (Trichoderma reesei). PLoS One 2012; 7:e44969. [PMID: 23028710 PMCID: PMC3445611 DOI: 10.1371/journal.pone.0044969] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 08/16/2012] [Indexed: 11/18/2022] Open
Abstract
The industrially important cellulolytic filamentous fungus Trichoderma reesei is the anamorph of the pantropical ascomycete Hypocrea jecorina. H. jecorina CBS999.97 strain undergoes a heterothallic reproductive cycle, and the mating yields fertilized perithecia imbedded in stromata. Asci in the perithecia contain 16 linearly arranged ascospores. Here, we investigated H. jecorina sexual development under different light regimes, and found that visible light was dispensable for sexual development (stroma formation and ascospore discharge). By contrast, constant illumination inhibited stroma formation, and an interruption of the darkness facilitated timely stroma formation in a 12 h/12 h light-dark photoperiod. The results of genetic analyses further revealed that H. jecorina blue-light photoreceptors (BLR1, BLR2) and the photoadaptation protein ENV1 were not essential for sexual development in general. BLR1, BLR2 and ENV1 are orthologues of the conserved Neurospora crassa WC-1, WC-2 and VVD, respectively. Moreover, BLR1 and BLR2 mediate both positive and negative light-dependent regulation on sexual development, whereas ENV1 is required for dampening the light-dependent inhibitory effect in response to changes in illumination. Comparative genome-wide microarray analysis demonstrated an overview of light-dependent gene expression versus sexual potency in CBS999.97 (MAT1-2) haploid cells. Constant illumination promotes abundant asexual conidiation and high levels of hpp1 transcripts. hpp1 encodes a h (hybrid)-type propheromone that exhibits features of both yeast a and a pheromone precursors. Deletion of hpp1 could rescue stroma formation but not ascospore generation under constant illumination. We inferred that the HPP1-dependent pheromone signaling system might directly prevent stroma formation or simply disallow the haploid cells to acquire sexual potency due to abundant asexual conidiation upon constant illumination.
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Affiliation(s)
- Chia-Ling Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Che Kuo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Yu Tung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Chih-Li Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Christian Seibel
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Monika Schmoll
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Vienna, Austria
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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Seibel C, Tisch D, Kubicek CP, Schmoll M. The role of pheromone receptors for communication and mating in Hypocrea jecorina (Trichoderma reesei). Fungal Genet Biol 2012; 49:814-24. [PMID: 22884620 PMCID: PMC3462998 DOI: 10.1016/j.fgb.2012.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/12/2012] [Accepted: 07/23/2012] [Indexed: 11/04/2022]
Abstract
Discovery of sexual development in the ascomycete Trichoderma reesei (Hypocrea jecorina) as well as detection of a novel class of peptide pheromone precursors in this fungus indicates promising insights into its physiology and lifestyle. Here we investigated the role of the two pheromone receptors HPR1 and HPR2 in the H. jecorina pheromone-system. We found that these pheromone receptors show an unexpectedly high genetic variability among H. jecorina strains. HPR1 and HPR2 confer female fertility in their cognate mating types (MAT1-1 or MAT1-2, respectively) and mediate induction of fruiting body development. One compatible pheromone precursor–pheromone receptor pair (hpr1–hpp1 or hpr2–ppg1) in mating partners was sufficient for sexual development. Additionally, pheromone receptors were essential for ascospore development, hence indicating their involvement in post-fertilisation events. Neither pheromone precursor genes nor pheromone receptor genes of H. jecorina were transcribed in a strictly mating type dependent manner, but showed enhanced expression levels in the cognate mating type. In the presence of a mating partner under conditions favoring sexual development, transcript levels of pheromone precursors were significantly increased, while those of pheromone receptor genes do not show this trend. In the female sterile T. reesei strain QM6a, transcriptional responses of pheromone precursor and pheromone receptor genes to a mating partner were clearly altered compared to the female fertile wild-type strain CBS999.97. Consequently, a delayed and inappropriate response to the mating partner may be one aspect causing female sterility in QM6a.
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Affiliation(s)
- Christian Seibel
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, 1060 Vienna, Austria
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ENVOY is a major determinant in regulation of sexual development in Hypocrea jecorina (Trichoderma reesei). EUKARYOTIC CELL 2012; 11:885-95. [PMID: 22581525 DOI: 10.1128/ec.05321-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Light is one crucial environmental signal which can determine whether a fungus reproduces asexually or initiates sexual development. Mating in the ascomycete Hypocrea jecorina (anamorph Trichoderma reesei) occurs preferentially in light. We therefore investigated the relevance of the light response machinery for sexual development in H. jecorina. We found that the photoreceptors BLR1 and BLR2 and the light-regulatory protein ENV1 have no effect on male fertility, while ENV1 is essential for female fertility. BLR1 and BLR2 were found to impact fruiting body formation although they are not essential for mating. Quantitative reverse transcription-PCR (qRT-PCR) analyses revealed that BLR1, BLR2, and ENV1 negatively regulate transcript levels of both pheromone receptors as well as peptide pheromone precursors in light but not in darkness and in a mating type-dependent manner. The effect of BLR1 and BLR2 on regulation of pheromone precursor and receptor genes is less severe than that of ENV1 as strains lacking env1 show 100-fold (for ppg1) to more than 100,000-fold (for hpp1) increased transcript levels of pheromone precursor genes as well as more than 20-fold increased levels of hpr1, the pheromone receptor receiving the HPP1 signal in a MAT1-1 strain. ENV1 likely integrates additional signals besides light, and our results indicate that its function is partially mediated via regulation of mat1-2-1. We conclude that ENV1 is essential for balancing the levels of genes regulated in a mating-type-dependent manner, which contributes to determination of sexual identity and fruiting body formation.
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Tisch D, Kubicek CP, Schmoll M. The phosducin-like protein PhLP1 impacts regulation of glycoside hydrolases and light response in Trichoderma reesei. BMC Genomics 2011; 12:613. [PMID: 22182583 PMCID: PMC3267782 DOI: 10.1186/1471-2164-12-613] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/19/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) transcription of cellulase genes as well as efficiency of the secreted cellulase mixture are modulated by light. Components of the heterotrimeric G-protein pathway interact with light-dependent signals, rendering this pathway a key regulator of cellulase gene expression. RESULTS As regulators of heterotrimeric G-protein signaling, class I phosducin-like proteins, are assumed to act as co-chaperones for G-protein beta-gamma folding and exert their function in response to light in higher eukaryotes. Our results revealed light responsive transcription of the T. reesei class I phosducin-like protein gene phlp1 and indicate a light dependent function of PhLP1 also in fungi. We showed the functions of PhLP1, GNB1 and GNG1 in the same pathway, with one major output being the regulation of transcription of glycoside hydrolase genes including cellulase genes in T. reesei. We found no direct correlation between the growth rate and global regulation of glycoside hydrolases, which suggests that regulation of growth does not occur only at the level of substrate degradation efficiency.Additionally, PhLP1, GNB1 and GNG1 are all important for proper regulation of light responsiveness during long term exposure. In their absence, the amount of light regulated genes increased from 2.7% in wild type to 14% in Δphlp1. Besides from the regulation of degradative enzymes, PhLP1 was also found to impact on the transcription of genes involved in sexual development, which was in accordance with decreased efficiency of fruiting body formation in Δphlp1. The lack of GNB1 drastically diminished ascospore discharge in T. reesei. CONCLUSIONS The heterotrimeric G-protein pathway is crucial for the interconnection of nutrient signaling and light response of T. reesei, with the class I phosducin-like protein PhLP1, GNB1 and GNG1 acting as important nodes, which influence light responsiveness, glycoside hydrolase gene transcription and sexual development.
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Affiliation(s)
- Doris Tisch
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
| | - Christian P Kubicek
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
| | - Monika Schmoll
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
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Leeder AC, Palma-Guerrero J, Glass NL. The social network: deciphering fungal language. Nat Rev Microbiol 2011; 9:440-51. [PMID: 21572459 DOI: 10.1038/nrmicro2580] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It has been estimated that up to one quarter of the world's biomass is of fungal origin, comprising approximately 1.5 million species. In order to interact with one another and respond to environmental cues, fungi communicate with their own chemical languages using a sophisticated series of extracellular signals and cellular responses. A new appreciation for the linkage between these chemical languages and developmental processes in fungi has renewed interest in these signalling molecules, which can now be studied using post-genomic resources. In this Review, we focus on the molecules that are secreted by the largest phylum of fungi, the Ascomycota, and the quest to understand their biological function.
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Affiliation(s)
- Abigail C Leeder
- Plant and Microbial Biology Department, The University of California, Berkeley, CA 94720-3102, USA
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Jones SK, Bennett RJ. Fungal mating pheromones: choreographing the dating game. Fungal Genet Biol 2011; 48:668-76. [PMID: 21496492 PMCID: PMC3100450 DOI: 10.1016/j.fgb.2011.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/23/2011] [Accepted: 04/05/2011] [Indexed: 01/11/2023]
Abstract
Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence from this model system is compared amongst the ascomycetes and basidiomycetes, which reveals the wealth of information that has been gleaned from studying pheromone-driven processes across a wide spectrum of the fungal kingdom.
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Affiliation(s)
- Stephen K. Jones
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
| | - Richard J. Bennett
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912
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Bidard F, Aït Benkhali J, Coppin E, Imbeaud S, Grognet P, Delacroix H, Debuchy R. Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina. PLoS One 2011; 6:e21476. [PMID: 21738678 PMCID: PMC3125171 DOI: 10.1371/journal.pone.0021476] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/29/2011] [Indexed: 12/15/2022] Open
Abstract
Background Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat− mating types are determined by dissimilar allelic sequences. The mat− sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. Methodology/Principal Findings The transcriptomic profiles of the mat+ and mat− strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1− and fpr1− mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat− strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. Conclusions/Significance This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
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Affiliation(s)
- Frédérique Bidard
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Jinane Aït Benkhali
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Evelyne Coppin
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
| | - Sandrine Imbeaud
- CNRS, Centre de Génétique Moléculaire FRE3144, GODMAP, Gif sur Yvette, France
| | - Pierre Grognet
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- UFR des Sciences du Vivant, Université Paris 7-Denis Diderot, Paris, France
| | - Hervé Delacroix
- CNRS, Centre de Génétique Moléculaire FRE3144, GODMAP, Gif sur Yvette, France
- Univ Paris-Sud, Orsay, France
| | - Robert Debuchy
- Univ Paris-Sud, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- CNRS, Institut de Génétique et Microbiologie UMR8621, Orsay, France
- * E-mail:
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Dehydrogenase GRD1 represents a novel component of the cellulase regulon in Trichoderma reesei (Hypocrea jecorina). Appl Environ Microbiol 2011; 77:4553-63. [PMID: 21602376 DOI: 10.1128/aem.00513-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trichoderma reesei (Hypocrea jecorina) is nowadays the most important industrial producer of cellulase and hemicellulase enzymes, which are used for pretreatment of cellulosic biomass for biofuel production. In this study, we introduce a novel component, GRD1 (glucose-ribitol dehydrogenase 1), which shows enzymatic activity on cellobiose and positively influences cellulase gene transcription, expression, and extracellular endo-1,4-β-D-glucanase activity. grd1 is differentially transcribed upon growth on cellulose and the induction of cellulase gene expression by sophorose. The transcription of grd1 is coregulated with that of cel7a (cbh1) under inducing conditions. GRD1 is further involved in carbon source utilization on several carbon sources, such as those involved in lactose and D-galactose catabolism, in several cases in a light-dependent manner. We conclude that GRD1 represents a novel enhancer of cellulase gene expression, which by coregulation with the major cellulase may act via optimization of inducing mechanisms.
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Martin SH, Wingfield BD, Wingfield MJ, Steenkamp ET. Causes and consequences of variability in peptide mating pheromones of ascomycete fungi. Mol Biol Evol 2011; 28:1987-2003. [PMID: 21252281 DOI: 10.1093/molbev/msr022] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The reproductive genes of fungi, like those of many other organisms, are thought to diversify rapidly. This phenomenon could be associated with the formation of reproductive barriers and speciation. Ascomycetes produce two classes of mating type-specific peptide pheromones. These are required for recognition between the mating types of heterothallic species. Little is known regarding the diversity or the extent of species specificity in pheromone peptides among these fungi. We compared the putative protein-coding DNA sequences of the 2 pheromone classes from 70 species of Ascomycetes. The data set included previously described pheromones and putative pheromones identified from genomic sequences. In addition, pheromone genes from 12 Fusarium species in the Gibberella fujikuroi complex were amplified and sequenced. Pheromones were largely conserved among species in this complex and, therefore, cannot alone account for the reproductive barriers observed between these species. In contrast, pheromone peptides were highly diverse among many other Ascomycetes, with evidence for both positive diversifying selection and relaxed selective constraint. Repeats of the α-factor-like pheromone, which occur in tandem arrays of variable copy number, were found to be conserved through purifying selection and not concerted evolution. This implies that sequence specificity may be important for pheromone reception and that interspecific differences may indeed be associated with functional divergence. Our findings also suggest that frequent duplication and loss causes the tandem repeats to experience "birth-and-death" evolution, which could in fact facilitate interspecific divergence of pheromone peptide sequences.
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Affiliation(s)
- Simon H Martin
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
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