1
|
Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
Collapse
|
2
|
Hall RA, Wallace EW. Post-transcriptional control of fungal cell wall synthesis. Cell Surf 2022; 8:100074. [PMID: 35097244 PMCID: PMC8783092 DOI: 10.1016/j.tcsw.2022.100074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Pathogenic fungi hide from their hosts by camouflage, obscuring immunogenic cell wall components such as beta-glucan with innocuous coverings such as mannoproteins and alpha-glucan that are less readily recognised by the host. Attempts to understand how such processes are regulated have met with varying success. Typically studies focus on understanding the transcriptional response of fungi to either their reservoir environment or the host. However, such approaches do not fully address this research question, due to the layers of post-transcriptional and post-translational regulation that occur within a cell. Although in animals the impact of post-transcriptional and post-translational regulation has been well characterised, our knowledge of these processes in the fungal kingdom is more limited. Mutations in RNA-binding proteins, like Ssd1 and Candida albicans Slr1, affect cell wall composition and fungal virulence indicating that post-transcriptional regulation plays a key role in these processes. Here, we review the current state of knowledge of fungal post-transcriptional regulation, and link this to potential mechanisms of immune evasion by drawing on studies from model yeast and plant pathogenic fungi. We highlight several RNA-binding proteins that regulate cell wall synthesis and could be involved in local translation of cell wall components. Expanding our knowledge on post-transcriptional regulation in human fungal pathogens is essential to fully comprehend fungal virulence strategies and for the design of novel antifungal therapies.
Collapse
Affiliation(s)
- Rebecca A. Hall
- Kent Fungal Group, Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom
| | - Edward W.J. Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, EH9 3FF, United Kingdom
| |
Collapse
|
3
|
Gortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. J Fungi (Basel) 2022; 8:jof8080854. [PMID: 36012842 PMCID: PMC9410309 DOI: 10.3390/jof8080854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
The nature of saprophytic and mycoparasitic hyphal growth of Trichoderma spp. has been studied extensively, yet its initiation via conidial germination in this genus is less well understood. Using near-synchronous germinating cultures of Trichoderma asperelloides, we followed the morphological progression from dormant conidia to initial polar growth to germling formation and to evidence for first branching. We found that the stage-specific transcriptional profile of T. asperelloides is one of the most dynamic described to date: transcript abundance of over 5000 genes-comprising approximately half of the annotated genome-was unremittingly reduced in the transition from dormancy to polar growth. Conversely, after the onset of germination, the transcript abundance of approximately a quarter of the genome was unremittingly elevated during the transition from elongation to initial branching. These changes are a testimony to the substantial developmental events that accompany germination. Bayesian network analysis identified several chitinase- and glucanase-encoding genes as active transcriptional hubs during germination. Furthermore, the expression of specific members of the chitin synthase and glucan elongase families was significantly increased during germination in the presence of Rhizoctonia solani-a known host of the mycoparasite-indicating that host recognition can occur during the early stages of mycoparasite development.
Collapse
Affiliation(s)
- Maggie Gortikov
- Department of Plant Pathology and Microbiology, The RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06511, USA
| | | | - Yujia Tu
- Department of Mathematics and Computer Science, University of Strasbourg, 67081 Strasbourg, France
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06511, USA
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Correspondence:
| |
Collapse
|
4
|
Bartholomai BM, Gladfelter AS, Loros JJ, Dunlap JC. Quantitative single molecule RNA-FISH and RNase-free cell wall digestion in Neurospora crassa. Fungal Genet Biol 2021; 156:103615. [PMID: 34425213 PMCID: PMC8463489 DOI: 10.1016/j.fgb.2021.103615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Single molecule RNA-FISH (smFISH) is a valuable tool for analysis of mRNA spatial patterning in fixed cells that is underutilized in filamentous fungi. A primary complication for fixed-cell imaging in filamentous fungi is the need for enzymatic cell wall permeabilization, which is compounded by considerable variability in cell wall composition between species. smFISH adds another layer of complexity due to a requirement for RNase free conditions. Here, we describe the cloning, expression, and purification of a chitinase suitable for supplementation of a commercially available RNase-free enzyme preparation for efficient permeabilization of the Neurospora cell wall. We further provide a method for smFISH in Neurospora which includes a tool for generating numerical data from images that can be used in downstream customized analysis protocols.
Collapse
Affiliation(s)
- Bradley M Bartholomai
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA
| | - Amy S Gladfelter
- University of North Carolina, Department of Biology, Chapel Hill, NC, USA
| | - Jennifer J Loros
- Geisel School of Medicine at Dartmouth, Department of Biochemistry and Cell Biology, Hanover, NH, USA
| | - Jay C Dunlap
- Geisel School of Medicine at Dartmouth, Department of Molecular and Systems Biology, Hanover, NH, USA.
| |
Collapse
|
5
|
Ballou ER, Cook AG, Wallace EWJ. Repeated Evolution of Inactive Pseudonucleases in a Fungal Branch of the Dis3/RNase II Family of Nucleases. Mol Biol Evol 2021; 38:1837-1846. [PMID: 33313834 PMCID: PMC8097288 DOI: 10.1093/molbev/msaa324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RNase II family of 3'-5' exoribonucleases is present in all domains of life, and eukaryotic family members Dis3 and Dis3L2 play essential roles in RNA degradation. Ascomycete yeasts contain both Dis3 and inactive RNase II-like "pseudonucleases." The latter function as RNA-binding proteins that affect cell growth, cytokinesis, and fungal pathogenicity. However, the evolutionary origins of these pseudonucleases are unknown: What sequence of events led to their novel function, and when did these events occur? Here, we show how RNase II pseudonuclease homologs, including Saccharomyces cerevisiae Ssd1, are descended from active Dis3L2 enzymes. During fungal evolution, active site mutations in Dis3L2 homologs have arisen at least four times, in some cases following gene duplication. In contrast, N-terminal cold-shock domains and regulatory features are conserved across diverse dikarya and mucoromycota, suggesting that the nonnuclease function requires these regions. In the basidiomycete pathogenic yeast Cryptococcus neoformans, the single Ssd1/Dis3L2 homolog is required for cytokinesis from polyploid "titan" growth stages. This phenotype of C. neoformans Ssd1/Dis3L2 deletion is consistent with those of inactive fungal pseudonucleases, yet the protein retains an active site sequence signature. We propose that a nuclease-independent function for Dis3L2 arose in an ancestral hyphae-forming fungus. This second function has been conserved across hundreds of millions of years, whereas the RNase activity was lost repeatedly in independent lineages.
Collapse
Affiliation(s)
- Elizabeth R Ballou
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Atlanta G Cook
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Edward W J Wallace
- Institute for Cell Biology and SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
6
|
Zhao Q, Liu Q, Wang Q, Qin Y, Zhong Y, Gao L, Liu G, Qu Y. Disruption of the Trichoderma reesei gul1 gene stimulates hyphal branching and reduces broth viscosity in cellulase production. J Ind Microbiol Biotechnol 2021; 48:6132311. [PMID: 33693788 PMCID: PMC9113457 DOI: 10.1093/jimb/kuab012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/05/2021] [Indexed: 12/03/2022]
Abstract
Hyphal morphology is considered to have a close relationship with the production
level of secreted proteins by filamentous fungi. In this study, the
gul1 gene, which encodes a putative mRNA-binding protein,
was disrupted in cellulase-producing fungus Trichoderma reesei.
The hyphae of Δgul1 strain produced more lateral
branches than the parent strain. Under the condition for cellulase production,
disruption of gul1 resulted in smaller mycelial clumps and
significantly lower viscosity of fermentation broth. In addition, cellulase
production was improved by 22% relative to the parent strain.
Transcriptome analysis revealed that a set of genes encoding cell wall
remodeling enzymes as well as hydrophobins were differentially expressed in the
Δgul1 strain. The results suggest that the
regulatory role of gul1 in cell morphogenesis is likely
conserved in filamentous fungi. To our knowledge, this is the first report on
the engineering of gul1 in an industrially important
fungus.
Collapse
Affiliation(s)
- Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Qin Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Qi Wang
- National Glycoengineering Research Center, Shandong University, 27 Binhai Road, 266237 Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, 27 Binhai Road, 266237 Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China
| | - Liwei Gao
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China.,Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 11 Keyuanjingsi Road, 266101 Qingdao, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China.,National Glycoengineering Research Center, Shandong University, 27 Binhai Road, 266237 Qingdao, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, 266237 Qingdao, China.,National Glycoengineering Research Center, Shandong University, 27 Binhai Road, 266237 Qingdao, China
| |
Collapse
|
7
|
Herold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez RR, Townsend JP, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:672696. [PMID: 37744127 PMCID: PMC10512220 DOI: 10.3389/ffunb.2021.672696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 09/26/2023]
Abstract
The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide RNA-binding protein (RBP) that can associate with 828 "core" mRNA species. When cell wall integrity (CWI) is challenged, expression of over 25% of genomic RNA species are modulated (2,628 mRNAs, including the GUL-1 mRNA). GUL-1 binds mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmic reticulum (ER), as well as CWI and MAPK pathway components. GUL-1 interacts with over 100 different proteins, including stress-granule and P-body proteins, ER components and components of the MAPK, COT-1, and STRIPAK complexes. Several additional RBPs were also shown to physically interact with GUL-1. Under stress conditions, GUL-1 can localize to the ER and affect the CWI pathway-evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript, and involvement in the expression level of the transcription factor adv-1. We conclude that GUL-1 functions in multiple cellular processes, including the regulation of cell wall remodeling, via a mechanism associated with the MAK-1 pathway and stress-response.
Collapse
Affiliation(s)
- Inbal Herold
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avihai Zolti
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marisela Garduño-Rosales
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Francesc López-Giráldez
- Yale Center for Genome Analysis, Department of Genetics, Yale University, New Haven, CT, United States
| | - Rosa R. Mouriño-Pérez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| |
Collapse
|
8
|
Stein V, Blank-Landeshammer B, Müntjes K, Märker R, Teichert I, Feldbrügge M, Sickmann A, Kück U. The STRIPAK signaling complex regulates dephosphorylation of GUL1, an RNA-binding protein that shuttles on endosomes. PLoS Genet 2020; 16:e1008819. [PMID: 32997654 PMCID: PMC7550108 DOI: 10.1371/journal.pgen.1008819] [Citation(s) in RCA: 12] [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: 04/27/2020] [Revised: 10/12/2020] [Accepted: 08/17/2020] [Indexed: 12/03/2022] Open
Abstract
The striatin-interacting phosphatase and kinase (STRIPAK) multi-subunit signaling complex is highly conserved within eukaryotes. In fungi, STRIPAK controls multicellular development, morphogenesis, pathogenicity, and cell-cell recognition, while in humans, certain diseases are related to this signaling complex. To date, phosphorylation and dephosphorylation targets of STRIPAK are still widely unknown in microbial as well as animal systems. Here, we provide an extended global proteome and phosphoproteome study using the wild type as well as STRIPAK single and double deletion mutants (Δpro11, Δpro11Δpro22, Δpp2Ac1Δpro22) from the filamentous fungus Sordaria macrospora. Notably, in the deletion mutants, we identified the differential phosphorylation of 129 proteins, of which 70 phosphorylation sites were previously unknown. Included in the list of STRIPAK targets are eight proteins with RNA recognition motifs (RRMs) including GUL1. Knockout mutants and complemented transformants clearly show that GUL1 affects hyphal growth and sexual development. To assess the role of GUL1 phosphorylation on fungal development, we constructed phospho-mimetic and -deficient mutants of GUL1 residues. While S180 was dephosphorylated in a STRIPAK-dependent manner, S216, and S1343 served as non-regulated phosphorylation sites. While the S1343 mutants were indistinguishable from wild type, phospho-deficiency of S180 and S216 resulted in a drastic reduction in hyphal growth, and phospho-deficiency of S216 also affects sexual fertility. These results thus suggest that differential phosphorylation of GUL1 regulates developmental processes such as fruiting body maturation and hyphal morphogenesis. Moreover, genetic interaction studies provide strong evidence that GUL1 is not an integral subunit of STRIPAK. Finally, fluorescence microscopy revealed that GUL1 co-localizes with endosomal marker proteins and shuttles on endosomes. Here, we provide a new mechanistic model that explains how STRIPAK-dependent and -independent phosphorylation of GUL1 regulates sexual development and asexual growth.
Collapse
Affiliation(s)
- Valentina Stein
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
| | | | - Kira Müntjes
- Institut für Mikrobiologie, Cluster of Excellence on Plant Sciences, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Ramona Märker
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
| | - Ines Teichert
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
| | - Michael Feldbrügge
- Institut für Mikrobiologie, Cluster of Excellence on Plant Sciences, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Ulrich Kück
- Allgemeine und Molekulare Botanik, Ruhr-Universität, Bochum, Germany
| |
Collapse
|
9
|
Quantitative Proteome Profiling Reveals Cellobiose-Dependent Protein Processing and Export Pathways for the Lignocellulolytic Response in Neurospora crassa. Appl Environ Microbiol 2020; 86:AEM.00653-20. [PMID: 32471912 DOI: 10.1128/aem.00653-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi are intensively used for producing industrial enzymes, including lignocellulases. Employing insoluble cellulose to induce the production of lignocellulases causes some drawbacks, e.g., a complex fermentation operation, which can be overcome by using soluble inducers such as cellobiose. Here, a triple β-glucosidase mutant of Neurospora crassa, which prevents rapid turnover of cellobiose and thus allows the disaccharide to induce lignocellulases, was applied to profile the proteome responses to cellobiose and cellulose (Avicel). Our results revealed a shared proteomic response to cellobiose and Avicel, whose elements included lignocellulases and cellulolytic product transporters. While the cellulolytic proteins showed a correlated increase in protein and mRNA levels, only a moderate correlation was observed on a proteomic scale between protein and mRNA levels (R 2 = 0.31). Ribosome biogenesis and rRNA processing were significantly overrepresented in the protein set with increased protein but unchanged mRNA abundances in response to Avicel. Ribosome biogenesis, as well as protein processing and protein export, was also enriched in the protein set that showed increased abundance in response to cellobiose. NCU05895, a homolog of yeast CWH43, is potentially involved in transferring a glycosylphosphatidylinositol (GPI) anchor to nascent proteins. This protein showed increased abundance but no significant change in mRNA levels. Disruption of CWH43 resulted in a significant decrease in cellulase activities and secreted protein levels in cultures grown on Avicel, suggesting a positive regulatory role for CWH43 in cellulase production. The findings should have an impact on a systems engineering approach for strain improvement for the production of lignocellulases.IMPORTANCE Lignocellulases are important industrial enzymes for sustainable production of biofuels and bio-products. Insoluble cellulose has been commonly used to induce the production of lignocellulases in filamentous fungi, which causes a difficult fermentation operation and enzyme loss due to adsorption to cellulose. The disadvantages can be overcome by using soluble inducers, such as the disaccharide cellobiose. Quantitative proteome profiling of the model filamentous fungus Neurospora crassa revealed cellobiose-dependent pathways for cellulase production, including protein processing and export. A protein (CWH43) potentially involved in protein processing was found to be a positive regulator of lignocellulase production. The cellobiose-dependent mechanisms provide new opportunities to improve the production of lignocellulases in filamentous fungi.
Collapse
|
10
|
Alder-Rangel A, Idnurm A, Brand AC, Brown AJP, Gorbushina A, Kelliher CM, Campos CB, Levin DE, Bell-Pedersen D, Dadachova E, Bauer FF, Gadd GM, Braus GH, Braga GUL, Brancini GTP, Walker GM, Druzhinina I, Pócsi I, Dijksterhuis J, Aguirre J, Hallsworth JE, Schumacher J, Wong KH, Selbmann L, Corrochano LM, Kupiec M, Momany M, Molin M, Requena N, Yarden O, Cordero RJB, Fischer R, Pascon RC, Mancinelli RL, Emri T, Basso TO, Rangel DEN. The Third International Symposium on Fungal Stress - ISFUS. Fungal Biol 2020; 124:235-252. [PMID: 32389286 DOI: 10.1016/j.funbio.2020.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022]
Abstract
Stress is a normal part of life for fungi, which can survive in environments considered inhospitable or hostile for other organisms. Due to the ability of fungi to respond to, survive in, and transform the environment, even under severe stresses, many researchers are exploring the mechanisms that enable fungi to adapt to stress. The International Symposium on Fungal Stress (ISFUS) brings together leading scientists from around the world who research fungal stress. This article discusses presentations given at the third ISFUS, held in São José dos Campos, São Paulo, Brazil in 2019, thereby summarizing the state-of-the-art knowledge on fungal stress, a field that includes microbiology, agriculture, ecology, biotechnology, medicine, and astrobiology.
Collapse
Affiliation(s)
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, VIC, Australia
| | - Alexandra C Brand
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, England, UK
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, England, UK
| | - Anna Gorbushina
- Bundesanstalt für Materialforschung und -prüfung, Materials and the Environment, Berlin, Germany
| | - Christina M Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Claudia B Campos
- Departamento de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, SP, Brazil
| | - David E Levin
- Boston University Goldman School of Dental Medicine, Boston, MA, USA
| | - Deborah Bell-Pedersen
- Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Florian F Bauer
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Matieland, South Africa
| | - Geoffrey M Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics and Goettingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Gilberto U L Braga
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Guilherme T P Brancini
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Graeme M Walker
- School of Applied Sciences, Abertay University, Dundee, Scotland, UK
| | | | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - Jesús Aguirre
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Julia Schumacher
- Bundesanstalt für Materialforschung und -prüfung, Materials and the Environment, Berlin, Germany
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy; Italian National Antarctic Museum (MNA), Mycological Section, Genoa, Italy
| | | | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Michelle Momany
- Fungal Biology Group & Plant Biology Department, University of Georgia, Athens, GA, USA
| | - Mikael Molin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Natalia Requena
- Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jeruslaem, Rehovot 7610001, Israel
| | - Radamés J B Cordero
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Renata C Pascon
- Biological Sciences Department, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | | | - Tamas Emri
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Thiago O Basso
- Department of Chemical Engineering, Escola Politécnica, Universidade de São Paulo, São Paulo, SP, Brazil
| | | |
Collapse
|
11
|
Feldman D, Kowbel DJ, Cohen A, Glass NL, Hadar Y, Yarden O. Identification and manipulation of Neurospora crassa genes involved in sensitivity to furfural. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:210. [PMID: 31508149 PMCID: PMC6724289 DOI: 10.1186/s13068-019-1550-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/24/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Biofuels derived from lignocellulosic biomass are a viable alternative to fossil fuels required for transportation. Following plant biomass pretreatment, the furan derivative furfural is present at concentrations which are inhibitory to yeasts. Detoxification of furfural is thus important for efficient fermentation. Here, we searched for new genetic attributes in the fungus Neurospora crassa that may be linked to furfural tolerance. The fact that furfural is involved in the natural process of sexual spore germination of N. crassa and that this fungus is highly amenable to genetic manipulations makes it a rational candidate for this study. RESULTS Both hypothesis-based and unbiased (random promotor mutagenesis) approaches were performed to identify N. crassa genes associated with the response to furfural. Changes in the transcriptional profile following exposure to furfural revealed that the affected processes were, overall, similar to those observed in Saccharomyces cerevisiae. N. crassa was more tolerant (by ~ 30%) to furfural when carboxymethyl cellulose was the main carbon source as opposed to sucrose, indicative of a link between carbohydrate metabolism and furfural tolerance. We also observed increased tolerance in a Δcre-1 mutant (CRE-1 is a key transcription factor that regulates the ability of fungi to utilize non-preferred carbon sources). In addition, analysis of aldehyde dehydrogenase mutants showed that ahd-2 (NCU00378) was involved in tolerance to furfural as well as the predicted membrane transporter NCU05580 (flr-1), a homolog of FLR1 in S. cerevisiae. Further to the rational screening, an unbiased approach revealed additional genes whose inactivation conferred increased tolerance to furfural: (i) NCU02488, which affected the abundance of the non-anchored cell wall protein NCW-1 (NCU05137), and (ii) the zinc finger protein NCU01407. CONCLUSIONS We identified attributes in N. crassa associated with tolerance or degradation of furfural, using complementary research approaches. The manipulation of the genes involved in furan sensitivity can provide a means for improving the production of biofuel producing strains. Similar research approaches can be utilized in N. crassa and other filamentous fungi to identify additional attributes relevant to other furans or toxic chemicals.
Collapse
Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - David J. Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Adi Cohen
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Environmental Genomics and Systems Biology Division, The Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7600001 Rehovot, Israel
| |
Collapse
|
12
|
Thammahong A, Dhingra S, Bultman KM, Kerkaert JD, Cramer RA. An Ssd1 Homolog Impacts Trehalose and Chitin Biosynthesis and Contributes to Virulence in Aspergillus fumigatus. mSphere 2019; 4:e00244-19. [PMID: 31068436 PMCID: PMC6506620 DOI: 10.1128/msphere.00244-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/24/2019] [Indexed: 12/24/2022] Open
Abstract
Regulation of fungal cell wall biosynthesis is critical to maintain cell wall integrity in dynamic fungal infection microenvironments. Genes involved in this response that impact fungal fitness and host immune responses remain to be fully defined. In this study, we observed that a yeast ssd1 homolog, ssdA, in the filamentous fungus Aspergillus fumigatus is involved in trehalose and cell wall homeostasis. An ssdA null mutant strain exhibited an increase in trehalose levels and a reduction in fungal colony growth rate. In contrast, overexpression of ssdA perturbed trehalose biosynthesis and reduced germination of conidia. The ssdA null mutant strain was more resistant to cell wall-perturbing agents, while overexpression of ssdA increased sensitivity. Overexpression of ssdA significantly increased chitin levels, and both loss and overexpression of ssdA altered subcellular localization of the class V chitin synthase CsmA. Strikingly, overexpression of ssdA abolished adherence to abiotic surfaces and severely attenuated the virulence of A. fumigatus in a murine model of invasive pulmonary aspergillosis. Despite the severe in vitro fitness defects observed upon loss of ssdA, neither surface adherence nor murine survival was impacted. In conclusion, A. fumigatus SsdA plays a critical role in cell wall homeostasis impacting A. fumigatus-host interactions.IMPORTANCE The incidence of life-threatening infections caused by the filamentous fungus Aspergillus fumigatus is increasing along with an increase in the number of fungal strains resistant to contemporary antifungal therapies. The fungal cell wall and the associated carbohydrates required for its synthesis and maintenance are attractive drug targets given that many genes encoding proteins involved in cell wall biosynthesis and integrity are absent in humans. Importantly, genes and associated cell wall biosynthesis and homeostasis regulatory pathways remain to be fully defined in A. fumigatus In this report, we identify SsdA as an important component of trehalose and fungal cell wall biosynthesis in A. fumigatus that consequently impacts the host immune response and fungal virulence in animal models of infection.
Collapse
Affiliation(s)
- Arsa Thammahong
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Sourabh Dhingra
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Katherine M Bultman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joshua D Kerkaert
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| |
Collapse
|
13
|
Hatamoto M, Aizawa R, Kobayashi Y, Fujimura M. A novel fungicide aminopyrifen inhibits GWT-1 protein in glycosylphosphatidylinositol-anchor biosynthesis in Neurospora crassa. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 156:1-8. [PMID: 31027568 DOI: 10.1016/j.pestbp.2019.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Aminopyrifen, 4-phenoxybenzyl 2-amino-6-methylnicotinate, strongly inhibited the mycelial growth of a wild-type Neurospora crassa strain on Vogel's minimal medium containing 1.2% sucrose, with a 0.001 mg/L concentration required for 50% growth inhibition. Similar to micafungin, an inhibitor of beta-1, 3-glucan synthetase, aminopyrifen further inhibited the growth of N. crassa deletion mutants of MAP kinase cascade genes, such as mak-1 and mak-2, than the wild-type strain, suggesting that aminopyrifen perturbs cell wall-related processes. Furthermore, we found that three chitin synthase gene mutants (chs-1, chs-5, and chs-7) were highly sensitive to both chemicals; however, aminopyrifen, but not micafungin, induced a swollen germ tube from the conidia of chs-5 and chs-7 mutants on Vogel's medium containing 1.2% sucrose. To elucidate the target protein of aminopyrifen, we isolated mutants resistant to aminopyrifen after UV treatment of conidia of the wild-type strain or the chs-5 strain. The resistance mutations were localized to the gwt-1 gene that encodes an acyltransferase, GWT-1, which participates in the biosynthesis of the glycosylphosphatidylinositol (GPI) precursor, and were found to result in S180F and V178A alterations in the protein. These results strongly suggest that aminopyrifen works as an inhibitor targeting GWT-1, a protein involved in GPI-anchor biosynthesis.
Collapse
Affiliation(s)
- Masahiro Hatamoto
- Biological Section Research Department, Agro-Kanesho Co., Ltd., 9511-4 Yuki, Yuki-City, Ibaraki 307-0001, Japan
| | - Ryo Aizawa
- Chemical Synthesis Section Research Department, Agro-Kanesho Co., Ltd., 852, Shimoyasumatsu, Tokorozawa-City, Saitama 359-0024, Japan
| | - Yuta Kobayashi
- Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma 374-0193, Japan
| | - Makoto Fujimura
- Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma 374-0193, Japan.
| |
Collapse
|
14
|
Kitade Y, Sumita T, Izumitsu K, Tanaka C. Cla4 PAK-like kinase is required for pathogenesis, asexual/sexual development and polarized growth in Bipolaris maydis. Curr Genet 2019; 65:1229-1242. [DOI: 10.1007/s00294-019-00977-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
|
15
|
The endocytic cargo adaptor complex is required for cell-wall integrity via interacting with the sensor FgWsc2B in Fusarium graminearum. Curr Genet 2019; 65:1071-1080. [DOI: 10.1007/s00294-019-00961-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023]
|
16
|
Sun X, Su X. Harnessing the knowledge of protein secretion for enhanced protein production in filamentous fungi. World J Microbiol Biotechnol 2019; 35:54. [PMID: 30900052 DOI: 10.1007/s11274-019-2630-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/08/2019] [Indexed: 12/19/2022]
Abstract
Filamentous fungi are important microorganisms used in industrial production of proteins and enzymes. Among these organisms, Trichoderma reesei, Aspergilli, and more recently Myceliophthora thermophile are the most widely used and promising ones which have powerful protein secretion capability. In recent years, there have been tremendous achievements in understanding the molecular mechanisms of the secretory pathways in filamentous fungi. The acquired pieces of knowledge can be harnessed to enhance protein production in filamentous fungi with assistance of state-of-the-art genetic engineering techniques.
Collapse
Affiliation(s)
- Xianhua Sun
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun Street, Beijing, 100081, China.
| |
Collapse
|
17
|
Verdín J, Sánchez-León E, Rico-Ramírez AM, Martínez-Núñez L, Fajardo-Somera RA, Riquelme M. Off the wall: The rhyme and reason of Neurospora crassa hyphal morphogenesis. ACTA ACUST UNITED AC 2019; 5:100020. [PMID: 32743136 PMCID: PMC7389182 DOI: 10.1016/j.tcsw.2019.100020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/07/2019] [Accepted: 02/10/2019] [Indexed: 12/11/2022]
Abstract
Chitin and β-1,3-glucan synthases are transported separately in chitosomes and macrovesicles. Chitin synthases occupy the core of the SPK; β-1,3-glucan synthases the outer layer. CHS-4 arrival to the SPK and septa is CSE-7 dependent. Rabs YPT-1 and YPT-31 localization at the SPK mimics that of chitosomes and macrovesicles. The exocyst acts as a tether between the SPK outer layer vesicles and the apical PM.
The fungal cell wall building processes are the ultimate determinants of hyphal shape. In Neurospora crassa the main cell wall components, β-1,3-glucan and chitin, are synthesized by enzymes conveyed by specialized vesicles to the hyphal tip. These vesicles follow different secretory routes, which are delicately coordinated by cargo-specific Rab GTPases until their accumulation at the Spitzenkörper. From there, the exocyst mediates the docking of secretory vesicles to the plasma membrane, where they ultimately get fused. Although significant progress has been done on the cellular mechanisms that carry cell wall synthesizing enzymes from the endoplasmic reticulum to hyphal tips, a lot of information is still missing. Here, the current knowledge on N. crassa cell wall composition and biosynthesis is presented with an emphasis on the underlying molecular and cellular secretory processes.
Collapse
Key Words
- BGT, β-1,3-glucan transferases
- CHS, chitin synthase
- CLSM, confocal laser scanning microscopy
- CWI, cell wall integrity
- CWP, cell wall proteins
- Cell wall
- ER, endoplasmic reticulum
- FRAP, fluorescence recovery after photobleaching
- GEF, guanine nucleotide exchange factor
- GFP, green fluorescent protein
- GH, glycosyl hydrolases
- GPI, glycosylphosphatidylinositol
- GSC, β-1,3-glucan synthase complex
- MMD, myosin-like motor domain
- MS, mass spectrometry
- MT, microtubule
- NEC, network of elongated cisternae
- PM, plasma membrane
- SPK, Spitzenkörper
- Spitzenkörper
- TIRFM, total internal reflection fluorescence microscopy
- TM, transmembrane
- Tip growth
- Vesicles
Collapse
Affiliation(s)
- Jorge Verdín
- Industrial Biotechnology, CIATEJ-Jalisco State Scientific Research and Technology Assistance Center, Mexico National Council for Science and Technology, Zapopan, Jalisco, Mexico
| | - Eddy Sánchez-León
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adriana M Rico-Ramírez
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE Ensenada, Baja California, Mexico
| | - Leonora Martínez-Núñez
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rosa A Fajardo-Somera
- Karlsruhe Institute of Technology (KIT) South Campus, Institute for Applied Biosciences, Department of Microbiology, Karlsruhe, Germany
| | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE Ensenada, Baja California, Mexico
| |
Collapse
|
18
|
Kodama S, Nishiuchi T, Kubo Y. Colletotrichum orbiculare MTF4 Is a Key Transcription Factor Downstream of MOR Essential for Plant Signal-Dependent Appressorium Development and Pathogenesis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:313-324. [PMID: 30398907 DOI: 10.1094/mpmi-05-18-0118-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The cucumber anthracnose fungus Colletotrichum orbiculare forms a specialized infection structure, called an appressorium. Appressorium differentiation relies on fungal perception of physical and biochemical signals at the plant surface. Our previous report showed that the morphogenesis-related NDR (nuclear Dbf2-related) kinase pathway (MOR) is crucial for translating plant-derived signals for appressorium development. Here, we focused on identifying transcriptional regulators downstream of MOR that are involved in plant signal sensing and transduction for appressorium development. Based on whole-genome transcript profiling, we identified a Zn(II)2Cys6 transcription factor, CoMTF4, as a potential downstream factor of MOR. CoMTF4 was expressed in planta rather than in vitro under the control of the NDR kinase CoCbk1. Phenotypes of comtf4 mutants, strains with constitutively active CoCbk1 and strains with constitutive overexpression of CoMTF4 suggested that CoMtf4 acts downstream of MOR. Furthermore, nuclear localization of CoMtf4 was dependent on the MOR and responsive to plant-derived signals that lead to appressorium morphogenesis. Thus, we conclude that CoMtf4 is a transcription factor downstream of MOR that is essential for appressorium morphogenesis and pathogenesis and is regulated in response to plant-derived signals. This study provides insights into fungal sensing of plant signals and subsequent responses critical for appressorium formation.
Collapse
Affiliation(s)
- Sayo Kodama
- 1 Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan; and
| | - Takumi Nishiuchi
- 2 Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa 920-0934, Japan
| | - Yasuyuki Kubo
- 1 Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan; and
| |
Collapse
|
19
|
Herold I, Kowbel D, Delgado-Álvarez DL, Garduño-Rosales M, Mouriño-Pérez RR, Yarden O. Transcriptional profiling and localization of GUL-1, a COT-1 pathway component, in Neurospora crassa. Fungal Genet Biol 2019; 126:1-11. [PMID: 30731203 DOI: 10.1016/j.fgb.2019.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 01/19/2023]
Abstract
Impairment of theNeurospora crassaCOT-1 kinase results in defects in hyphal polarity. Some of these effects are partially suppressed by inactivation of gul-1 (encoding an mRNA-binding protein involved in translational regulation). Here, we report on the transcriptional profiling of cot-1 inactivation and demonstrate that gul-1 affects transcript abundance of multiple genes in the COT-1 pathway, including processes such as cell wall remodeling, nitrogen and amino acid metabolism. The GUL-1 protein itself was found to be distributed within the entire hyphal cell, along with a clear presence of aggregates that traffic within the cytoplasm. Live imaging of GUL-1-GFP demonstrated that GUL-1 transport is microtubule-dependent. Cellular stress, as imposed by the presence of the cell wall biosynthesis inhibitor Nikkomycin Z or by nitrogen limitation, resulted in a 2-3-fold increase of GUL-1 aggregate association with nuclei. Taken together, this study demonstrates that GUL-1 affects multiple processes, its function is stress-related and linked with cellular traffic and nuclear association.
Collapse
Affiliation(s)
- Inbal Herold
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| | - David Kowbel
- Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720-3102, USA
| | - Diego L Delgado-Álvarez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Mexico
| | - Marisela Garduño-Rosales
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Mexico
| | - Rosa R Mouriño-Pérez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Mexico
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| |
Collapse
|
20
|
Lin L, Sun Z, Li J, Chen Y, Liu Q, Sun W, Tian C. Disruption of gul-1 decreased the culture viscosity and improved protein secretion in the filamentous fungus Neurospora crassa. Microb Cell Fact 2018; 17:96. [PMID: 29908565 PMCID: PMC6004096 DOI: 10.1186/s12934-018-0944-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/12/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The cellulolytic fungus Neurospora crassa is considered a potential host for enzyme and bioethanol production. However, large scale applications are hindered by its filamentous growth. Although previous investigations have shown that mycelial morphology in submerged culture can be controlled by altering physical factors, there is little knowledge available about the potential for morphology control by genetic modification. RESULTS In this study, we screened morphological mutants in the filamentous fungus N. crassa. Of the 90 morphological mutants screened, 14 mutants exhibited considerably higher viscosity compared with that of the wild type strain, and only two mutants showed low-viscosity morphologies in submerged culture. We observed that disruption of gul-1 (NCU01197), which encodes an mRNA binding protein involved in cell wall remodeling, caused pellet formation as the fermentation progressed, and resulted in the most significant decrease in viscosity of culture broth. Moreover, over-expression of gul-1 caused dramatically increased viscosity, suggesting that the gul-1 had an important function in mycelial morphology during submerged cultivation. Transcriptional profiling showed that expression of genes encoding eight GPI-anchored cell wall proteins was lowered in Δgul-1 while expression of genes associated with two non-anchored cell wall proteins was elevated. Meanwhile, the expression levels of two hydrophobin genes were also significantly altered. These results suggested that GUL-1 affected the transcription of cell wall-related genes, thereby influencing cell wall structure and mycelial morphology. Additionally, the deletion of gul-1 caused increased protein secretion, probably due to a defect in cell wall integrity, suggesting this as an alternative strategy of strain improvement for enzyme production. To confirm practical applications, deletion of gul-1 in the hyper-cellulase producing strain (∆ncw-1∆Ncap3m) significantly reduced the viscosity of culture broth. CONCLUSIONS Using the model filamentous fungus N. crassa, genes that affect mycelial morphology in submerged culture were explored through systematic screening of morphological mutants. Disrupting several candidate genes altered viscosities in submerged culture. This work provides an example for controlling fungal morphology in submerged fermentation by genetic engineering, and will be beneficial for industrial fungal strain improvement.
Collapse
Affiliation(s)
- Liangcai Lin
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Zhiyong Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jingen Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Yong Chen
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Qian Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Wenliang Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Chaoguang Tian
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| |
Collapse
|
21
|
Aharoni-Kats L, Zelinger E, Chen S, Yarden O. Altering Neurospora crassa MOB2A exposes its functions in development and affects its interaction with the NDR kinase COT1. Mol Microbiol 2018; 108:641-660. [PMID: 29600559 DOI: 10.1111/mmi.13954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2018] [Indexed: 12/30/2022]
Abstract
The Neurospora crassa Mps One Binder (MOB) proteins MOB2A and MOB2B physically interact with the Nuclear Dbf2 Related (NDR) kinase COT1 and have been shown to have overlapping functions in various aspects of asexual development. Here, we identified two N. crassa MOB2A residues, Tyr117 and Tyr119, which are potentially phosphorylated. Using phosphomimetic mob-2a mutants we have been able to establish that apart from their previously described roles, MOB2A/B are involved in additional developmental processes. Enhanced conidial germination, accompanied by conidial agglutination, in the phosphomimetic mutants indicated that MOB2A is a negative regulator of germination. Thick-section imaging of perithecia revealed slow maturation and a lack of asci alignment in the mutant strains demonstrating a role for MOB2A in sexual development. We demonstrate that even though MOB2A and MOB2B have some overlapping functions, MOB2B cannot compensate for the roles MOB2A has in conidiation and germination. Altering Tyr residues 117 and 119 impaired the physical interactions between MOB2A and COT1, most likely contributing to some of the observed effects. As cot-1 and the phosphomimetic mutants share an extragenic suppressor (gul-1), we concluded that at least some of the effects imposed by altering Tyr117 and Tyr119 are mediated by the NDR kinase.
Collapse
Affiliation(s)
- Liran Aharoni-Kats
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - Einat Zelinger
- Centre for Scientific Imaging, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| | - She Chen
- Proteomics Centre, The National Institute of Biological Sciences, Beijing 102206, China
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610000, Israel
| |
Collapse
|
22
|
Rico-Ramírez AM, Roberson RW, Riquelme M. Imaging the secretory compartments involved in the intracellular traffic of CHS-4, a class IV chitin synthase, in Neurospora crassa. Fungal Genet Biol 2018; 117:30-42. [PMID: 29601947 DOI: 10.1016/j.fgb.2018.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 12/16/2022]
Abstract
In Neurospora crassa hyphae the localization of all seven chitin synthases (CHSs) at the Spitzenkörper (SPK) and at developing septa has been well analyzed. Hitherto, the mechanisms of CHSs traffic and sorting from synthesis to delivery sites remain largely unexplored. In Saccharomyces cerevisiae exit of Chs3p from the endoplasmic reticulum (ER) requires chaperone Chs7p. Here, we analyzed the role of CSE-7, N. crassa Chs7p orthologue, in the biogenesis of CHS-4 (orthologue of Chs3p). In a N. crassa Δcse-7 mutant, CHS-4-GFP no longer accumulated at the SPK and septa. Instead, fluorescence was retained in hyphal subapical regions in an extensive network of elongated cisternae (NEC) referred to previously as tubular vacuoles. In a complemented strain expressing a copy of cse-7 the localization of CHS-4-GFP at the SPK and septa was restored, providing evidence that CSE-7 is necessary for the localization of CHS-4 at hyphal tips and septa. CSE-7 was revealed at delimited regions of the ER at the immediacies of nuclei, at the NEC, and remarkably also at septa and the SPK. The organization of the NEC was dependent on the cytoskeleton. SEC-63, an extensively used ER marker, and NCA-1, a SERCA-type ATPase previously localized at the nuclear envelope, were used as markers to discern the nature of the membranes containing CSE-7. Both SEC-63 and NCA-1 were found at the nuclear envelope, but also at regions of the NEC. However, at the NEC only NCA-1 co-localized extensively with CSE-7. Observations by transmission electron microscopy revealed abundant rough ER sheets and distinct electron translucent smooth flattened cisternae, which could correspond collectively to the NEC, thorough the subapical cytoplasm. This study identifies CSE-7 as the putative ER receptor for its cognate cargo, the polytopic membrane protein CHS-4, and elucidates the complexity of the ER system in filamentous fungi.
Collapse
Affiliation(s)
- Adriana M Rico-Ramírez
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, BC 22860, Mexico
| | | | - Meritxell Riquelme
- Department of Microbiology, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, BC 22860, Mexico.
| |
Collapse
|
23
|
Shomin-Levi H, Yarden O. The Neurospora crassa PP2A Regulatory Subunits RGB1 and B56 Are Required for Proper Growth and Development and Interact with the NDR Kinase COT1. Front Microbiol 2017; 8:1694. [PMID: 28928725 PMCID: PMC5591878 DOI: 10.3389/fmicb.2017.01694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 12/29/2022] Open
Abstract
COT1 is the founding member of the highly conserved nuclear Dbf2-related (NDR) Ser/Thr kinase family and plays a role in the regulation of polar growth and development in Neurospora crassa and other fungi. Changes in COT1 phosphorylation state have been shown to affect hyphal elongation, branching, and conidiation. The function of NDR protein kinases has been shown to be regulated by type 2A protein phosphatases (PP2As). PP2As are heterotrimers comprised of a catalytic and scaffolding protein along with an interchangeable regulatory subunit involved in determining substrate specificity. Inactivation of the N. crassa PP2A regulatory subunits rgb-1 and b56 conferred severe hyphal growth defects. Partial suppression of defects observed in the rgb-1RIP strain (but not in the Δb56 mutant) was observed in cot-1 phosphomimetic mutants, demonstrating that altering COT1 phosphorylation state can bypass, at least in part, the requirement of a functional RGB1 subunit. The functional fusion proteins RGB1::GFP and B56::GFP predominantly localized to hyphal tips and septa, respectively, indicating that their primary activity is in different cellular locations. COT1 protein forms exhibited a hyperphosphorylated gel migration pattern in an rgb-1RIP mutant background, similar to that observed when the fungus was cultured in the presence of the PP2A inhibitor cantharidin. COT1 was hypophosphorylated in a Δb56 mutant background, suggesting that this regulatory subunit may be involved in determining COT1 phosphorylation state, yet in an indirect manner. Reciprocal co-immunoprecipitation analyses, using tagged COT1, PPH1, RGB1, and B56 subunits established that these proteins physically interact. Taken together, our data determine the presence of a functional and physical link between PP2A and COT1 and show that two of the PP2A regulatory subunits interact with the kinase and determine COT1 phosphorylation state.
Collapse
Affiliation(s)
- Hila Shomin-Levi
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovot, Israel
| |
Collapse
|
24
|
Schmidpeter J, Dahl M, Hofmann J, Koch C. ChMob2 binds to ChCbk1 and promotes virulence and conidiation of the fungal pathogen Colletotrichum higginsianum. BMC Microbiol 2017; 17:22. [PMID: 28103800 PMCID: PMC5248491 DOI: 10.1186/s12866-017-0932-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/12/2017] [Indexed: 01/11/2023] Open
Abstract
Background Mob family proteins are conserved between animals, plants and fungi and are essential for the activation of NDR kinases that control crucial cellular processes like cytokinesis, proliferation and morphology. Results We identified a hypomorphic allele of ChMOB2 in a random insertional mutant (vir-88) of the hemibiotrophic ascomycete fungus Colletotrichum higginsianum. The mutant is impaired in conidiation, host penetration and virulence on Arabidopsis thaliana. ChMob2 binds to and co-localizes with the NDR/LATS kinase homolog ChCbk1. Mutants in the two potential ChCbk1 downstream targets ChSSD1 and ChACE2 show defects in pathogenicity. The genome of C. higginsianum encodes two more Mob proteins. While we could not detect any effect on pathogenicity in ΔChmob3 mutants, ChMob1 is involved in conidiation, septae formation and virulence. Conclusion This study shows that ChMob2 binds to the conserved NDR/LATS Kinase ChCbk1 and plays an important role in pathogenicity of Colletotrichum higginsianum on Arabidopsis thaliana. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0932-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Johannes Schmidpeter
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Marlis Dahl
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Jörg Hofmann
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany
| | - Christian Koch
- Department of Biology, Division of Biochemistry, Friedrich-Alexander University Erlangen-Nuremberg, Staudtstrasse 5, 91058, Erlangen, Germany.
| |
Collapse
|