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Cea-Sánchez S, Corrochano-Luque M, Gutiérrez G, Glass NL, Cánovas D, Corrochano LM. Transcriptional Regulation by the Velvet Protein VE-1 during Asexual Development in the Fungus Neurospora crassa. mBio 2022; 13:e0150522. [PMID: 35913159 PMCID: PMC9426599 DOI: 10.1128/mbio.01505-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/13/2022] [Indexed: 11/23/2022] Open
Abstract
Asexual reproduction in fungi facilitates the dispersal and colonization of new substrates and, in pathogenic fungi, allows infection of plants and animals. The velvet complex is a fungus-specific protein complex that participates in the regulation of gene expression in response to environmental signals like light, as well as developmental processes, pathogenesis, and secondary metabolism. The velvet complex in the fungus Neurospora crassa is composed of three proteins, VE-1, VE-2, and LAE-1. Mutations in ve-1 or ve-2, but not in lae-1, led to shorter heights of aerial tissue, a mixture of aerial hyphae and developing macroconidia, and increased microconidiation when they were combined with mutations in the transcription factor gene fl. VE-2 and LAE-1 were detected during vegetative growth and conidiation, unlike VE-1, which was mostly observed in samples obtained from submerged vegetative hyphae. We propose that VE-1 is the limiting component of the velvet complex during conidiation and has a major role in the transcriptional regulation of conidiation. Characterization of the role of VE-1 during mycelial growth and asexual development (conidiation) by transcriptome sequencing (RNA-seq) experiments allowed the identification of a set of genes regulated by VE-1 that participate in the regulation of conidiation, most notably the transcription factor genes vib-1 and fl. We propose that VE-1 and VE-2 regulate the development of aerial tissue and the balance between macro- and microconidiation in coordination with FL and VIB-1. IMPORTANCE Most fungi disperse in nature and infect new hosts by producing vegetative spores or conidia during asexual development. This is a process that is regulated by environmental signals like light and the availability of nutrients. A protein complex, the velvet complex, participates in the integration of environmental signals to regulate conidiation. We have found that a key component of this complex in the fungus Neurospora crassa, VE-1, has a major role in the regulation of transcription during conidiation. VE-1 regulates a large number of genes, including the genes for the transcription factors FL and VIB-1. Our results will help to understand how environmental signals are integrated in the fungal cell to regulate development.
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Affiliation(s)
- Sara Cea-Sánchez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | | | - Gabriel Gutiérrez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - N. Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, Berkeley, California, USA
| | - David Cánovas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Luis M. Corrochano
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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2
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Chen JF, Liu Y, Tang GR, Jin D, Chen X, Pei Y, Fan YH. The secondary metabolite regulator, BbSmr1, is a central regulator of conidiation via the BrlA-AbaA-WetA pathway in Beauveria bassiana. Environ Microbiol 2020; 23:810-825. [PMID: 32691932 DOI: 10.1111/1462-2920.15155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 01/21/2023]
Abstract
The filamentous fungus Beauveria bassiana, an insect fungal pathogen, is widely used for pest biocontrol. Aerial conidia are infectious propagules, and their yield and viability greatly affect the field application of this fungus; however, little is known about the molecular regulatory mechanism of the triggered conidiation. In the present study, we find that the secondary metabolite regulator BbSmr1 is involved in the regulation of asexual conidiation development and stress response in B. bassiana. A deficiency in Bbsmr1 results in a prominent fluffy-like phenotype on solid medium, decreased conidial yield, accelerated conidial germination, as well as increased tolerance to H2 O2 stress and cell wall inhibitors. The deletion of Bbsmr1 also leads to thickened conidial cell walls and changed cell epitopes. Overexpressing either BbbrlA or BbabaA in the ∆Bbsmr1 strain can rescue the phenotypes of conidial development and stress response. BbSmr1 activates BbbrlA transcription by directly binding to the A4GA3 sequence of the BbbrlA promoter. BbBrlA in turn binds to the promoter of Bbsmr1 and negatively regulates the expression of Bbsmr1. These results indicate that BbSmr1 positively regulates conidial development in B. bassiana by activating the central development pathway BrlA-AbaA-WetA and provides insights into the developmental regulatory mechanism of entomopathogenic fungi.
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Affiliation(s)
- Jin-Feng Chen
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China.,College of Biological and Chemical Engineering, Chongqing University of Education, Chongqing, 400067, China
| | - Yu Liu
- College of Biotechnology, Southwest University, Beibei, Chongqing, 400716, China
| | - Gui-Rong Tang
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China
| | - Dan Jin
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China
| | - Xi Chen
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China
| | - Yan Pei
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China
| | - Yan-Hua Fan
- State Key Laboratory of Silkworm Genome Biology, Biotechnology Research Center, Southwest University, Chongqing, 400716, China
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3
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Rath M, Crenshaw NJ, Lofton LW, Glenn AE, Gold SE. FvSTUA is a Key Regulator of Sporulation, Toxin Synthesis, and Virulence in Fusarium verticillioides. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:958-971. [PMID: 32293993 DOI: 10.1094/mpmi-09-19-0271-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fusarium verticillioides is one of the most important pathogens of maize, causing rot and producing fumonisin mycotoxins during infection. Ingestion of fumonisin-contaminated corn causes underperformance and even fatal toxicity in livestock and is associated with neural tube birth defects, growth stunting in children, and some cancers. StuA, an APSES-class transcription factor, is a major developmental transcriptional regulator in fungi. It has been shown to regulate crucial developmental processes, such as sporulation, virulence, and mycotoxin synthesis among others. In this study, the role of FvSTUA in F. verticillioides was examined by characterizing ∆FvstuA deletion mutants functionally and transcriptomally. The deletion mutants exhibited reduced vegetative growth, stunted aerial hyphae, and significant reductions in microconidiation. Macroconidiation and hydrophobicity of the deletion strains were reduced as well. Additionally, fumonisin production and virulence of the deletion mutants were greatly reduced. Transcriptomic analysis revealed downregulation of expression of several genes in the fumonisin and fusarin C biosynthetic clusters and differential expression of genes involved in conidiation and virulence. Nuclear localization of FvSTUA supported its likely function as a transcription factor. Together, our results indicate that FvSTUA plays a global role in transcriptional regulation in F. verticillioides influencing morphogenesis, toxin production, and virulence.
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Affiliation(s)
- M Rath
- Department of Plant Pathology, University of Georgia, Athens, GA, U.S.A
| | - N J Crenshaw
- USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, U.S.A
| | - L W Lofton
- USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, U.S.A
| | - A E Glenn
- USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, U.S.A
| | - S E Gold
- USDA, ARS, US National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Athens, GA, U.S.A
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4
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Martins MP, Martinez-Rossi NM, Sanches PR, Rossi A. The PAC-3 transcription factor critically regulates phenotype-associated genes in Neurospora crassa. Genet Mol Biol 2020; 43:e20190374. [PMID: 32584919 PMCID: PMC7355564 DOI: 10.1590/1678-4685-gmb-2019-0374] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/08/2020] [Indexed: 12/17/2022] Open
Abstract
Transcription factors play an important role in fungal environmental adaptive process by promoting adjustment to challenging stimuli via gene modulation and activation of signaling networks. The transcription factor encoded by the pac-3/rim101/pacC gene is involved in pH regulation and is associated with a wide variety of cellular functions. The deletion of pac-3 affects fungal development. In Neurospora crassa, the Δpac-3 strain presents diminished aerial growth and reduced conidiation. However, the PAC-3-regulated genes associated with this altered phenotype have not been elucidated. In this study, we used RNA-seq to analyze the phenotypic plasticity induced after pac-3 deletion in the filamentous fungus N. crassa cultivated in media supplemented with sufficient or limited inorganic phosphate. Genes related to morphology, hyphal development, and conidiation were of particular interest in this study. Our results suggest a pac-3 dependency in gene regulation in a Pi-dependent manner. Furthermore, our analysis suggested that the fungus attempts to overcome the deletion effects in a Δpac-3 mutant through a complex combined regulatory mechanism. Finally, the modulatory responses observed in the Δpac-3 strain, a double mutant generated based on the Δmus-52 mutant strain, is strain-specific, highlighting that the phenotypic impact may be attributed to pac-3 absence despite the combined mus-52 deletion.
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Affiliation(s)
- Maíra Pompeu Martins
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Nilce Maria Martinez-Rossi
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Pablo Rodrigo Sanches
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Antonio Rossi
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
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5
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Conidiation in Neurospora crassa: vegetative reproduction by a model fungus. Int Microbiol 2019; 23:97-105. [DOI: 10.1007/s10123-019-00085-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Accepted: 05/20/2019] [Indexed: 12/13/2022]
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6
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Sun X, Wang F, Lan N, Liu B, Hu C, Xue W, Zhang Z, Li S. The Zn(II)2Cys6-Type Transcription Factor ADA-6 Regulates Conidiation, Sexual Development, and Oxidative Stress Response in Neurospora crassa. Front Microbiol 2019; 10:750. [PMID: 31024511 PMCID: PMC6468284 DOI: 10.3389/fmicb.2019.00750] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/26/2019] [Indexed: 01/02/2023] Open
Abstract
Conidiation and sexual development are critical for reproduction, dispersal and better-adapted survival in many filamentous fungi. The Neurospora crassa gene ada-6 encodes a Zn(II)2Cys6-type transcription factor, whose deletion resulted in reduced conidial production and female sterility. In this study, we confirmed the positive contribution of ada-6 to conidiation and sexual development by detailed phenotypic characterization of its deletion mutant and the complemented mutant. To understand the regulatory mechanisms of ADA-6 in conidiation and sexual development, transcriptomic profiles generated by RNA-seq from the Δada-6 mutant and wild type during conidiation and sexual development were compared. During conidial development, differential expressed genes (DEGs) between the Δada-6 mutant and wild type are mainly involved in oxidation-reduction process and single-organism metabolic process. Several conidiation related genes are positively regulated by ADA-6, including genes that positively regulate conidiation (fluffy and acon-3), and genes preferentially expressed during conidial development (eas, con-6, con-8, con-10, con-13, pcp-1, and NCU9357), as the expression of these genes were lower in the Δada-6 mutant compared to wild type during conidial development. Phenotypic observation of deletion mutants for other genes with unknown function down-regulated by ada-6 deletion revealed that deletion mutants for four genes (NCU00929, NCU05260, NCU00116, and NCU04813) produced less conidia than wild type. Deletion of ada-6 resulted in female sterility, which might be due to that ADA-6 affects oxidation-reduction process and transmembrane transport process, and positively regulates the transcription of pre-2, poi-2, and NCU05832, three key genes participating in sexual development. In both conidiation and the sexual development process, ADA-6 regulates the transcription of cat-3 and other genes participating in reactive oxygen species production according to RNA-seq data, indicating a role of ADA-6 in oxidative stress response. This was further confirmed by the results that deletion of ada-6 led to hypersensitivity to oxidants H2O2 and menadione. Together, these results proved that ADA-6, as a global regulator, plays a crucial role in conidiation, sexual development, and oxidative stress response of N. crassa.
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Affiliation(s)
- Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Food Science and Engineering, Qilu University of Technology, Jinan, China
| | - Nan Lan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Liu
- College of Food Science and Engineering, Qilu University of Technology, Jinan, China
| | - Chengcheng Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Xue
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhenying Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shaojie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Transcription Factors Controlling Primary and Secondary Metabolism in Filamentous Fungi: The β-Lactam Paradigm. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4020047] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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8
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Abstract
Regulation of gene expression by DNA-binding transcription factors is essential for proper control of growth and development in all organisms. In this study, we annotate and characterize growth and developmental phenotypes for transcription factor genes in the model filamentous fungus Neurospora crassa. We identified 312 transcription factor genes, corresponding to 3.2% of the protein coding genes in the genome. The largest class was the fungal-specific Zn2Cys6 (C6) binuclear cluster, with 135 members, followed by the highly conserved C2H2 zinc finger group, with 61 genes. Viable knockout mutants were produced for 273 genes, and complete growth and developmental phenotypic data are available for 242 strains, with 64% possessing at least one defect. The most prominent defect observed was in growth of basal hyphae (43% of mutants analyzed), followed by asexual sporulation (38%), and the various stages of sexual development (19%). Two growth or developmental defects were observed for 21% of the mutants, while 8% were defective in all three major phenotypes tested. Analysis of available mRNA expression data for a time course of sexual development revealed mutants with sexual phenotypes that correlate with transcription factor transcript abundance in wild type. Inspection of this data also implicated cryptic roles in sexual development for several cotranscribed transcription factor genes that do not produce a phenotype when mutated.
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9
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10
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Regulation of conidiation in Botrytis cinerea involves the light-responsive transcriptional regulators BcLTF3 and BcREG1. Curr Genet 2017; 63:931-949. [PMID: 28382431 DOI: 10.1007/s00294-017-0692-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 01/25/2023]
Abstract
Botrytis cinerea is a plant pathogenic fungus with a broad host range. Due to its rapid growth and reproduction by asexual spores (conidia), which increases the inoculum pressure, the fungus is a serious problem in different fields of agriculture. The formation of the conidia is promoted by light, whereas the formation of sclerotia as survival structures occurs in its absence. Based on this observation, putative transcription factors (TFs) whose expression is induced upon light exposure have been considered as candidates for activating conidiation and/or repressing sclerotial development. Previous studies reported on the identification of six light-responsive TFs (LTFs), and two of them have been confirmed as crucial developmental regulators: BcLTF2 is the positive regulator of conidiation, whose expression is negatively regulated by BcLTF1. Here, the functional characterization of the four remaining LTFs is reported. BcLTF3 has a dual function, as it represses conidiophore development by repressing bcltf2 in light and darkness, and is moreover essential for conidiogenesis. In bcltf3 deletion mutants conidium initials grow out to hyphae, which develop secondary conidiophores. In contrast, no obvious functions could be assigned to BcLTF4, BcLTF5 and BcLTF6 in these experiments. BcREG1, previously reported to be required for virulence and conidiogenesis, has been re-identified as light-responsive transcriptional regulator. Studies with bcreg1 overexpression strains indicated that BcREG1 differentially affects conidiation by acting as a repressor of BcLTF2-induced conidiation in the light and as an activator of a BcLTF2-independent conidiation program in the dark.
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11
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Cohrs KC, Simon A, Viaud M, Schumacher J. Light governs asexual differentiation in the grey mould fungus Botrytis cinerea via the putative transcription factor BcLTF2. Environ Microbiol 2016; 18:4068-4086. [PMID: 27347834 DOI: 10.1111/1462-2920.13431] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/27/2016] [Accepted: 06/21/2016] [Indexed: 11/26/2022]
Abstract
Botrytis cinerea is a plant pathogenic fungus known for its utilization of light as environmental cue to regulate asexual differentiation: conidia are formed in the light, while sclerotia are formed in the dark. As no orthologues of known regulators of conidiation (e.g., Aspergillus nidulans BrlA, Neurospora crassa FL) exist in the Leotiomycetes, we initiated a de novo approach to identify the functional counterpart in B. cinerea. The search revealed the light-responsive C2H2 transcription factor BcLTF2 whose expression - usually restricted to light conditions - is necessary and sufficient to induce conidiation and simultaneously to suppress sclerotial development. Light-induced expression of bcltf2 is mediated via a so far unknown pathway, and is attenuated in a (blue) light-dependent fashion by the White Collar complex, BcLTF1 and the VELVET complex. Mutation of either component leads to increased bcltf2 expression and causes light-independent conidiation (always conidia phenotype). Hence, the tight regulation of bcltf2 governs the balance between vegetative growth that allows for the colonization of the substrate and subsequent reproduction via conidia in the light. The orthologue ssltf2 in the closely related species Sclerotinia sclerotiorum is not significantly expressed suggesting that its deregulation may cause the lack of the conidiation program in this fungus.
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Affiliation(s)
- Kim C Cohrs
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität (WWU) Münster, Schlossplatz 8, Münster, 48143, Germany
| | - Adeline Simon
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, 78850, France
| | - Julia Schumacher
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität (WWU) Münster, Schlossplatz 8, Münster, 48143, Germany
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12
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Intact spore MALDI-TOF mass spectrometry and proteomic analysis of Puccinia pathogenic fungi. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1093-1103. [PMID: 27267623 DOI: 10.1016/j.bbapap.2016.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/27/2016] [Accepted: 06/02/2016] [Indexed: 11/20/2022]
Abstract
The aim of this work was to develop a method for the identification of pathogens causing rust diseases of crops using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of intact cells or spores (IC/IS). All optimizations were performed with Puccinia triticina, the causal agent of wheat leaf rust. Experiments included selection of washing solvents for spores, finding of an optimal concentration of spores in suspension and the most suitable matrix system as well as an evaluation of different sample preparation techniques. The best results were obtained when the spores were washed with acetonitrile/0.1% (v/v) trifluoroacetic acid, 7:3, v/v. A mixture of ferulic and sinapinic acids (5:15mgml(-1)) dissolved in acetonitrile/2.5% (v/v) trifluoroacetic acid, 7:3, v/v, was found optimal for the deposition of samples (50μg spores per μl) by two-layer volume technique. The optimized protocol was subsequently applied to other Puccinia species (Puccinia graminis, Puccinia striiformis and Puccinia coronata). Together with the use of the software BIOSPEAN, not only different species but also various pathotypes of the same species, which differ in their virulence, could be discriminated. There were 108 and 29 proteins identified from P. striiformis and P. graminis spores, respectively, after an acidic extraction in the matrix solvent mimicking the sample preparation for MALDI. Besides the presence of ribosomal proteins, histones, regulatory proteins and enzymes, also extracellular proteins participating in the pathogenesis were found. Finally, for both species, several proteins were assigned to signals in typical mass spectrometric profiles and suggested as diagnostic markers.
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13
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Mendes NS, Silva PM, Silva-Rocha R, Martinez-Rossi NM, Rossi A. Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa. FEBS Open Bio 2016; 6:358-68. [PMID: 27239448 PMCID: PMC4821360 DOI: 10.1002/2211-5463.12047] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
For this study, we sought to identify pre‐mRNA processing events modulated by changes in extracellular pH, inorganic phosphate, and antifungal drugs. We examined genes with at least four putative introns whose transcriptional level responded to these effectors. We showed that the intron retention levels of genes encoding asparagine synthetase 2, C6‐zinc finger regulator (fluffy), and a farnesyltransferase respond to amphotericin B, ketoconazole, and other effectors. In general, the assayed antifungals promoted the disruption of the structural domains of these proteins probably leading to their inactivation, which emphasize the complexity of the metabolic modulation exerted by antifungal signaling.
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Affiliation(s)
- Niege S Mendes
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Patricia M Silva
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Rafael Silva-Rocha
- Department of Molecular and Cellular Biology Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Nilce M Martinez-Rossi
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Antonio Rossi
- Department of Genetics Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
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14
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Schumacher J, Simon A, Cohrs KC, Traeger S, Porquier A, Dalmais B, Viaud M, Tudzynski B. The VELVET Complex in the Gray Mold Fungus Botrytis cinerea: Impact of BcLAE1 on Differentiation, Secondary Metabolism, and Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:659-74. [PMID: 25625818 DOI: 10.1094/mpmi-12-14-0411-r] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Botrytis cinerea, the gray mold fungus, is an important plant pathogen. Field populations are characterized by variability with regard to morphology, the mode of reproduction (conidiation or sclerotia formation), the spectrum of secondary metabolites (SM), and virulence. Natural variation in bcvel1 encoding the ortholog of Aspergillus nidulans VeA, a member of the VELVET complex, was previously shown to affect light-dependent differentiation, the formation of oxalic acid (OA), and virulence. To gain broader insight into the B. cinerea VELVET complex, an ortholog of A. nidulans LaeA, BcLAE1, a putative interaction partner of BcVEL1, was studied. BcVEL1 but not its truncated versions interacts with BcLAE1 and BcVEL2 (VelB ortholog). In accordance with the expected common as well as specific functions of BcVEL1 and BcLAE1, the deletions of both genes result in similar though not identical phenotypes. Both mutants lost the ability to produce OA, to colonize the host tissue, and to form sclerotia. However, mutants differ with regard to aerial hyphae and conidia formation. Genome-wide expression analyses revealed that BcVEL1 and BcLAE1 have common and distinct target genes. Some of the genes that are underexpressed in both mutants, e.g., those encoding SM-related enzymes, proteases, and carbohydrate-active enzymes, may account for their reduced virulence.
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Affiliation(s)
| | - Adeline Simon
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
| | - Kim C Cohrs
- 1 IBBP, WWU Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Antoine Porquier
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
- 3 Université Paris-Sud, 91405 Orsay, France
| | | | - Muriel Viaud
- 2 BIOGER, INRA, Avenue Lucien Brétignières, 78850 Grignon, France
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15
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Niu C, Payne GA, Woloshuk CP. Transcriptome changes in Fusarium verticillioides caused by mutation in the transporter-like gene FST1. BMC Microbiol 2015; 15:90. [PMID: 25906821 PMCID: PMC4422464 DOI: 10.1186/s12866-015-0427-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/19/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Fusarium verticillioides causes an important seed disease on maize and produces the fumonisin group of mycotoxins, which are toxic to humans and livestock. A previous study discovered that a gene (FST1) in the pathogen affects fumonisin production and virulence. Although the predicted amino acid sequence of FST1 is similar to hexose transporters, previous experimental evidence failed to prove function. RESULTS Three new phenotypes were identified that are associated with the FST1 mutant of F. verticillioides (Δfst1), namely reduction in macroconidia production, increased sensitivity to hydrogen peroxide, and reduced mycelial hydrophobicity. A transcriptome comparison of the wild type and strain Δfst1 grown on autoclaved maize kernels for six days identified 2677 genes that were differentially expressed. Through gene ontology analysis, 961 genes were assigned to one of 12 molecular function categories. Sets of down-regulated genes in strain Δfst1 were identified that could account for each of the mutant phenotypes. CONCLUSION The study provides evidence that disruption of FST1 causes several metabolic and developmental defects in F. verticillioides. FST1 appears to connect the expression of several gene networks, including those involved in secondary metabolism, cell wall structure, conidiogenesis, virulence, and resistance to reactive oxygen species. The results support our hypothesis that FST1 functions within the framework of environmental sensing.
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Affiliation(s)
- Chenxing Niu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | - Gary A Payne
- Department of Plant Pathology, North Carolina State University, 851 Main Campus Drive, Raleigh, NC, 27695-7567, USA.
| | - Charles P Woloshuk
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
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Son H, Kim MG, Chae SK, Lee YW. FgFlbD regulates hyphal differentiation required for sexual and asexual reproduction in the ascomycete fungus Fusarium graminearum. J Microbiol 2014; 52:930-9. [DOI: 10.1007/s12275-014-4384-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/19/2014] [Accepted: 08/19/2014] [Indexed: 12/22/2022]
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17
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Abstract
The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 hr in the dark and then exposed to light for 0 (control) 15, 60, 120, and 240 min. More than three-quarters of all defined protein coding genes (79%) were expressed in these cells. The increased sensitivity of RNA-seq compared with previous microarray studies revealed that the RNA levels for 31% of expressed genes were affected two-fold or more by exposure to light. Additionally, a large class of mRNAs, enriched for transcripts specifying products involved in rRNA metabolism, showed decreased expression in response to light, indicating a heretofore undocumented effect of light on this pathway. Based on measured changes in mRNA levels, light generally increases cellular metabolism and at the same time causes significant oxidative stress to the organism. To deal with this stress, protective photopigments are made, antioxidants are produced, and genes involved in ribosome biogenesis are transiently repressed.
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Gyöngyösi N, Káldi K. Interconnections of reactive oxygen species homeostasis and circadian rhythm in Neurospora crassa. Antioxid Redox Signal 2014; 20:3007-23. [PMID: 23964982 DOI: 10.1089/ars.2013.5558] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
SIGNIFICANCE Both circadian rhythm and the production of reactive oxygen species (ROS) are fundamental features of aerobic eukaryotic cells. The circadian clock enhances the fitness of organisms by enabling them to anticipate cycling changes in the surroundings. ROS generation in the cell is often altered in response to environmental changes, but oscillations in ROS levels may also reflect endogenous metabolic fluctuations governed by the circadian clock. On the other hand, an effective regulation and timing of antioxidant mechanisms may be crucial in the defense of cellular integrity. Thus, an interaction between the circadian timekeeping machinery and ROS homeostasis or signaling in both directions may be of advantage at all phylogenetic levels. RECENT ADVANCES The Frequency-White Collar-1 and White Collar-2 oscillator (FWO) of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Several members of the ROS homeostasis were found to be controlled by the circadian clock, and ROS levels display circadian rhythm in Neurospora. On the other hand, multiple data indicate that ROS affect the molecular oscillator. CRITICAL ISSUES Increasing evidence suggests the interplay between ROS homeostasis and oscillators that may be partially or fully independent of the FWO. In addition, ROS may be part of a complex cellular network synchronizing non-transcriptional oscillators with timekeeping machineries based on the classical transcription-translation feedback mechanism. FUTURE DIRECTIONS Further investigations are needed to clarify how the different layers of the bidirectional interactions between ROS homeostasis and circadian regulation are interconnected.
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Ruger-Herreros C, Gil-Sánchez MDM, Sancar G, Brunner M, Corrochano LM. Alteration of light-dependent gene regulation by the absence of the RCO-1/RCM-1 repressor complex in the fungus Neurospora crassa. PLoS One 2014; 9:e95069. [PMID: 24747913 PMCID: PMC3991626 DOI: 10.1371/journal.pone.0095069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/23/2014] [Indexed: 12/04/2022] Open
Abstract
The activation of transcription by light in the fungus Neurospora crassa requires the White Collar Complex (WCC), a photoreceptor and transcription factor complex. After light reception two WCCs interact and bind the promoters of light-regulated genes to activate transcription. This process is regulated by VVD, a small photoreceptor that disrupts the interaction between WCCs and leads to a reduction in transcription after long exposures to light. The N. crassa RCO-1/RCM-1 repressor complex is the homolog of the Tup1-Ssn6 repressor complex in yeast, and its absence modifies photoadaptation. We show that the absence of the RCO-1/RCM-1 repressor complex leads to several alterations in transcription that are gene-specific: an increase in the accumulation of mRNAs in the dark, a repression of transcription, and a derepression of transcription after long exposures to light. The absence of the RCO-1/RCM-1 repressor complex leads to lower VVD levels that are available for the regulation of the activity of the WCC. The reduction in the amount of VVD results in increased WCC binding to the promoters of light-regulated genes in the dark and after long exposures to light, leading to the modification of photoadaptation that has been observed in rco-1 and rcm-1 mutants. Our results show that the photoadaptation phenotype of mutants in the RCO-1/RCM-1 repressor complex is, at least in part, an indirect consequence of the reduction of vvd transcription, and the resulting modification in the regulation of transcription by the WCC.
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Affiliation(s)
| | | | - Gencer Sancar
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Heidelberg, Germany
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Li L, Hu X, Xia Y, Xiao G, Zheng P, Wang C. Linkage of oxidative stress and mitochondrial dysfunctions to spontaneous culture degeneration in Aspergillus nidulans. Mol Cell Proteomics 2013; 13:449-61. [PMID: 24345786 DOI: 10.1074/mcp.m113.028480] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Filamentous fungi including mushrooms frequently and spontaneously degenerate during subsequent culture maintenance on artificial media, which shows the loss or reduction abilities of asexual sporulation, sexuality, fruiting, and production of secondary metabolites, thus leading to economic losses during mass production. To better understand the underlying mechanisms of fungal degeneration, the model fungus Aspergillus nidulans was employed in this study for comprehensive analyses. First, linkage of oxidative stress to culture degeneration was evident in A. nidulans. Taken together with the verifications of cell biology and biochemical data, a comparative mitochondrial proteome analysis revealed that, unlike the healthy wild type, a spontaneous fluffy sector culture of A. nidulans demonstrated the characteristics of mitochondrial dysfunctions. Relative to the wild type, the features of cytochrome c release, calcium overload and up-regulation of apoptosis inducing factors evident in sector mitochondria suggested a linkage of fungal degeneration to cell apoptosis. However, the sector culture could still be maintained for generations without the signs of growth arrest. Up-regulation of the heat shock protein chaperones, anti-apoptotic factors and DNA repair proteins in the sector could account for the compromise in cell death. The results of this study not only shed new lights on the mechanisms of spontaneous degeneration of fungal cultures but will also provide alternative biomarkers to monitor fungal culture degeneration.
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Affiliation(s)
- Lin Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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21
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Park HS, Yu JH. Genetic control of asexual sporulation in filamentous fungi. Curr Opin Microbiol 2012; 15:669-77. [PMID: 23092920 DOI: 10.1016/j.mib.2012.09.006] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 12/20/2022]
Abstract
Asexual sporulation (conidiation) in the ascomycetous filamentous fungi involves the formation of conidia, formed on specialized structures called conidiophores. Conidiation in filamentous fungi involves many common themes including spatial and temporal regulation of gene expression, specialized cellular differentiation, intra-/inter-cellular communications, and response to environmental factors. The commencement, progression and completion of conidiation are regulated by multiple positive and negative genetic elements that direct expression of genes required for proper vegetative growth and the assembly of the conidiophore and spore maturation. Light is one of the key environmental factors affecting conidiation. Developmental mechanisms in Aspergillus nidulans and Neurospora crassa have been intensively studied, leading to important outlines. Here, we summarize genetic control of conidiation including the light-responding mechanisms in the two model fungi.
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Affiliation(s)
- Hee-Soo Park
- Departments of Bacteriology and Genetics, and Molecular and Environmental Toxicology Center, University of Wisconsin, Madison, WI 53706, USA
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22
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Guo J, Duan YH, Zhang JS, Shi XX, Chen YY, Zhang H, Huang LL, Kang ZS. A conidiation-related gene is highly expressed at the resting urediospore stage inPuccinia striiformisf. sp.tritici. J Basic Microbiol 2012; 53:695-702. [DOI: 10.1002/jobm.201200059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 06/06/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Ying-Hui Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Life Science, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Jin-Shan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Xue-Xia Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Yue-Ying Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Li-Li Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
| | - Zhen-Sheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University, Yangling; Shaanxi; P. R.; China
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Sun X, Yu L, Lan N, Wei S, Yu Y, Zhang H, Zhang X, Li S. Analysis of the role of transcription factor VAD-5 in conidiation of Neurospora crassa. Fungal Genet Biol 2012; 49:379-87. [PMID: 22445960 DOI: 10.1016/j.fgb.2012.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 03/01/2012] [Accepted: 03/07/2012] [Indexed: 11/29/2022]
Abstract
Conidiation is the major mode of reproduction in many filamentous fungi. The Neurospora crassa gene vad-5, which encodes a GAL4-like Zn2Cys6 transcription factor, was suggested to contribute to conidiation in a previous study using a knockout mutant. In this study, we confirmed the positive contribution of vad-5 to conidiation by gene complementation. To understand the role of vad-5 in conidiation, transcriptomic profiles generated by digital gene expression profiling from the vad-5 deletion mutant and the wild-type strain were compared. Among 7559 detected genes, 176 genes were found to be transcriptionally down-regulated and 277 genes transcriptionally upregulated in the vad-5 deletion mutant, using ≥1-fold change as a cutoff threshold. Among the down-regulated genes, four which were already known to be involved in conidiation -fluffy, ada-6, rca-1, and eas - were examined further in a time course experiment. Transcription of each of the four genes in the vad-5 deletion mutant was lower than in the wild-type strain during conidial development. Phenotypic observation of deletion mutants for 132 genes down-regulated by vad-5 deletion revealed that deletion mutants for 17 genes, including fluffy, ada-6, and eas, produced fewer conidia than the wild type. By phenotypic observation of deletion mutants for 211 genes upregulated in the vad-5 deletion mutant, two types of deletion mutants were found. One type, which produced more conidia than the wild-type strain, includes deletion mutants for previously characterized genes cat-2, cat-3, and sah-1 and for a non-characterized gene NCU07221. Deletion mutants of NCU06302 and NCU11090, representing the second type, produced conidia earlier than the wild-type strain. Based on these conidiation phenotypes, we designated NCU07221 as high conidial production-1 (hcp-1) and named NCU06302 and NCU11090 as early conidial development-1 (ecd-1) and ecd-2, respectively. Given the collective results from this study, we propose that vad-5 exerts an effect on conidiation by activating genes that positively contribute to conidiation as well as by repressing genes that negatively influence conidial development.
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Affiliation(s)
- Xianyun Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China
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24
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Sun X, Zhang H, Zhang Z, Wang Y, Li S. Involvement of a helix–loop–helix transcription factor CHC-1 in CO2-mediated conidiation suppression in Neurospora crassa. Fungal Genet Biol 2011; 48:1077-86. [DOI: 10.1016/j.fgb.2011.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 09/19/2011] [Accepted: 09/29/2011] [Indexed: 01/25/2023]
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25
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Inoue H. Exploring the processes of DNA repair and homologous integration in Neurospora. Mutat Res 2011; 728:1-11. [PMID: 21757027 DOI: 10.1016/j.mrrev.2011.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2011] [Indexed: 12/23/2022]
Abstract
This review offers a personal perspective on historical developments related to our current understanding of DNA repair, recombination, and homologous integration in Neurospora crassa. Previous reviews have summarized and analyzed the characteristics of Neurospora DNA repair mutants. The early history is reviewed again here as a prelude to a discussion of the molecular cloning, annotation, gene disruption and reverse genetics of Neurospora DNA repair genes. The classical studies and molecular analysis are then linked in a perspective on new directions in research on mutagen-sensitive mutants.
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Affiliation(s)
- Hirokazu Inoue
- Laboratory of Genetics, Department of Regulation Biology, Faculty of Science, Saitama University, Urawa 338-8570, Japan.
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26
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Abstract
Light regulates several aspects of the biology of many organisms, including the balance between asexual and sexual development in some fungi. To understand how light regulates fungal development at the molecular level we have used Aspergillus nidulans as a model. We have performed a genome-wide expression analysis that has allowed us to identify >400 genes upregulated and >100 genes downregulated by light in developmentally competent mycelium. Among the upregulated genes were genes required for the regulation of asexual development, one of the major biological responses to light in A. nidulans, which is a pathway controlled by the master regulatory gene brlA. The expression of brlA, like conidiation, is induced by light. A detailed analysis of brlA light regulation revealed increased expression after short exposures with a maximum after 60 min of light followed by photoadaptation with longer light exposures. In addition to brlA, genes flbA-C and fluG are also light regulated, and flbA-C are required for the correct light-dependent regulation of the upstream regulator fluG. We have found that light induction of brlA required the photoreceptor complex composed of a phytochrome FphA, and the white-collar homologs LreA and LreB, and the fluffy genes flbA-C. We propose that the activation of regulatory genes by light is the key event in the activation of asexual development by light in A. nidulans.
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Chung DW, Greenwald C, Upadhyay S, Ding S, Wilkinson HH, Ebbole DJ, Shaw BD. acon-3, the Neurospora crassa ortholog of the developmental modifier, medA, complements the conidiation defect of the Aspergillus nidulans mutant. Fungal Genet Biol 2011; 48:370-6. [DOI: 10.1016/j.fgb.2010.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 12/17/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
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Tian C, Li J, Glass NL. Exploring the bZIP transcription factor regulatory network in Neurospora crassa. MICROBIOLOGY (READING, ENGLAND) 2011; 157:747-759. [PMID: 21081763 PMCID: PMC3081083 DOI: 10.1099/mic.0.045468-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/08/2010] [Accepted: 11/14/2010] [Indexed: 11/18/2022]
Abstract
Transcription factors (TFs) are key nodes of regulatory networks in eukaryotic organisms, including filamentous fungi such as Neurospora crassa. The 178 predicted DNA-binding TFs in N. crassa are distributed primarily among six gene families, which represent an ancient expansion in filamentous ascomycete genomes; 98 TF genes show detectable expression levels during vegetative growth of N. crassa, including 35 that show a significant difference in expression level between hyphae at the periphery versus hyphae in the interior of a colony. Regulatory networks within a species genome include paralogous TFs and their respective target genes (TF regulon). To investigate TF network evolution in N. crassa, we focused on the basic leucine zipper (bZIP) TF family, which contains nine members. We performed baseline transcriptional profiling during vegetative growth of the wild-type and seven isogenic, viable bZIP deletion mutants. We further characterized the regulatory network of one member of the bZIP family, NCU03905. NCU03905 encodes an Ap1-like protein (NcAp-1), which is involved in resistance to multiple stress responses, including oxidative and heavy metal stress. Relocalization of NcAp-1 from the cytoplasm to the nucleus was associated with exposure to stress. A comparison of the NcAp-1 regulon with Ap1-like regulons in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Aspergillus fumigatus showed both conservation and divergence. These data indicate how N. crassa responds to stress and provide information on pathway evolution.
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Affiliation(s)
- Chaoguang Tian
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Jingyi Li
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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Greenwald CJ, Kasuga T, Glass NL, Shaw BD, Ebbole DJ, Wilkinson HH. Temporal and spatial regulation of gene expression during asexual development of Neurospora crassa. Genetics 2010; 186:1217-30. [PMID: 20876563 PMCID: PMC2998306 DOI: 10.1534/genetics.110.121780] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 09/18/2010] [Indexed: 12/18/2022] Open
Abstract
In this study we profiled spatial and temporal transcriptional changes during asexual sporulation in the filamentous fungus Neurospora crassa. Aerial tissue was separated from the mycelium to allow detection of genes specific to each tissue. We identified 2641 genes that were differentially expressed during development, which represents ∼25% of the predicted genes in the genome of this model fungus. On the basis of the distribution of functional annotations of 1102 of these genes, we identified gene expression patterns that define key physiological events during conidial development. Not surprisingly, genes encoding transcription factors, cell wall remodeling proteins, and proteins involved in signal transduction were differentially regulated during asexual development. Among the genes differentially expressed in aerial tissues the majority were unclassified and tended to be unique to ascomycete genomes. This finding is consistent with the view that these genes evolved for asexual development in the Pezizomycotina. Strains containing deletions of several differentially expressed genes encoding transcription factors exhibited asexual development-associated phenotypes. Gene expression patterns during asexual development suggested that cAMP signaling plays a critical role in the transition from aerial growth to proconidial chain formation. This observation prompted us to characterize a deletion of the gene encoding a high-affinity cAMP phosphodiesterase (NCU00478). NCU00478 was determined to be allelic to aconidiate-2, a previously identified genetic locus controlling conidiation.
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Affiliation(s)
- Charles J. Greenwald
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Takao Kasuga
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - N. Louise Glass
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Brian D. Shaw
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Daniel J. Ebbole
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Heather H. Wilkinson
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132 and Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
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A role in the regulation of transcription by light for RCO-1 and RCM-1, the Neurospora homologs of the yeast Tup1-Ssn6 repressor. Fungal Genet Biol 2010; 47:939-52. [PMID: 20709620 DOI: 10.1016/j.fgb.2010.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Revised: 07/29/2010] [Accepted: 08/02/2010] [Indexed: 12/15/2022]
Abstract
The activation of gene transcription by light is transient since light-dependent mRNA accumulation ceases after long exposures to light. This phenomenon, photoadaptation, has been observed in plants and fungi, and allows the perception of changes in light intensities. In the fungus Neurosporacrassa photoadaptation involves the transient binding of the photoresponsive White Collar Complex (WCC) to the promoters of light-regulated genes. We show that RCO-1 and RCM-1, the Neurospora homologs of the components of the yeast Tup1-Ssn6 repressor complex, participate in photoadaptation. Mutation in either rco-1 or rcm-1 result in high and sustained accumulation of mRNAs for con-10 and other light-regulated genes after long exposures to light. The mutation of rco-1 increased the sensitivity to light for con-10 activation and delayed synthesis and/or degradation of con-10 and con-6 mRNAs without altering the amount or the light-dependent phosphorylation of the photoreceptor WC-1. RCO-1 and RCM-1 are located in the Neurospora nuclei were they regulate gene transcription. We show that RCO-1 and RCM-1 participate in the light-transduction pathway of Neurospora and has a role in photoadaptation by repressing gene transcription after long exposures to light.
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Regulation by blue light of the fluffy gene encoding a major regulator of conidiation in Neurospora crassa. Genetics 2009; 184:651-8. [PMID: 20026679 DOI: 10.1534/genetics.109.109975] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The development of asexual spores, that is, the process of conidiation, in the fungus Neurospora crassa is increased by light. The fluffy (fl) gene, encoding a major regulator of conidiation, is activated by light. We describe here a detailed characterization of the regulation by blue light of fl in vegetative hyphae. This induction requires the white collar complex (WCC) while the FLD protein acts as a dark repressor of fl transcription. We show that the WCC directly regulates fl transcription in response to blue light after transiently binding the promoter. We propose that fl is repressed by FLD in vegetative mycelia and that the repression is lost after light exposure and WCC activation. The increase in fl mRNA in vegetative mycelia after light exposure, and the corresponding increase in the amount of the regulatory FL protein, should promote the activation of the conidiation pathway. The activation by light of fl provides a simple mechanism for the activation of conidiation by blue light in Neurospora that may be at work in other fungi.
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Hypovirus-responsive transcription factor gene pro1 of the chestnut blight fungus Cryphonectria parasitica is required for female fertility, asexual spore development, and stable maintenance of hypovirus infection. EUKARYOTIC CELL 2008; 8:262-70. [PMID: 19114501 DOI: 10.1128/ec.00338-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report characterization of the gene encoding putative transcription factor PRO1, identified in transcriptional profiling studies as being downregulated in the chestnut blight fungus Cryphonectria parasitica in response to infection by virulence-attenuating hypoviruses. Sequence analysis confirmed that pro1 encodes a Zn(II)(2)Cys(6) binuclear cluster DNA binding protein with significant sequence similarity to the pro1 gene product that controls fruiting body development in Sordaria macrospora. Targeted disruption of the C. parasitica pro1 gene resulted in two phenotypic changes that also accompany hypovirus infection, a significant reduction in asexual sporulation that could be reversed by exposure to high light intensity, and loss of female fertility. The pro1 disruption mutant, however, retained full virulence. Although hypovirus CHV1-EP713 infection was established in the pro1 disruption mutant, infected colonies continually produced virus-free sectors, suggesting that PRO1 is required for stable maintenance of hypovirus infection. These results complement the recent characterization of the hypovirus-responsive homologue of the Saccharomyces cerevisiae Ste12 C(2)H(2) zinc finger transcription factor gene, cpst12, which was shown to be required for C. parasitica female fertility and virulence.
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Abstract
We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of sufficient density to allow fine mapping of most loci. Sequencing of Mauriceville cDNAs and alignment to the completed genomic sequence of the Oak Ridge strain identified 19,087 putative SNPs. Of these, a subset was validated by cleaved amplified polymorphic sequence (CAPS), a simple and robust PCR-based assay that reliably distinguishes between SNP alleles. Experimental confirmation resulted in the development of 250 CAPS markers distributed evenly over the genome. To demonstrate the applicability of this map, we used bulked segregant analysis followed by interval mapping to locate the csp-1 mutation to a narrow region on LGI. Subsequently, we refined mapping resolution to 74 kbp by developing additional markers, resequenced the candidate gene, NCU02713.3, in the mutant background, and phenocopied the mutation by gene replacement in the WT strain. Together, these techniques demonstrate a generally applicable and straightforward approach for the isolation of novel genes from existing mutants. Data on both putative and validated SNPs are deposited in a customized public database at the Broad Institute, which encourages augmentation by community users.
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Functional characterization of tzn1 and tzn2-zinc transporter genes in Neurospora crassa. Biometals 2008; 22:411-20. [PMID: 18989627 DOI: 10.1007/s10534-008-9177-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2008] [Accepted: 10/24/2008] [Indexed: 10/21/2022]
Abstract
Previous work from our laboratory involved the description of the Neurospora metal transportome, which included seven hypothetical zinc transporters belonging to the ZIP family. The aim of the present study was to make a comparative functional evaluation of two hypothetical zinc transporters named tzn1 (NCU07621.3) and tzn2 (NCU11414.3). Phenotypic analysis of tzn1 and tzn2 mutants and a double mutant (tzn1tzn2) revealed that the deletion of tzn1 causes aconidiation and a greater defect in growth than the single deletion of tzn2. Supplementation with zinc restores growth but not conidiation in tzn1 and tzn1tzn2. TZN1 complemented a zinc-uptake-deficient Saccharomyces cerevisiae mutant (zrt1zrt2) in zinc-deficient conditions, while tzn2 restored growth upon supplementation with zinc (0.05 mM). Furthermore, the Deltatzn1 mutant was found to have severely reduced zinc content indicating that tzn1 functions as a key regulator of intracellular zinc levels in Neurospora crassa. Zinc uptake studies indicate tzn1 is a specific transporter of zinc, while tzn2 transports both zinc and cadmium. Quantitative RT-PCR showed up-regulation of tzn1 (128-fold) under zinc-depleted conditions and down-regulation (>1,000-fold) in zinc-replete conditions. The present study indicates that the zinc transport proteins encoded by tzn1 and tzn2 are members of the zinc uptake system regulated by zinc status in N. crassa.
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Gooch VD, Mehra A, Larrondo LF, Fox J, Touroutoutoudis M, Loros JJ, Dunlap JC. Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. EUKARYOTIC CELL 2007; 7:28-37. [PMID: 17766461 PMCID: PMC2224151 DOI: 10.1128/ec.00257-07] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in Neurospora crassa. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony assay that will facilitate luciferase-based screens. The signals from sorbose-grown colonies of strains in which the frq promoter drives luciferase exhibit the properties of circadian rhythms and can be tracked for many days to weeks. This reporter now makes it possible to follow the clock in real time, even in strains or under conditions in which the circadian rhythm in conidial banding is not expressed. This property has been used to discover short, ca. 15-h period rhythms at high temperatures, at which banding becomes difficult to observe in race tubes, and to generate a high-resolution temperature phase-response curve.
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Affiliation(s)
- Van D Gooch
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
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36
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Bieszke JA, Li L, Borkovich KA. The fungal opsin gene nop-1 is negatively-regulated by a component of the blue light sensing pathway and influences conidiation-specific gene expression in Neurospora crassa. Curr Genet 2007; 52:149-57. [PMID: 17676324 DOI: 10.1007/s00294-007-0148-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 07/17/2007] [Accepted: 07/18/2007] [Indexed: 10/23/2022]
Abstract
We previously demonstrated that the nop-1 gene encodes a putative green-light opsin photoreceptor that is highly expressed in cultures that support asexual sporulation (conidiation) in Neurospora crassa. In this study, we demonstrate that nop-1 is a late-stage conidiation gene, through analysis of nop-1 transcript levels in wild-type strains and mutants blocked at various stages of conidiation. nop-1 message amounts are similar with constant illumination or darkness during conidiation, consistent with developmental, but not light, regulation of nop-1 expression. Furthermore, photoinduction experiments using wild type and mutants defective in components of the blue light sensing pathway (wc-1 and wc-2) indicate that nop-1 mRNA levels are not appreciably affected by brief light exposure during conidiation. Surprisingly, nop-1 message amounts are greatly elevated in wc-2 mutants in light or dark, suggesting that the wc-2 gene product regulates nop-1 expression in a light-independent manner. Analysis of expression patterns for al-2, con-10 and con-13, genes regulated by conidiation and/or blue light, showed that nop-1 has significant and reproducible effects on all three genes during various stages of conidiation. The results suggest that NOP-1 directly or indirectly modulates carotenogenesis and repression of conidiation-specific gene expression in N. crassa.
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Affiliation(s)
- Jennifer A Bieszke
- Department of Microbiology and Molecular Genetics, University of Texas-Houston Medical School, 6431 Fannin Street, JFB 1.765, Houston, TX 77030, USA
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37
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Kubicek CP, Komoń-Zelazowska M, Sándor E, Druzhinina IS. Facts and Challenges in the Understanding of the Biosynthesis of Peptaibols byTrichoderma. Chem Biodivers 2007; 4:1068-82. [PMID: 17589877 DOI: 10.1002/cbdv.200790097] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Species of the mitosporic filamentous fungal genus Trichoderma are prominent producers of both short (7-11 residues) and long (18-20 residues) peptaibols and peptaibiotics, which are thought to be involved in their interaction with other living systems. Numerous reviews are available regarding biodiversity, structure, and mode of action of these peptide derivatives, but little emphasis has been paid to the physiology and genetics of their formation. In this review article, we used the recent knowledge on biosynthesis and production of these components to speculate on some of the unknown points. We also highlight areas where further research is most urgently needed.
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Affiliation(s)
- Christian P Kubicek
- Division of Gene Technology and Applied Biochemistry (DGTAB), Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/1665, Vienna, Austria
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Perkins DD, Freitag M, Pollard VC, Bailey-Shrode LA, Selker EU, Ebbole DJ. Recurrent locus-specific mutation resulting from a cryptic ectopic insertion in Neurospora. Genetics 2007; 175:527-44. [PMID: 17322355 PMCID: PMC1800634 DOI: 10.1534/genetics.106.065714] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
New mutations are found among approximately 20% of progeny when one or both parents carry eas allele UCLA191 (eas(UCLA), easily wettable, hydrophobin-deficient, linkage group II). The mutations inactivate the wild-type allele of cya-8 (cytochrome aa3 deficient, linkage group VII), resulting in thin, "transparent" mycelial growth. Other eas alleles fail to produce cya-8 mutant progeny. The recurrent cya-8 mutations are attributed to repeat-induced point mutation (RIP) resulting from a duplicated copy of cya-8+ that was inserted ectopically at eas when the UCLA191 mutation occurred. As expected for RIP, eas(UCLA)-induced cya-8 mutations occur during nuclear proliferation prior to karyogamy. When only one parent is eas(UCLA), the new mutations arise exclusively in eas(UCLA) nuclei. Mutation of cya-8 is suppressed when a long unlinked duplication is present. Stable cya-8 mutations are effectively eliminated in crosses homozygous for rid, a recessive suppressor of RIP. The eas(UCLA) allele is associated with a long paracentric inversion. A discontinuity is present in eas(UCLA) DNA. The eas promoter is methylated in cya-8 progeny of eas(UCLA), presumably by the spreading of methylation beyond the adjoining RIP-inactivated duplication. These findings support a model in which an ectopic insertion that created a mutation at the target site acts as a locus-specific mutator via RIP.
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Affiliation(s)
- David D Perkins
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA
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MacPherson S, Larochelle M, Turcotte B. A fungal family of transcriptional regulators: the zinc cluster proteins. Microbiol Mol Biol Rev 2006; 70:583-604. [PMID: 16959962 PMCID: PMC1594591 DOI: 10.1128/mmbr.00015-06] [Citation(s) in RCA: 401] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The trace element zinc is required for proper functioning of a large number of proteins, including various enzymes. However, most zinc-containing proteins are transcription factors capable of binding DNA and are named zinc finger proteins. They form one of the largest families of transcriptional regulators and are categorized into various classes according to zinc-binding motifs. This review focuses on one class of zinc finger proteins called zinc cluster (or binuclear) proteins. Members of this family are exclusively fungal and possess the well-conserved motif CysX(2)CysX(6)CysX(5-12)CysX(2)CysX(6-8)Cys. The cysteine residues bind to two zinc atoms, which coordinate folding of the domain involved in DNA recognition. The first- and best-studied zinc cluster protein is Gal4p, a transcriptional activator of genes involved in the catabolism of galactose in the budding yeast Saccharomyces cerevisiae. Since the discovery of Gal4p, many other zinc cluster proteins have been characterized; they function in a wide range of processes, including primary and secondary metabolism and meiosis. Other roles include regulation of genes involved in the stress response as well as pleiotropic drug resistance, as demonstrated in budding yeast and in human fungal pathogens. With the number of characterized zinc cluster proteins growing rapidly, it is becoming more and more apparent that they are important regulators of fungal physiology.
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Affiliation(s)
- Sarah MacPherson
- Department of Microbiology and Immunology, Royal Victoria Hospital, McGill University, Montréal, Québec, Canada H3A 1A
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40
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Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 2006; 103:10352-10357. [PMID: 16801547 PMCID: PMC1482798 DOI: 10.1073/pnas.0601456103] [Citation(s) in RCA: 889] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The low rate of homologous recombination exhibited by wild-type strains of filamentous fungi has hindered development of high-throughput gene knockout procedures for this group of organisms. In this study, we describe a method for rapidly creating knockout mutants in which we make use of yeast recombinational cloning, Neurospora mutant strains deficient in nonhomologous end-joining DNA repair, custom-written software tools, and robotics. To illustrate our approach, we have created strains bearing deletions of 103 Neurospora genes encoding transcription factors. Characterization of strains during growth and both asexual and sexual development revealed phenotypes for 43% of the deletion mutants, with more than half of these strains possessing multiple defects. Overall, the methodology, which achieves high-throughput gene disruption at an efficiency >90% in this filamentous fungus, promises to be applicable to other eukaryotic organisms that have a low frequency of homologous recombination.
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Affiliation(s)
- Hildur V Colot
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Gyungsoon Park
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Gloria E Turner
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | - Carol Ringelberg
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755
| | - Christopher M Crew
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Liubov Litvinkova
- Department of Plant Pathology, University of California, Riverside, CA 92521; and
| | - Richard L Weiss
- Department of Chemistry and Biochemistry, 405 Hilgard Avenue, University of California, Los Angeles, CA 90095
| | | | - Jay C Dunlap
- *Department of Genetics, Dartmouth Medical School, HB7400, Hanover, NH 03755;
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41
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Flaherty JE, Dunkle LD. Identification and expression analysis of regulatory genes induced during conidiation in Exserohilum turcicum. Fungal Genet Biol 2005; 42:471-81. [PMID: 15809011 DOI: 10.1016/j.fgb.2005.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 01/31/2005] [Accepted: 02/01/2005] [Indexed: 11/18/2022]
Abstract
Light influences numerous developmental and biochemical processes in fungi. The objectives of this research were to characterize the influence of light on growth and conidiation and associated gene expression in the plant pathogenic ascomycete, Exserohilum turcicum. We found that vegetative growth was more extensive in light/dark cycles than in constant light or darkness as measured by analysis of ergosterol content and genomic DNA. Cultures grown under continuous white light or blue light (approximately 465-480 nm) were developmentally arrested after the formation of conidiophores, whereas those grown in continuous darkness or a light/dark cycle produced mature conidia. Incubation of conidiophore-producing cultures in darkness for a minimum of 2 h was necessary and sufficient to initiate synchronous conidiation. To identify genes that are expressed during dark-induced conidiation, we constructed subtractive cDNA libraries from cultures grown under conidiation-permissive and -repressive conditions. From 816 sequenced EST clones in the conidiation-permissive and 310 in the repressive libraries, 12 putative regulatory genes were chosen for expression analysis by quantitative real-time PCR. The majority of those genes reached maximum expression by 2 h after initiation of the dark period and then declined to initial levels by 4-24 h in darkness. Expression of two dark-induced genes remained elevated after 24 h in darkness but was reset to initial levels if cultures were returned to light. This study revealed several genes whose expression increased rapidly after dark induction of conidiation, suggesting that they encode regulators of asexual development in E. turcicum.
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MESH Headings
- Ascomycota/genetics
- Ascomycota/growth & development
- DNA, Complementary
- DNA, Fungal/biosynthesis
- DNA, Fungal/chemistry
- Ergosterol/analysis
- Ergosterol/biosynthesis
- Expressed Sequence Tags
- Gene Expression Profiling
- Gene Expression Regulation, Fungal
- Gene Library
- Genes, Fungal
- Genes, Regulator
- Light
- Molecular Sequence Data
- Morphogenesis
- Polymerase Chain Reaction
- RNA, Fungal/analysis
- RNA, Messenger/analysis
- Sequence Analysis, DNA
- Spores, Fungal/genetics
- Spores, Fungal/growth & development
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Affiliation(s)
- Joseph E Flaherty
- United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research Unit, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054, USA
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42
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Rerngsamran P, Murphy MB, Doyle SA, Ebbole DJ. Fluffy, the major regulator of conidiation in Neurospora crassa, directly activates a developmentally regulated hydrophobin gene. Mol Microbiol 2005; 56:282-97. [PMID: 15773996 DOI: 10.1111/j.1365-2958.2005.04544.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The fluffy (fl) gene of Neurospora crassa is required for asexual sporulation and encodes an 88 kDa polypeptide containing a typical fungal Zn2Cys6 DNA-binding motif. Identification of genes regulated by fl will provide insight into how fungi regulate growth during morphogenesis. As a step towards identifying the target genes on which FL may act, we sought to define target sequences to which the FL protein binds. The DNA binding domain of FL was expressed in Escherichia coli as a fusion with glutathione S-transferase (GST) and purified using glutathione-sepharose affinity chromatography. The DNA binding sites were selected and amplified by means of a polymerase chain reaction (PCR)-mediated random-site selection method involving affinity bead-binding and gel mobility shift analysis. Sequencing and comparison of the selected clones suggested that FL binds to the motif 5'-CGG(N)9CCG-3'. A potential binding site was found in the promoter region of the eas (ccg-2) gene, which encodes a fungal hydrophobin. In vitro competitive binding assays revealed a preferred binding site for FL in the eas promoter, 5'-CGGAAGTTTC CTCCG-3', which is located 1498 bp upstream of the eas translation initiation codon. In vivo experiments using a foreign DNA sequence tag also confirmed that this sequence resides in a region required for FL regulation. In addition, yeast one hybrid experiments demonstrated that the C-terminal portion of FL functions in transcriptional activation. Transcriptional profiling was used to identify additional potential targets for regulation by fl.
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Affiliation(s)
- Panan Rerngsamran
- Program for the Biology of Filamentous Fungi, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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43
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Banno S, Ochiai N, Noguchi R, Kimura M, Yamaguchi I, Kanzaki SI, Murayama T, Fujimura M. A catalytic subunit of cyclic AMP-dependent protein kinase, PKAC-1, regulates asexual differentiation in Neurospora crassa. Genes Genet Syst 2005; 80:25-34. [PMID: 15824453 DOI: 10.1266/ggs.80.25] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A cyclic AMP (cAMP)-dependent protein kinase pathway has been shown to regulate growth, morphogenesis and virulence in filamentous fungi. However, the precise mechanisms of regulation through the pathway remain poorly understood. In Neurospora crassa, the cr-1 adenylate cyclase mutant exhibits colonial growth with short aerial hyphae bearing conidia, and the mcb mutant, a mutant of the regulatory subunit of cAMP-dependent protein kinase (PKA), shows the loss of growth polarity at the restrictive temperature. In the present study, we isolated mutants of the catalytic subunit of the PKA gene pkac-1 through the process of repeat-induced point mutation (RIP). PKA activity of the mutants obtained through RIP was undetectable. The genome sequence predicts two distinct catalytic subunit genes of PKA, named pkac-1 (NCU06240.1, AAF75276) and pkac-2 (NCU00682.1), as is the case in most filamentous fungi. The results suggest that PKAC-1 works as the major PKA in N. crassa. The phenotype of the pkac-1 mutants included colonial growth, short aerial hyphae, premature conidiation on solid medium, inappropriate conidiation in submerged culture, and increased thermotolerance. This phenotype of pkac-1 mutants resembled to that of cr-1 mutants, except that the addition of cAMP did not rescue the abnormal morphology of pkac-1 mutants. The loss of growth polarity at the restrictive temperature in the mcb mutant was suppressed by pkac-1 mutation. These results suggest that the signal transduction pathway mediated by PKAC-1 plays an important role in regulation of aerial hyphae formation, conidiation, and hyphal growth with polarity.
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Affiliation(s)
- Shinpei Banno
- Faculty of Life Sciences, Toyo University, Gunma, Japan
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Vienken K, Scherer M, Fischer R. The Zn(II)2Cys6 putative Aspergillus nidulans transcription factor repressor of sexual development inhibits sexual development under low-carbon conditions and in submersed culture. Genetics 2004; 169:619-30. [PMID: 15520269 PMCID: PMC1449130 DOI: 10.1534/genetics.104.030767] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we have characterized the putative Zn(II)2Cys6 transcription factor RosA from the filamentous fungus Aspergillus nidulans. The rosA gene encodes a protein of 713 aa, which shares 38% sequence similarity to Pro1 from Sordaria macrospora. In contrast to Pro1, which promotes the transition from protoperithecia to perithecia, RosA is a negative regulator of sexual development in A. nidulans. Transcript levels of rosA were usually very low and were only transiently upregulated upon carbon starvation and at 12 hr of asexual development. Deletion of rosA only slightly induced fruiting-body formation under standard culture conditions, but enabled sexual development under low-glucose and high-osmolarity conditions and the production of Hulle cells under submersed growth conditions. Stimulation of fruiting-body formation on agar surfaces was dependent on veA. In delta rosA strains, transcript levels of the sexual developmental regulators nsdD, veA, and stuA were increased. Overexpression of rosA led to a reduction of hyphal growth and to a fluffy phenotype. Post-transcriptional regulation of RosA, with a regulated accumulation in the nucleus, was shown using a RosA-GFP fusion protein. We propose that RosA represses sexual development upon integration of several environmental signals.
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Affiliation(s)
- Kay Vienken
- Department of Microbiology, University of Marburg and Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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45
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Liu TD, Marzluf GA. Characterization of pco-1, a newly identified gene which regulates purine catabolism in Neurospora. Curr Genet 2004; 46:213-27. [PMID: 15378267 DOI: 10.1007/s00294-004-0530-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Revised: 08/24/2004] [Accepted: 08/30/2004] [Indexed: 11/30/2022]
Abstract
A new gene of Neurospora crassa, designated pco-1, was characterized and shown to regulate the expression of several genes which encode enzymes required for the catabolism of purines. Unlike the wild type, a pco-1 mutant created by repeat-induced point mutation cannot utilize purines as a nitrogen source. The PCO1 protein contains a Zn(II)2Cys6 binuclear cluster motif near its N-terminus, followed by a putative coiled-coil motif. A chemical crosslinking experiment demonstrated that PCO1 forms homodimers. PCO1 binds to CGG-N6-CCG elements located in the upstream promoter region of four genes encoding purine catabolic enzymes. Northern blot analysis demonstrated that a functional PCO1 protein is required for induction of xdh, which encodes xanthine dehydrogenase. Moreover, PCO1 was required for induction of three different purine catabolic enzymes. Two glutamine-rich domains occur in the C-terminal region of PCO1 and at least one of the glutamine-rich regions is required for PCO1 function, suggesting that they might play a role in transcriptional activation. The PCO1 protein does not interact with the global-acting NIT2 protein or the negative-acting NMR protein that functions in nitrogen catabolite repression. Induction of the xdh gene and synthesis of xanthine dehydrogenase is completely dependent upon PCO1, but does not require the global-acting NIT2 protein, suggesting that it is controlled by a novel regulatory mechanism.
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Affiliation(s)
- T D Liu
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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46
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Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 2004; 68:1-108. [PMID: 15007097 PMCID: PMC362109 DOI: 10.1128/mmbr.68.1.1-108.2004] [Citation(s) in RCA: 434] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.
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Affiliation(s)
- Katherine A Borkovich
- Department of Plant Pathology, University of California, Riverside, California 92521, USA. Katherine/
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47
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Bailey-Shrode L, Ebbole DJ. The fluffy Gene of Neurospora crassa Is Necessary and Sufficient to Induce Conidiophore Development. Genetics 2004. [DOI: 10.1093/genetics/166.4.1741] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The fl (fluffy) gene of Neurospora crassa encodes a binuclear zinc cluster protein that regulates the production of asexual spores called macroconidia. Two other genes, acon-2 and acon-3, play major roles in controlling development. fl is induced specifically in differentiating tissue during conidiation and acon-2 plays a role in this induction. We examined the function of fl by manipulating its level of expression in wild-type and developmental mutant strains. Increasing expression of fl from a heterologous promoter in a wild-type genetic background is sufficient to induce conidiophore development. Elevated expression of fl leads to induction of development of the acon-2 mutant in nitrogen-starved cultures, but does not bypass the conidiation defect of the acon-3 mutant. These findings indicate that fl acts downstream of acon-2 and upstream of acon-3 in regulating gene expression during development. The eas, con-6, and con-10 genes are induced at different times during development. Morphological changes induced by artificially elevated fl expression in the absence of environmental cues were correlated with increased expression of eas, but not con-6 or con-10. Thus, although inappropriate expression of fl in vegetative hyphae is sufficient to induce conidial morphogenesis, complete reconstitution of development leading to the formation of mature conidia may require environmental signals to regulate fl activity and/or appropriate induction of fl expression in the developing conidiophore.
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Affiliation(s)
- Lori Bailey-Shrode
- Program for the Biology of Filamentous Fungi, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132
| | - Daniel J Ebbole
- Program for the Biology of Filamentous Fungi, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843-2132
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Xiang Q, Glass NL. Chromosome rearrangements in isolates that escape from het-c heterokaryon incompatibility in Neurospora crassa. Curr Genet 2003; 44:329-38. [PMID: 14564476 DOI: 10.1007/s00294-003-0451-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2003] [Revised: 08/29/2003] [Accepted: 09/08/2003] [Indexed: 10/26/2022]
Abstract
Chromosomal rearrangement is implicated in human cancers and hereditary diseases. Mechanisms generating chromosomal rearrangements may be shared by a variety of organisms. Spontaneous chromosomal rearrangements, especially large deletions, take place at high frequency in isolates that escape from heterokaryon incompatibility in Neurospora crassa. In this study, chromosomal rearrangements were detected in strains that had escaped from het-c heterokaryon incompatibility in N. crassa. A vc1 mutant carried a 20-kbp deletion covering five ORFs. A vc2 mutant carried a complex chromosome rearrangement with an 8-kbp deletion covering three ORFs, a 34-bp deletion and an 80-kbp inversion. The break-points of chromosome rearrangements in the vc1 and vc2 mutants all have direct repeats of 2 bp, similar to the break-points of some chromosome rearrangements associated with human cancer and genetic diseases. An ahc mutant carried a 31-kbp deletion covering at least 11 ORFs and a het-c deletion mutant carried a 7-kbp deletion covering two ORFs. Additional chromosomal rearrangements occurred in these two strains. These results indicate that escape from heterokaryon incompatibility can be used as a model system for chromosome rearrangement and DNA-repair studies. The impact of the chromosomal rearrangements is discussed, especially the deletion of the predicted ORFs on the phenotype of mutants.
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Affiliation(s)
- Qijun Xiang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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Masloff S, Jacobsen S, Pöggeler S, Kück U. Functional analysis of the C6 zinc finger gene pro1 involved in fungal sexual development. Fungal Genet Biol 2002; 36:107-16. [PMID: 12081464 DOI: 10.1016/s1087-1845(02)00010-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The pro1 gene, controlling fruiting body development in the homothallic ascomycete Sordaria macrospora, encodes a C6 zinc finger protein with a typical DNA binding domain of GAL4-like C6 zinc finger proteins as well as a putative nuclear targeting signal. In the corresponding mutant pro1, the pro1 gene is deleted, and the transition of primordia into mature fruiting bodies is prevented. To further characterize the PRO1 polypeptide, the yeast system was used for identifying a transactivation domain in the N-terminal half of PRO1, which probably also functions in S. macrospora. The functional analysis was extended by using truncated versions of the pro1 gene in complementation transformations of a deltapro1 mutant. Interestingly, the 5' part of the pro1 gene encoding the DNA binding and transactivation domain as well as putative nuclear targeting signals was sufficient to restore fertility in the sterile pro1 mutant. In vitro mutagenesis verified that the DNA binding domain is essential for normal fruiting body development. This was concluded from transformation experiments with eight pro1 derivatives containing triplet substitutions in conserved codons of the DNA binding domain; some, but not all, failed in restoring the wild-type phenotype in mutant pro1. Using a PCR-based cloning strategy, pro1 homologs from the two related heterothallic species Neurospora crassa and Sordaria brevicollis were isolated, showing similarities in the predicted amino acid sequences of 91 and 90%, respectively. When a N. crassa pro1 cDNA clone was used in complementation transformations, we succeeded in restoring the wild-type phenotype to the S. macrospora pro1 mutant. These data suggest that pro1 homologs from heterothallic species can provide the pro1 function in homothallic ascomycetes. Based on the published sequence of the N. crassa genome, we identified hpro1A, another transcriptionally expressed gene, with a similarity of 40% to the pro1 genes, which is present as a single copy gene in N. crassa as well as in S. macrospora.
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Affiliation(s)
- Sandra Masloff
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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Correa A, Bell-Pedersen D. Distinct signaling pathways from the circadian clock participate in regulation of rhythmic conidiospore development in Neurospora crassa. EUKARYOTIC CELL 2002; 1:273-80. [PMID: 12455961 PMCID: PMC118037 DOI: 10.1128/ec.1.2.273-280.2002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Several different environmental signals can induce asexual spore development (conidiation) and expression of developmentally regulated genes in Neurospora crassa. However, under constant conditions, where no environmental cues for conidiation are present, the endogenous circadian clock in N. crassa promotes daily rhythms in expression of known developmental genes and of conidiation. We anticipated that the same pathway of gene regulation would be followed during clock-controlled conidiation and environmental induction of conidiation and that the circadian clock would need only to control the initial developmental switch. Previous experiments showed that high-level developmental induction of the clock-controlled genes eas (ccg-2) and ccg-1 requires the developmental regulatory proteins FL and ACON-2, respectively, and normal developmental induction of fl mRNA expression requires ACON-2. We demonstrate that the circadian clock regulates rhythmic fl gene expression and that fl rhythmicity requires ACON-2. However, we find that clock regulation of eas (ccg-2) is normal in an fl mutant strain and ccg-1 expression is rhythmic in an acon-2 mutant strain. Together, these data point to the endogenous clock and the environment following separate pathways to regulate conidiation-specific gene expression.
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Affiliation(s)
- Alejandro Correa
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
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