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Cai G, Fry WE, Hillman BI. PiRV-2 stimulates sporulation in Phytophthora infestans. Virus Res 2019; 271:197674. [DOI: 10.1016/j.virusres.2019.197674] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 02/05/2023]
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Schmoll M, Tian C, Sun J, Tisch D, Glass NL. Unravelling the molecular basis for light modulated cellulase gene expression - the role of photoreceptors in Neurospora crassa. BMC Genomics 2012; 13:127. [PMID: 22462823 PMCID: PMC3364853 DOI: 10.1186/1471-2164-13-127] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/31/2012] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Light represents an important environmental cue, which exerts considerable influence on the metabolism of fungi. Studies with the biotechnological fungal workhorse Trichoderma reesei (Hypocrea jecorina) have revealed an interconnection between transcriptional regulation of cellulolytic enzymes and the light response. Neurospora crassa has been used as a model organism to study light and circadian rhythm biology. We therefore investigated whether light also regulates transcriptional regulation of cellulolytic enzymes in N. crassa. RESULTS We show that the N. crassa photoreceptor genes wc-1, wc-2 and vvd are involved in regulation of cellulase gene expression, indicating that this phenomenon is conserved among filamentous fungi. The negative effect of VVD on production of cellulolytic enzymes is thereby accomplished by its role in photoadaptation and hence its function in White collar complex (WCC) formation. In contrast, the induction of vvd expression by the WCC does not seem to be crucial in this process. Additionally, we found that WC-1 and WC-2 not only act as a complex, but also have individual functions upon growth on cellulose. CONCLUSIONS Genome wide transcriptome analysis of photoreceptor mutants and evaluation of results by analysis of mutant strains identified several candidate genes likely to play a role in light modulated cellulase gene expression. Genes with functions in amino acid metabolism, glycogen metabolism, energy supply and protein folding are enriched among genes with decreased expression levels in the wc-1 and wc-2 mutants. The ability to properly respond to amino acid starvation, i. e. up-regulation of the cross pathway control protein cpc-1, was found to be beneficial for cellulase gene expression. Our results further suggest a contribution of oxidative depolymerization of cellulose to plant cell wall degradation in N. crassa.
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Affiliation(s)
- Monika Schmoll
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
- Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Wien, Austria
| | - Chaoguang Tian
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jianping Sun
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
| | - Doris Tisch
- Research Area Gene Technology and Applied Biochemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Wien, Austria
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley, CA 94720, USA
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Kasuga T, Townsend JP, Tian C, Gilbert LB, Mannhaupt G, Taylor JW, Glass NL. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Res 2005; 33:6469-85. [PMID: 16287898 PMCID: PMC1283539 DOI: 10.1093/nar/gki953] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 09/22/2005] [Accepted: 10/19/2005] [Indexed: 01/26/2023] Open
Abstract
To test the inferences of spotted microarray technology against a biochemically well-studied process, we performed transcriptional profiling of conidial germination in the filamentous fungus, Neurospora crassa. We first constructed a 70 base oligomer microarray that assays 3366 predicted genes. To estimate the relative gene expression levels and changes in gene expression during conidial germination, we analyzed a circuit design of competitive hybridizations throughout a time course using a Bayesian analysis of gene expression level. Remarkable consistency of mRNA profiles with previously published northern data was observed. Genes were hierarchically clustered into groups with respect to their expression profiles over the time course of conidial germination. A functional classification database was employed to characterize the global picture of gene expression. Consensus motif searches identified a putative regulatory component associated with genes involved in ribosomal biogenesis. Our transcriptional profiling data correlate well with biochemical and physiological processes associated with conidial germination and will facilitate functional predictions of novel genes in N.crassa and other filamentous ascomycete species. Furthermore, our dataset on conidial germination allowed comparisons to transcriptional mechanisms associated with germination processes of diverse propagules, such as teliospores of the phytopathogenic fungus Ustilago maydis and spores of the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Takao Kasuga
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Jeffrey P. Townsend
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
- Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT 06269, USA
| | - Chaoguang Tian
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Luz B. Gilbert
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - Gertrud Mannhaupt
- Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and HealthD-85764 Neuherberg, Germany
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA 94720-3102, USA
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Affiliation(s)
- E P Geiduschek
- Division of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA.
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de la Serna I, Ng D, Tyler BM. Carbon regulation of ribosomal genes in Neurospora crassa occurs by a mechanism which does not require Cre-1, the homologue of the Aspergillus carbon catabolite repressor, CreA. Fungal Genet Biol 1999; 26:253-69. [PMID: 10361038 DOI: 10.1006/fgbi.1999.1121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription of the ribosomal protein and 40S rRNA genes is coordinately regulated during steady state growth and carbon shifts in Neurospora crassa. Recognition sequences for the Aspergillus nidulans carbon catabolite repressor, CreA, overlap transcriptional elements of a 40S rRNA gene and the crp-2 ribosomal protein gene. They also occur in similar locations in the promoters of several other ribosomal protein genes. Substitutions encompassing the -74 and -167 CreA consensus sequences in the crp-2 promoter result in a decrease in transcription. A cDNA encoding the N. crassa homologue of CreA was cloned and designated Cre-1. The Cre-1 protein is 45% identical to CreA from A. nidulans. Cre-1 protein produced in Escherichia coli binds to the CreA sites in the promoters of the 40S rRNA and crp-2 genes. An amino acid change from histidine (92) to threonine changed the Cre-1 binding specificity from (5'G/CC/TGGG/AG3') to (5'G/CC/TGGCG3'). Base substitutions in the Cre-1 binding sites of the crp-2 promoter disrupted binding of wildtype Cre-1 in vitro but had no effect on transcription during steady state growth or carbon shifts, indicating that regulation of ribosomal genes by carbon source is not mediated by Cre-1, but via different proteins binding the Cre-1 sites and the Dde boxes.
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Affiliation(s)
- I de la Serna
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
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Cujec TP, Tyler BM. Nutritional and growth control of ribosomal protein mRNA and rRNA in Neurospora crassa. Nucleic Acids Res 1996; 24:943-50. [PMID: 8600464 PMCID: PMC145710 DOI: 10.1093/nar/24.5.943] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The effects of changing growth rates on the levels of 40S pre-rRNA and two r-protein mRNAs were examined to gain insight into the coordinate transcriptional regulation of ribosomal genes in the ascomycete fungus Neurospora crassa. Growth rates were varied either by altering carbon nutritional conditions, or by subjecting the isolates to inositol-limiting conditions. During carbon up- or down-shifts, r-protein mRNA levels were stoichiometrically coordinated. Changes in 40S pre-rRNA levels paralleled those of the r-protein mRNAs but in a non-stoichiometric manner. Comparison of crp-2 mRNA levels with those of a crp-2::qa-2 fusion gene indicated no major effect from changes in crp-2 mRNA stability. Crp-2 promoter mutagenesis experiments revealed that two elements of the crp-2 promoter, -95 to -83 bp (Dde box) and -74 to -66 bp (CG repeat) important for transcription under constant growth conditions, are also critical for transcriptional regulation by a carbon source. Ribosomal protein mRNA and rRNA levels were unaffected by changes in growth rates when the cultures were grown under inositol-limiting conditions, suggesting that, under these conditions, transcription of the ribosomal genes in N.crassa was regulated independently of growth rate.
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Affiliation(s)
- T P Cujec
- Department of Plant Pathology, University of California, Davis 95616, USA
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Melnik VI, Bowman BJ. Isolation of the vma-6 gene encoding a 41 kDa subunit of the Neurospora crassa vacuolar ATPase, and an adjoining gene encoding a ribosome-associated protein. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1273:77-83. [PMID: 8611592 DOI: 10.1016/0005-2728(95)00144-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The vma-6 gene, encoding a membrane-associated subunit of the vacuolar H+-ATPase from Neurospora crassa, was cloned and sequenced. The gene contains three small introns and encodes a protein of 41 005 Da. When compared with homologous polypeptides from other species, the N. crassa protein contains a unique glycine-rich region. Three conserved cysteine residues, previously unrecognized, have been identified. An unrelated gene encoding a protein of 31 701 Da was found 2.1 kb downstream of vma-6. The second appears to encode the N. crassa homolog of a ribosome-associated protein identified previously in several plant and mammalian cells, and was named rap-1.
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Affiliation(s)
- V I Melnik
- Department of Biology, University of California, Santa Cruz 95064, USA
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Wechser MA, Bowman BJ. Regulation of the expression of three housekeeping genes encoding subunits of the Neurospora crassa vacuolar ATPase. MOLECULAR & GENERAL GENETICS : MGG 1995; 249:317-27. [PMID: 7500957 DOI: 10.1007/bf00290533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The vacuolar ATPase is a complex enzyme and is encoded by at least nine genes, which appear to be scattered throughout the genome. We have examined the vma-1 vma-2, and vma-3 genes, which encode subunits present in multiple copies within the Neurospora crassa vacuolar ATPase. We wished to see if the expression of these genes is coordinately regulated and if these genes contain similar promoter elements. A region was sequenced of approximately 1 kb located upstream of the protein coding region for each gene. Several sequence elements were found in similar positions in each of the three genes. Each of the genes had several strong transcription initiation sites, clustered within 13-60 bp and located 112-193 bp upstream of the translation start site. The size and abundance of the RNA transcripts was also determined: the amount of RNA transcribed from each gene was roughly proportional to the numbers of each subunit present in the enzyme. A series of plasmids was constructed containing parts of the putative promoter region fused to beta-galactosidase. Analysis of these plasmids indicated that the essential region of the vma promoters lies within 370 bp of the protein coding region. Overall, the vma genes appear to have similar characteristics to "housekeeping" genes described in other organisms.
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Affiliation(s)
- M A Wechser
- Department of Biology, Sinsheimer Laboratories, University of California, Santa Cruz 95064, USA
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Ichi-ishi A, Inoue H. Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1 alpha (EF-1 alpha) of Neurospora crassa. IDENGAKU ZASSHI 1995; 70:273-87. [PMID: 7605676 DOI: 10.1266/jjg.70.273] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tef-1 gene encoding translation elongation factor 1 alpha was cloned from the ascomycete fungus Neurospora crassa. The sequences of genomic DNA and cDNA clones showed that the tef-1 gene contained one ORF of 1380 bp length that is interrupted by three short introns. The deduced polypeptide contained 460 amino acid residues, and the sequence had a high similarity with those of EF-1 alpha polypeptides from other species. The level of tef-1 mRNA was low in conidia but high in growing cells. When mycelia were transferred to poor nutrient media, the level of tef-1 gene mRNA decreased remarkably. The pattern of tef-1 expression was similar to the expression of genes for ribosomal proteins. The tef-1 gene was mapped between arg-3 and leu-4 loci on linkage group I by restriction fragment length polymorphism mapping. Southern blot analysis showed that Neurospora genomic DNA contained only one copy of the tef-1 gene in a genome.
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Affiliation(s)
- A Ichi-ishi
- Department of Regulation Biology, Faculty of Science, Saitama University, Urawa, Japan
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Bäuerle A, Mutzel R. Nucleotide sequence of the gene for ribosomal protein S17 from Dictyostelium discoideum. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1260:223-6. [PMID: 7841201 DOI: 10.1016/0167-4781(94)00218-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The nucleotide sequence of the gene for the Dictyostelium homologue of eukaryotic ribosomal protein S17 has been assembled from cDNA and genomic DNA clones. The predicted primary structure of the S17 protein displays a similar level of sequence identity with its counterparts from higher eukaryotes (53%) as other Dictyostelium ribosomal proteins. Although Dictyostelium genes usually are organized in a rather simple manner, the rps17 gene harbors two introns. One of them, located immediately 3' from the ATG initiator codon, appears to be ubiquitously conserved in eukaryotic rps17 genes.
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Affiliation(s)
- A Bäuerle
- Fakultät für Biologie, Universität Konstanz, Germany
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11
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ICHI-ISHI A, INOUE H. Cloning, nucleotide sequence, and expression of tef-1, the gene encoding translation elongation factor 1α (EF-1α) of Neurospora crassa. Genes Genet Syst 1995. [DOI: 10.1266/ggs.70.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Steiner S, Philippsen P. Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii. MOLECULAR & GENERAL GENETICS : MGG 1994; 242:263-71. [PMID: 8107673 DOI: 10.1007/bf00280415] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ashbya gossypii carries only a single gene (TEF) coding for the abundant translation elongation factor 1 alpha. Cloning and sequencing of this gene and deletion analysis of the promoter region revealed an extremely high degree of similarity with the well studied TEF genes of the yeast Saccharomyces cerevisiae including promoter upstream activation sequence (UAS) elements. The open reading frames in both species are 458 codons long and show 88.6% identity at the DNA level and 93.7% identity at the protein level. A short DNA segment in the promoter, between nucleotides -268 and -213 upstream of the ATG start codon, is essential for high-level expression of the A. gossypii TEF gene. It carries two sequences, GCCCATACAT and ATCCATACAT, with high homology to the UASrpg sequence of S. cerevisiae, which is an essential promoter element in genes coding for highly expressed components of the translational apparatus. UASrpg sequences are binding sites for the S. cerevisiae protein TUF, also called RAP1 or GRF1. In gel retardation with A. gossypii protein extracts we demonstrated specific protein binding to the short TEF promoter segment carrying the UASrpg homologous sequences.
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Affiliation(s)
- S Steiner
- Institut für Mikrobiologie und Molekularbiologie, Universität Giessen, Germany
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Chow CM, RajBhandary UL. Developmental regulation of the gene for formate dehydrogenase in Neurospora crassa. J Bacteriol 1993; 175:3703-9. [PMID: 8509325 PMCID: PMC204785 DOI: 10.1128/jb.175.12.3703-3709.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have isolated and characterized a gene, fdh, from Neurospora crassa which is developmentally regulated and which produces formate dehydrogenase activity when expressed in Escherichia coli. The gene is closely linked (less than 0.6 kb apart) to the leu-5 gene encoding mitochondrial leucyl-tRNA synthetase; the two genes are transcribed convergently from opposite strands. The expression patterns of these genes differ: fdh mRNA is found only during conidiation and early germination and is not detectable during mycelial growth, while leu-5 mRNA appears during germination and mycelial growth. The structure of the fdh gene was determined from the sequence of cDNA and genomic DNA clones and from mRNA mapping studies. The gene encodes a 375-amino-acid-long protein with sequence similarity to NAD-dependent dehydrogenases of the E. coli 3-phosphoglycerate dehydrogenase (serA gene product) subfamily. In particular, there is striking sequence similarity (52% identity) to formate dehydrogenase from Pseudomonas sp. strain 101. All of the residues thought to interact with NAD in the crystal structure of the Pseudomonas enzyme are conserved in the N. crassa enzyme. We have further shown that expression of the N. crassa gene in E. coli leads to the production of formate dehydrogenase activity, indicating that the N. crassa gene specifies a functional polypeptide.
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Affiliation(s)
- C M Chow
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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Wang Z, Tarawneh KA, Free SJ. Isolation, sequencing, and characterization of crp-5, a gene encoding a Neurospora ribosomal protein. Curr Genet 1993; 23:330-3. [PMID: 8467530 DOI: 10.1007/bf00310894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A Neurospora crassa cytoplasmic ribosomal protein gene, crp-5, has been isolated and characterized. The cDNA was isolated by a differential screening of a cDNA library for glucose-inducible genes. The cDNA was subsequently used to identify and isolate crp-5 genomic sequences. Computer analysis of the DNA sequences showed that they contain an open reading frame which encodes a protein homologous to the rat ribosomal protein S26. The crp-5 mRNA levels are regulated in a carbon-source-dependent manner. The organization of the gene and the region upstream of the coding sequences are discussed.
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Affiliation(s)
- Z Wang
- Department of Biological Sciences, State University of New York, Buffalo 14260
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