Fungal Genetics Reports最新文献

{"title":"Fungal endophyte misidentified as Neurospora crassa.","authors":"S. Riyaz-Ul-Hassan, S. Rehman, A. S. Shawl, G. N. Qazi, J. Taylor","doi":"10.4148/1941-4765.1075","DOIUrl":"https://doi.org/10.4148/1941-4765.1075","url":null,"abstract":"The endophytic fungus isolate, ZP5SE, recently described in Rehman et al. 2008 was misidentified identified as Neurospora crassa. The 28S ribosomal gene sequence of the isolate shows 100% sequence similarity with GenBank accession Neurospora crassa M38154. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This regular paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol56/iss1/2 Number 56, 2009 5 Fungal endophyte misidentified as Neurospora crassa. S. Riyaz-Ul-Hassan, S. Rehman, A. S. Shawl, G. N. Qazi, and J. Taylor. Biotechnology Division , Indian Institute of Integrative Medicine, Canal Road, Jammu, INDIA 180001. Indian Institute of Integrative Medicine (Branch Srinagar), Sanatnagar, Srinagar, INDIA 190005. Department of Plant and Microbial Biology, University of California, Berkeley, CA USA 94720-3102 *corresponding author: email: jtaylor@berkeley.edu Fungal Genetics Reports 56: 5 The endophytic fungus isolate, ZP5SE, recently described in Rehman et al. 2008 was misidentified identified as Neurospora crassa. The 28S ribosomal gene sequence of the isolate shows 100% sequence similarity with GenBank accession Neurospora crassa M38154. However, there are three additional 28S ribosomal gene sequences deposited in GenBank as N. crassa U40124 (culture NRRL 13141), N. crassa AF286411 (culture MUCL 19026), and N. crassa AY681158.1 (culture ICMP 6360). Phylogenetic analyses shows that these three additional sequences are closest relatives (100% similarity) and that this group is more distantly related to the ZP5SE and N. crassa M38154 sequences (88%-91% similarity). In phylogenetic analysis, the ZP5SE sequence and M38154 form a sister group to many Sordariaceae, including species of Neurospora, Gelasinospora and Sordaria (Figure 1). As a result, ZP5SE cannot yet be assigned to a particular genus or species on the basis of the 28S ribosomal gene sequence. In addition, we infer that the GenBank sequence M38154 must be incorrectly attributed to N. crassa. Figure 1. Phylogenetic analysis comparing the fungal endophyte (ZP5SE) with related fungi using partial SSU and LSU rDNA sequences from Figure 4 of Rehman et al. 2008. N. crassa AY681158 represents three GenBank sequences of N. crassa (AY681158, U40124 and AF286411), and is nestled with Gelasinospora species, as expected. N. crassa M38154 is quite distant from the three other N. crassa sequences and likely is misattributed to N. crassa. References: Rehman, S., Shawl, A.S., Verma, V., Kour, A., Athar, M., Andrabi, R., Sultan, P., and G.N. Qazi. 2008. An endophytic Neurospora sp. from Nothapodytes foetida producing camptothecin. Applied Biochemistry and Microbiology 44:203–209. ( Prikladnaya Biokhimiya i Mikrobiologiya 44:225–231.) Published by New Prairie Press, 2017","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"16 1","pages":"5-5"},"PeriodicalIF":0.0,"publicationDate":"2009-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75449462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2008 Neurospora Bibliography","authors":"Craig Wilson","doi":"10.4148/1941-4765.1093","DOIUrl":"https://doi.org/10.4148/1941-4765.1093","url":null,"abstract":"This bibliography represents my attempt to collect all works dealing substantially with Neurospora. Please let me know of anything published in 2007 or 2008 that is not included here or in the previous bibliography, so that it might be mentioned next year. I would be especially happy to hear of chapters from books, and articles from journals not indexed in major bibliographic services. Please also let me know of any errors in citation. Please send reprints or copies of articles to the Fungal Genetics Stock Center. This bibliography is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol55/iss1/13 2008 Neurospora Bibliography This bibliography represents my attempt to collect all works dealing substantially with Neurospora. Please let me know of anything published in 2007 or 2008 that is not included here or in the previous bibliography, so that it might be mentioned next year. I would be especially happy to hear of chapters from books, and articles from journals not indexed in major bibliographic services. Please also let me know of any errors in citation. Please send reprints or copies of articles to the Fungal Genetics Stock Center. Craig Wilson, 15236 Ashworth Ave. N., Shoreline WA 98133, USA (chwilso@gmail.com) late addition from 2006: Holliday, R., and R. B. Flavell. 2006. John Robert Stanley Fincham: 11 August 1926 9 February 2005. Biogr. Mem. Fellows R. Soc. 52:83-95.","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"24 1","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82038520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recommendations for assigning symbols and names to Neurospora crassa genes now that its genome has been sequenced.","authors":"H. M. Hood, A. Radford, M. Sachs","doi":"10.4148/1941-4765.1087","DOIUrl":"https://doi.org/10.4148/1941-4765.1087","url":null,"abstract":"Originally, Neurospora crassa genes were named for their mutant phenotypes or natural variant properties. Genes are now increasingly named on the basis of cross-species sequence similarity. These names may also be supported by predicted or experimentally identified molecular function. As a consequence, N. crassa gene nomenclature in practice is frequently no longer adequately covered by the established conventions (Perkins et al. 2001). Here we provide additional nomenclature guidelines relevant to these new circumstances, and some general guidelines for providing information on the identity of N. crassa genes in scientific communications. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This regular paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol55/iss1/7 32 Fungal Genetics Reports The Neurospora crassa colonial temperature sensitive 2, 4 and 5 (cot-2, cot-4 and cot-5) genes encode regulatory and structural proteins required for hyphal elongation and branching Zipi Resheat-Eini, Alex Zelter, Rena Gorovits, Nick D. Read and Oded Yarden* Department of Plant Pathology and Microbiology, The Otto Warburg Minerva Center for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, 76100, Israel and Fungal Cell Biology Group, Institute of Cell and Molecular Biology, University of Edinburgh, Rutherford Building, Edinburgh EH9 3JH, UK. *corresponding author, email: Oded.Yarden@huji.ac.il Fungal Genetics Reports 55:32-36 The morphology and the genetic defects of the Neurospora crassa colonial temperature-sensitive-2, -4 and -5 mutants were analyzed. cot-2 is allelic to gs-1 and encodes a component of the glucan synthesis process. cot-4 encodes the catalytic subunit of a type 2B phosphatase and is allelic to calcineurin (cna-1). cot-5 encodes a homologue of the S. cerevisiae ALG2 manosyltransferase-encoding gene, a component of the dolichol pathway. A group of five non-allelic Neurospora crassa colonial temperature sensitive (cot) mutants was described by Garnjobst and Tatum (1967). The cot-1 gene was found to encode a Ser/Thr protein kinase (Yarden et al. 1992) which is the founding member of the NDR kinase family. The nature of the cot-3 defect has also been analyzed and the cot-3 gene was found to encode protein elongation factor 2 (Propheta et al. 2001). In order to expand our understanding of the genetic defects that can confer abnormal hyphal elongation/branching patterns, we have performed morphological and genetic analyses of the three remaining cot mutants isolated by Garnjobst and Tatum. We found that even though they all exhibit compact temperaturesensitive macroscopic colonial features, their microscopic hyphal morphology and branching patterns differ. Furthermore, the genetic defects involved in conferring their phenotypes include both regulatory as well as structural fac","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"1 1","pages":"29-31"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85324085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demonstration that the Neurospora crassa mutation un-4 is a single nucleotide change in the tim16 gene encoding a subunit of the mitochondrial inner membrane translocase","authors":"A. Wiest, M. Plamann, K. McCluskey","doi":"10.4148/1941-4765.1089","DOIUrl":"https://doi.org/10.4148/1941-4765.1089","url":null,"abstract":"The Neurospora crassa temperature sensitive mutation known as un-4 has been shown by a map-based complementation approach to be a single nucleotide change in the open reading frame of the mitochondrial inner membrane translocase subunit tim16 (NCU05515). This regular paper is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol55/iss1/9","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"14 1","pages":"37-39"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87202880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visualization of peroxisomes via SKL-tagged DsRed protein in Sordaria macrospora","authors":"Skander Elleuche, S. Pöggeler","doi":"10.4148/1941-4765.1083","DOIUrl":"https://doi.org/10.4148/1941-4765.1083","url":null,"abstract":"We report the utilization of Discosoma sp. red fluorescent protein DsRed to visualize peroxisomes in the filamentous ascomycete Sordaria macrospora. To achieve labeling of peroxisomes, DsRed was fused to a serine-lysine-leucine tag (SKL). Expression of the DsRed-SKL fusion gene under the control of the Aspergillus nidulans gpd-promoter led to protein import of DsRed into peroxisomes. In this study, we describe our results concerning the construction as well as the application of vector pDsRed-SKL.","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"30 1","pages":"9-12"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82590543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disruption of a Yeast ADE6 Gene Homolog in Ustilago maydis","authors":"M. Heidenreich, A. Budde, An Zhiqiang, S. Leong","doi":"10.4148/1941-4765.1090","DOIUrl":"https://doi.org/10.4148/1941-4765.1090","url":null,"abstract":"A putative homolog of the Sacharromyces cereviseae ADE6 and Escherichia coli purL genes is identified near a multigenic complex, which contains two genes, sid1 and sid2, involved in a siderophore biosynthetic pathway inUstilago maydis. The putative ADE6 homolog was mutated by targeted gene disruption. The resulting mutant strains demonstrated a requirement for exogenous adenine, indicating that the U. maydis ade6 homolog is required for purine biosynthesis. Authors M. L. Heidenreich, A. D. Budde, An Zhiqiang, and S. A. Leong This regular paper is available in Fungal Genetics Reports: https://newprairiepress.org/fgr/vol55/iss1/10 40 Fungal Genetics Reports Disruption of a Yeast ADE6 Gene Homolog in Ustilago maydis Heidenreich, M. L., Budde, A. D., Zhiqiang, An,and Leong, S. A. Department of Bacteriology, University of Wisconsin, Madison, WI 53706. USDA, ARS CCRU, Madison, WI 53726. Department of Plant Pathology, University of Wisconsin, Madison, WI, 53706 Fungal Genetics Reports 55:40-43 A putative homolog of the Sacharromyces cereviseae ADE6 and Escherichia coli purL genes is identified near a multigenic complex, which contains two genes, sid1 and sid2, involved in a siderophore biosynthetic pathway in Ustilago maydis. The putative ADE6 homolog was mutated by targeted gene disruption. The resulting mutant strains demonstrated a requirement for exogenous adenine, indicating that the U. maydis ade6 homolog is required for purine biosynthesis. Ustilago maydis is the causal agent of corn smut disease. Under conditions of iron stress, this fungus produces cyclic peptides, siderophores, for the purpose of iron acquisition (Leong and Winkelmann, 1998). The limits of this gene cluster were investigated by systematically analyzing the sequence of the flanking DNA. The Ustilago genomic sequence of the region downstream of sid1 sequence showed a predicted 1402 amino acid polypeptide encoding a probable ade6 gene (http://mips.gsf.de/genre/proj/ustilago/singleGeneReport.html?entry=um05162), and having 55.7% similarity to the translated purL gene of E. coliB, and 54.2% similarity with the translated ADE6 gene of Saccharomyces cerevisiae. These genes encode formylglycineamide ribonucleotide synthetase, which catalyzes the fourth step in the purine biosynthetic pathway (Schendel et. al., 1989). Information contained in the S. cerevisiae Genbank sequence submission 557019 indicated that disruption of this gene leads to an adenine-requiring phenotype. To determine whether the predicted ade6 gene is required for purine biosynthesis, the gene was disrupted by insertion of a cassette encoding hygromycin phosphotransferase. Materials and Methods The HindlII-NruI fragment containing the 5’ region of the putative ade6 gene was derived from an 8.2 kb HindIII fragment of pSid1, a cosmid clone that contains a Sau3A partial digest of a region of the genome of Ustilago strain 518 (Wang et. al., 1989), Table 1. The 8.2 kb HindIII fragment was initially cloned into pUC18 follo","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"18 1","pages":"40-43"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88597618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA extraction, probe preparation, and competitive hybridization for transcriptional profiling using Neurospora crassa long-oligomer DNA microarrays","authors":"T. Clark, J. Guilmette, Daniel Renstrom, J. Townsend","doi":"10.4148/1941-4765.1086","DOIUrl":"https://doi.org/10.4148/1941-4765.1086","url":null,"abstract":"We developed protocols optimized for the performance of experiments assaying genomic gene expression using Neurospora crassa long-oligomer microarrays. We present methods for sample growth and harvesting, total RNA extraction, poly(A) mRNA selection, preparation of NH3-Allyl Cy3/Cy5 labeled probes, and microarray hybridization. The quality of the data obtained with these protocols is demonstrated by the comparative transcriptional profiling of basal and apical zones of vegetative growth of N. crassa.","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"12 1","pages":"18-28"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76335636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Neurospora crassa colonial temperature sensitive 2, 4 and 5 (cot-2, cot-4 and cot-5) genes encode regulatory and structural proteins required for hyphal elongation and branching","authors":"Zipi Resheat-Eini, A. Zelter, R. Gorovits, N. Read, O. Yarden","doi":"10.4148/1941-4765.1088","DOIUrl":"https://doi.org/10.4148/1941-4765.1088","url":null,"abstract":"The morphology and the genetic defects of theNeurospora crassa colonial temperature-sensitive-2, -4 and -5 mutants were analyzed. cot-2 is allelic to gs-1 and encodes a component of the glucan synthesis process. cot-4 encodes the catalytic subunit of a type 2B phosphatase and is allelic to calcineurin (cna-1). cot-5 encodes a homologue of the S. cerevisiae ALG2 manosyltransferase-encoding gene, a component of the dolichol pathway. Creative Commons License This work is licensed under a Creative Commons Attribution-Share Alike 4.0 License. This regular paper is available in Fungal Genetics Reports: http://newprairiepress.org/fgr/vol55/iss1/8 32 Fungal Genetics Reports The Neurospora crassa colonial temperature sensitive 2, 4 and 5 (cot-2, cot-4 and cot-5) genes encode regulatory and structural proteins required for hyphal elongation and branching Zipi Resheat-Eini, Alex Zelter, Rena Gorovits, Nick D. Read and Oded Yarden* Department of Plant Pathology and Microbiology, The Otto Warburg Minerva Center for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, 76100, Israel and Fungal Cell Biology Group, Institute of Cell and Molecular Biology, University of Edinburgh, Rutherford Building, Edinburgh EH9 3JH, UK. *corresponding author, email: Oded.Yarden@huji.ac.il Fungal Genetics Reports 55:32-36 The morphology and the genetic defects of the Neurospora crassa colonial temperature-sensitive-2, -4 and -5 mutants were analyzed. cot-2 is allelic to gs-1 and encodes a component of the glucan synthesis process. cot-4 encodes the catalytic subunit of a type 2B phosphatase and is allelic to calcineurin (cna-1). cot-5 encodes a homologue of the S. cerevisiae ALG2 manosyltransferase-encoding gene, a component of the dolichol pathway. A group of five non-allelic Neurospora crassa colonial temperature sensitive (cot) mutants was described by Garnjobst and Tatum (1967). The cot-1 gene was found to encode a Ser/Thr protein kinase (Yarden et al. 1992) which is the founding member of the NDR kinase family. The nature of the cot-3 defect has also been analyzed and the cot-3 gene was found to encode protein elongation factor 2 (Propheta et al. 2001). In order to expand our understanding of the genetic defects that can confer abnormal hyphal elongation/branching patterns, we have performed morphological and genetic analyses of the three remaining cot mutants isolated by Garnjobst and Tatum. We found that even though they all exhibit compact temperaturesensitive macroscopic colonial features, their microscopic hyphal morphology and branching patterns differ. Furthermore, the genetic defects involved in conferring their phenotypes include both regulatory as well as structural factors, all of which are required for maintaining proper hyphal elongation and branching patterns. Confocal microscopic examination, using the membrane-selective dye FM4-64 (as described by Hickey et al. 2005) of Ne","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"1 1","pages":"32-36"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80765050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An improved plasmid for transformation of Neurospora crassa using the pan-2 gene as a selectable marker","authors":"Wilson Low, G. Jedd","doi":"10.4148/1941-4765.1091","DOIUrl":"https://doi.org/10.4148/1941-4765.1091","url":null,"abstract":"","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"136 1","pages":"44-45"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83164923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A quantitative PCR approach to determine gene copy number","authors":"P. Solomon, Simon V. S. Ipcho, James K. Hane, K. Tan, R. Oliver","doi":"10.4148/1941-4765.1082","DOIUrl":"https://doi.org/10.4148/1941-4765.1082","url":null,"abstract":"Here, we report on the use of quantitative PCR (qPCR) to determine gene copy number in filamentous fungi. Using the sequenced dothideomycete Stagonospora nodorum, qPCR was used to unequivocally confirm the presence of single, two and three copy regions as predicted by in silico PCR. Further validation of the technique was demonstrated by verifying the copy numbers of introduced gene cassettes in previously characterised transformants of S. nodorum. Apart from increased sensitivity, this technique offers a high-throughput alternative to Southern blots for determining gene copy number, a","PeriodicalId":12490,"journal":{"name":"Fungal Genetics Reports","volume":"13 1","pages":"5-8"},"PeriodicalIF":0.0,"publicationDate":"2008-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75437340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}