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Genomic Sequencing To Identify Potential Causative Mutation(s) of Neurospora crassa
col-4. Microbiol Resour Announc 2020; 9:9/2/e01009-19. [PMID: 31919156 PMCID: PMC6952642 DOI: 10.1128/mra.01009-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In many cases, genes for commonly used genetic markers in model organisms have not been identified; therefore, it is of interest to identify the causative genes. Whole-genome sequencing was used to identify potential causative mutations for a col-4 allele of Neurospora crassa. In many cases, genes for commonly used genetic markers in model organisms have not been identified; therefore, it is of interest to identify the causative genes. Whole-genome sequencing was used to identify potential causative mutations for a col-4 allele of Neurospora crassa.
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Zhang Y, Sachs MS. Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3'UTR Introns. Genetics 2015; 200:1133-48. [PMID: 26048019 PMCID: PMC4574236 DOI: 10.1534/genetics.115.176743] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/01/2015] [Indexed: 02/01/2023] Open
Abstract
In higher eukaryotes the accelerated degradation of mRNAs harboring premature termination codons is controlled by nonsense-mediated mRNA decay (NMD), exon junction complex (EJC), and nuclear cap-binding complex (CBC) factors, but the mechanistic basis for this quality-control system and the specific roles of the individual factors remain unclear. Using Neurospora crassa as a model system, we analyzed the mechanisms by which NMD is induced by spliced 3'-UTR introns or upstream open reading frames and observed that the former requires NMD, EJC, and CBC factors whereas the latter requires only the NMD factors. The transcripts for EJC components eIF4A3 and Y14, and translation termination factor eRF1, contain spliced 3'-UTR introns and each was stabilized in NMD, EJC, and CBC mutants. Reporter mRNAs containing spliced 3'-UTR introns, but not matched intronless controls, were stabilized in these mutants and were enriched in mRNPs immunopurified from wild-type cells with antibody directed against human Y14, demonstrating a direct role for spliced 3'-UTR introns in triggering EJC-mediated NMD. These results demonstrate conclusively that NMD, EJC, and CBC factors have essential roles in controlling mRNA stability and that, based on differential requirements for these factors, there are branched mechanisms for NMD. They demonstrate for the first time autoregulatory control of expression at the level of mRNA stability through the EJC/CBC branch of NMD for EJC core components, eIF4A3 and Y14, and for eRF1, which recognizes termination codons. Finally, these results show that EJC-mediated NMD occurs in fungi and thus is an evolutionarily conserved quality-control mechanism.
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Affiliation(s)
- Ying Zhang
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
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High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces. Genetics 2014; 198:859-66. [PMID: 25209147 DOI: 10.1534/genetics.114.170118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Current genome editing techniques available for Saccharomyces yeast species rely on auxotrophic markers, limiting their use in wild and industrial strains and species. Taking advantage of the ancient loss of thymidine kinase in the fungal kingdom, we have developed the herpes simplex virus thymidine kinase gene as a selectable and counterselectable marker that forms the core of novel genome engineering tools called the H: aploid E: ngineering and R: eplacement P: rotocol (HERP) cassettes. Here we show that these cassettes allow a researcher to rapidly generate heterogeneous populations of cells with thousands of independent chromosomal allele replacements using mixed PCR products. We further show that the high efficiency of this approach enables the simultaneous replacement of both alleles in diploid cells. Using these new techniques, many of the most powerful yeast genetic manipulation strategies are now available in wild, industrial, and other prototrophic strains from across the diverse Saccharomyces genus.
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Wang NY, Yang SL, Lin CH, Chung KR. Gene inactivation in the citrus pathogenic fungus Alternaria alternata defect at the Ku70 locus associated with non-homologous end joining. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0640-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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QIP, a component of the vegetative RNA silencing pathway, is essential for meiosis and suppresses meiotic silencing in Neurospora crassa. Genetics 2010; 186:127-33. [PMID: 20592262 DOI: 10.1534/genetics.110.118422] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among the processes that play essential roles in both genome defense and organism survival are those involved in chromosome comparison. They are acutely active in the meiotic cells of Neurospora crassa, where they evaluate the mutual identity of homologs by a process we call trans-sensing. When nonsymmetrical regions are found, they are silenced. The known molecular components of this meiotic silencing machinery are related to RNA-dependent RNA polymerases, Argonautes and Dicers, suggesting that the mechanisms of how heterologous chromosomal regions are silenced involves, at some stage, the production of small interfering RNAs. Neurospora has two active and clearly distinct RNA interference pathways: quelling (vegetative specific) and meiotic silencing (meiosis specific). Both pathways require a common set of protein types like RNA-dependent RNA polymerases, Argonautes and Dicers. In this work we demonstrate the involvement of quelling defective-2 interacting protein (qip(+)), a Neurospora gene whose function is essential to silencing by quelling, in meiotic silencing, and normal sexual development. Our observations reinforce the molecular connection between these two silencing pathways.
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Lee MH, Chiu CM, Roubtsova T, Chou CM, Bostock RM. Overexpression of a redox-regulated cutinase gene, MfCUT1, increases virulence of the brown rot pathogen Monilinia fructicola on Prunus spp. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:176-86. [PMID: 20064061 DOI: 10.1094/mpmi-23-2-0176] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A 4.5-kb genomic DNA containing a Monilinia fructicola cutinase gene, MfCUT1, and its flanking regions were isolated and characterized. Sequence analysis revealed that the genomic MfCUT1 carries a 63-bp intron and a promoter region with several transcription factor binding sites that may confer redox regulation of MfCUT1 expression. Redox regulation is indicated by the effect of antioxidants, shown previously to inhibit MfCUT1 gene expression in cutin-induced cultures, and in the present study, where H(2)O(2) enhanced MfCUT1 gene expression. A beta-glucuronidase (GUS) reporter gene (gusA) was fused to MfCUT1 under the control of the MfCUT1 promoter, and this construct was then used to generate an MfCUT1-GUS strain by Agrobacterium spp.-mediated transformation. The appearance of GUS activity in response to cutin and suppression of GUS activity by glucose in cutinase-inducing medium verified that the MfCUT1-GUS fusion protein was expressed correctly under the control of the MfCUT1 promoter. MfCUT1-GUS expression was detected following inoculation of peach and apple fruit, peach flower petals, and onion epidermis, and during brown rot symptom development on nectarine fruit at a relatively late stage of infection (24 h postinoculation). However, semiquantitative reverse-transcriptase polymerase chain reaction provided sensitive detection of MfCUT1 expression within 5 h of inoculation in both almond and peach petals. MfCUT1-GUS transformants expressed MfCUT1 transcripts at twice the level as the wild type and caused more severe symptoms on Prunus flower petals, consistent with MfCUT1 contributing to the virulence of M. fructicola.
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Affiliation(s)
- Miin-Huey Lee
- Department of Plant Pathology, University of California, One Shields Ave., Davis 95616, USA
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Circadian rhythms in Neurospora crassa: dynamics of the clock component frequency visualized using a fluorescent reporter. Fungal Genet Biol 2010; 47:332-41. [PMID: 20051268 DOI: 10.1016/j.fgb.2009.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 12/13/2009] [Accepted: 12/30/2009] [Indexed: 11/29/2022]
Abstract
The frequency (frq) gene of Neurospora crassa has long been considered essential to the function of this organism's circadian rhythm. Increasingly, deciphering the coupling of core oscillator genes such as frq to the output pathways of the circadian rhythm has become a major focus of circadian research. To address this coupling it is critical to have a reporter of circadian activity that can deliver high resolution spatial and temporal information about the dynamics of core oscillatory proteins such as FRQ. However, due to the difficulty of studying the expression of circadian rhythm genes in aerobic N. crassa cultures, little is known about the dynamics of this gene under physiologically realistic conditions. To address these issues we report a fluorescent fusion to the frq gene using a codon optimized version of the mCherry gene. To trace the expression and accumulation of FRQ-mCherryNC (FRQ-mCh) during the circadian rhythm, growing vegetative hyphae were scanned every hour under confocal microscopy (100x). Fluorescence of FRQ-mCh was detected only at the growing edge of the colony, and located in the cytoplasm and nuclei of vegetative hyphae for a distance of approximately 150-200microm from the apices of leading hyphae. When driven by the frq promoter, apparently there was also a second FRQ entrance into the nucleus during the circadian cycle; however the second entrance had a lower accumulation level than the first entrance. Thus this fluorescent fusion protein has proven useful in tracking the spatial dynamics of the frq protein and has indicated that the dynamics of the FRQ protein's nuclear trafficking may be more complex than previously realized.
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You BJ, Lee MH, Chung KR. Gene-specific disruption in the filamentous fungus Cercospora nicotianae using a split-marker approach. Arch Microbiol 2009; 191:615-22. [PMID: 19506835 DOI: 10.1007/s00203-009-0489-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 04/22/2009] [Accepted: 05/25/2009] [Indexed: 12/24/2022]
Abstract
To determine if DNA configuration, gene locus, and flanking sequences will affect homologous recombination in the phytopathogenic fungus Cercospora nicotianae, we evaluated and compared disruption efficiency targeting four cercosporin toxin biosynthetic genes encoding a polyketide synthase (CTB1), a monooxygenase/O-methyltransferase (CTB3), a NADPH-dependent oxidoreductase (CTB5), and a FAD/FMN-dependent oxidoreductase (CTB7). Transformation of C. nicotianae using a circular plasmid resulted in low disruption frequency. The use of endonucleases or a selectable marker DNA fragment flanked by homologous sequence either at one end or at both ends in the transformation procedures, increased disruption efficiency in some but not all CTB genes. A split-marker approach, using two DNA fragments overlapping within the selectable marker, increased the frequency of targeted gene disruption and homologous integration as high as 50%, depending on the target gene and on the length of homologous DNA sequence flanking the selectable marker. The results indicate that the split-marker approach favorably decreased ectopic integration and thus, greatly facilitated targeted gene disruption in this important fungal pathogen.
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Affiliation(s)
- Bang-Jau You
- School of Chinese Medicine Resources, College of Pharmacy, China Medical University, 91 Hsueh-Shih Road, Taichung 404, Taiwan
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Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics 2009; 182:11-23. [PMID: 19171944 DOI: 10.1534/genetics.108.098707] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The completion of genome-sequencing projects for a number of fungi set the stage for detailed investigations of proteins. We report the generation of versatile expression vectors for detection and isolation of proteins and protein complexes in the filamentous fungus Neurospora crassa. The vectors, which can be adapted for other fungi, contain C- or N-terminal FLAG, HA, Myc, GFP, or HAT-FLAG epitope tags with a flexible poly-glycine linker and include sequences for targeting to the his-3 locus in Neurospora. To introduce mutations at native loci, we also made a series of knock-in vectors containing epitope tags followed by the selectable marker hph (resulting in hygromycin resistance) flanked by two loxP sites. We adapted the Cre/loxP system for Neurospora, allowing the selectable marker hph to be excised by introduction of Cre recombinase into a strain containing a knock-in cassette. Additionally, a protein purification method was developed on the basis of the HAT-FLAG tandem affinity tag system, which was used to purify HETEROCHROMATIN PROTEIN 1 (HP1) and associated proteins from Neurospora. As expected on the basis of yeast two-hybrid and co-immunoprecipitation (Co-IP) experiments, the Neurospora DNA methyltransferase DIM-2 was found in a complex with HP1. Features of the new vectors allowed for verification of an interaction between HP1 and DIM-2 in vivo by Co-IP assays on proteins expressed either from their native loci or from the his-3 locus.
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Lee DW, Freitag M, Selker EU, Aramayo R. A cytosine methyltransferase homologue is essential for sexual development in Aspergillus nidulans. PLoS One 2008; 3:e2531. [PMID: 18575630 PMCID: PMC2432034 DOI: 10.1371/journal.pone.0002531] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 05/08/2008] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genome defense processes RIP (repeat-induced point mutation) in the filamentous fungus Neurospora crassa, and MIP (methylation induced premeiotically) in the fungus Ascobolus immersus depend on proteins with DNA methyltransferase (DMT) domains. Nevertheless, these proteins, RID and Masc1, respectively, have not been demonstrated to have DMT activity. We discovered a close homologue in Aspergillus nidulans, a fungus thought to have no methylation and no genome defense system comparable to RIP or MIP. PRINCIPAL FINDINGS We report the cloning and characterization of the DNA methyltransferase homologue A (dmtA) gene from Aspergillus nidulans. We found that the dmtA locus encodes both a sense (dmtA) and an anti-sense transcript (tmdA). Both transcripts are expressed in vegetative, conidial and sexual tissues. We determined that dmtA, but not tmdA, is required for early sexual development and formation of viable ascospores. We also tested if DNA methylation accumulated in any of the dmtA/tmdA mutants we constructed, and found that in both asexual and sexual tissues, these mutants, just like wild-type strains, appear devoid of DNA methylation. CONCLUSIONS/SIGNIFICANCE Our results demonstrate that a DMT homologue closely related to proteins implicated in RIP and MIP has an essential developmental function in a fungus that appears to lack both DNA methylation and RIP or MIP. It remains formally possible that DmtA is a bona fide DMT, responsible for trace, undetected DNA methylation that is restricted to a few cells or transient but our work supports the idea that the DMT domain present in the RID/Masc1/DmtA family has a previously undescribed function.
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Affiliation(s)
- Dong W. Lee
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, United States of America
| | - Michael Freitag
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Eric U. Selker
- Department of Biology, Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Rodolfo Aramayo
- Department of Biology, College of Science, Texas A&M University, College Station, Texas, United States of America
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NADPH oxidases NOX-1 and NOX-2 require the regulatory subunit NOR-1 to control cell differentiation and growth in Neurospora crassa. EUKARYOTIC CELL 2008; 7:1352-61. [PMID: 18567788 DOI: 10.1128/ec.00137-08] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have proposed that reactive oxygen species (ROS) play essential roles in cell differentiation. Enzymes belonging to the NADPH oxidase (NOX) family produce superoxide in a regulated manner. We have identified three distinct NOX subfamilies in the fungal kingdom and have shown that NoxA is required for sexual cell differentiation in Aspergillus nidulans. Here we show that Neurospora crassa NOX-1 elimination results in complete female sterility, decreased asexual development, and reduction of hyphal growth. The lack of NOX-2 did not affect any of these processes but led instead to the production of sexual spores that failed to germinate, even in the presence of exogenous oxidants. The elimination of NOR-1, an ortholog of the mammalian Nox2 regulatory subunit gp67(phox), also caused female sterility, the production of unviable sexual spores, and a decrease in asexual development and hyphal growth. These results indicate that NOR-1 is required for NOX-1 and NOX-2 functions at different developmental stages and establish a link between NOX-generated ROS and the regulation of growth. Indeed, NOX-1 was required for the increased asexual sporulation previously observed in mutants without catalase CAT-3. We also analyzed the function of the penta-EF calcium-binding domain protein PEF-1 in N. crassa. Deletion of pef-1 resulted in increased conidiation but, in contrast to what occurs in Dictyostelium discoideum, the mutation of this peflin did not suppress the phenotypes caused by the lack of NOX-1. Our results support the role of ROS as critical cell differentiation signals and highlight a novel role for ROS in regulation of fungal growth.
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Lee MH, Bostock RM. Agrobacterium T-DNA-mediated integration and gene replacement in the brown rot pathogen Monilinia fructicola. Curr Genet 2006; 49:309-22. [PMID: 16468040 DOI: 10.1007/s00294-006-0059-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 12/21/2005] [Accepted: 12/22/2005] [Indexed: 10/25/2022]
Abstract
A transformation system utilizing Agrobacterium tumefaciens was developed for targeted gene disruption in Monilinia fructicola, a fungal pathogen that causes brown rot disease of stone fruits. Transformation with a vector containing the neomycin phosphotransferase II (nptII) cassette flanked with 4 kb cutinase gene (Mfcut1) flanking sequences resulted in an average of 13 transformants per 10(5) spores. When assayed by PCR and DNA blot analyses, more than 50% of the transformants recovered had integrated in the targeted Mfcut1 locus. Both target-gene-specific and non-specific integrations carried direct (head-to-tail) repeat T-DNA integrations. Sequence analysis of these T-DNA integrations revealed that 26 bp of the T-DNA right border were missing at the junctions between direct repeats in all cases. The recombination event during non-specific T-DNA integration in this fungus was unlike that reported in Agrobacterium-mediated transformation in plants.
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Affiliation(s)
- Miin-Huey Lee
- Department of Plant Pathology, University of California, One Shields Ave, Davis, CA 95616, USA
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Krappmann S, Bayram O, Braus GH. Deletion and allelic exchange of the Aspergillus fumigatus veA locus via a novel recyclable marker module. EUKARYOTIC CELL 2005; 4:1298-307. [PMID: 16002655 PMCID: PMC1168958 DOI: 10.1128/ec.4.7.1298-1307.2005] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/26/2005] [Indexed: 11/20/2022]
Abstract
Detailed evaluation of gene functions in an asexual fungus requires advanced methods of molecular biology. For the generation of targeted gene deletions in the opportunistic pathogen Aspergillus fumigatus we designed a novel blaster module allowing dominant selection of transformants due to resistance to phleomycin as well as dominant (counter)selection of a Cre recombinase-mediated marker excision event. For validation purposes we have deleted the A. fumigatus pabaA gene in a wild-type isolate by making use of this cassette. The resulting pabaA::loxP strain served as the recipient for subsequent targeting of the velvet locus. Homologous reconstitution of the deleted gene was performed by an allele whose expression is driven in a nitrogen source-dependent manner, as validated by Northern analyses. Overexpression of the veA locus in A. fumigatus does not result in any obvious phenotype, whereas the sporulation capacities of the veA null mutant are reduced on nitrate-containing medium, a phenotype that is completely restored in the reconstituted strain.
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Affiliation(s)
- Sven Krappmann
- Institute of Microbiology and Genetics, Department of Molecular Microbiology and Genetics, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Khang CH, Park SY, Lee YH, Kang S. A dual selection based, targeted gene replacement tool for Magnaporthe grisea and Fusarium oxysporum. Fungal Genet Biol 2005; 42:483-92. [PMID: 15893252 DOI: 10.1016/j.fgb.2005.03.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2004] [Revised: 01/10/2005] [Accepted: 03/13/2005] [Indexed: 11/26/2022]
Abstract
Rapid progress in fungal genome sequencing presents many new opportunities for functional genomic analysis of fungal biology through the systematic mutagenesis of the genes identified through sequencing. However, the lack of efficient tools for targeted gene replacement is a limiting factor for fungal functional genomics, as it often necessitates the screening of a large number of transformants to identify the desired mutant. We developed an efficient method of gene replacement and evaluated factors affecting the efficiency of this method using two plant pathogenic fungi, Magnaporthe grisea and Fusarium oxysporum. This method is based on Agrobacterium tumefaciens-mediated transformation with a mutant allele of the target gene flanked by the herpes simplex virus thymidine kinase (HSVtk) gene as a conditional negative selection marker against ectopic transformants. The HSVtk gene product converts 5-fluoro-2'-deoxyuridine to a compound toxic to diverse fungi. Because ectopic transformants express HSVtk, while gene replacement mutants lack HSVtk, growing transformants on a medium amended with 5-fluoro-2'-deoxyuridine facilitates the identification of targeted mutants by counter-selecting against ectopic transformants. In addition to M. grisea and F. oxysporum, the method and associated vectors are likely to be applicable to manipulating genes in a broad spectrum of fungi, thus potentially serving as an efficient, universal functional genomic tool for harnessing the growing body of fungal genome sequence data to study fungal biology.
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Affiliation(s)
- Chang Hyun Khang
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
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Lee DW, Seong KY, Pratt RJ, Baker K, Aramayo R. Properties of unpaired DNA required for efficient silencing in Neurospora crassa. Genetics 2005; 167:131-50. [PMID: 15166142 PMCID: PMC1470857 DOI: 10.1534/genetics.167.1.131] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The presence of unpaired copies of a gene during meiosis triggers silencing of all copies of the gene in the diploid ascus cell of Neurospora. This phenomenon is called meiotic silencing and on the basis of genetic studies appears to be a post-transcriptional gene silencing (PTGS) mechanism. Previously, meiotic silencing was defined to be induced by the presence of a DNA region lacking an identical segment in the homologous chromosome. However, the determinants of unpaired DNA remained a mystery. Using the Ascospore maturation-1 (Asm-1) gene, we defined what needs to be "unpaired" to silence a gene. For efficient silencing, an unpaired region of DNA needs to be of a sufficient size and contain homology to the reporter transcript. The greater the size of the loop and the larger the homology to the reporter transcript, the better the resulting meiotic silencing is. Conversely, regions not containing homology to the transcript, e.g., intergenic regions, did not silence the reporter. Surprisingly, unpaired fragments lacking a canonical promoter silenced the reporter. Additionally, we detected the unpairing-dependent loss of a transcript during meiotic silencing. Our observations further support a PTGS mechanism for meiotic silencing and offer insight into the evolutionary consequences resulting from this novel meiotic checkpoint.
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Affiliation(s)
- Dong W Lee
- Department of Biology, College of Science, Texas A&M University, College Station, Texas 77843-3258, USA
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Veneault-Fourrey C, Talbot NJ. Moving Toward a Systems Biology Approach to the Study of Fungal Pathogenesis in the Rice Blast Fungus Magnaporthe grisea. ADVANCES IN APPLIED MICROBIOLOGY 2005; 57:177-215. [PMID: 16002013 DOI: 10.1016/s0065-2164(05)57006-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Claire Veneault-Fourrey
- School of Biological Sciences, Washington Singer Laboratories, University of Exeter, Exeter EX4 4QG, United Kingdom
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Pratt RJ, Lee DW, Aramayo R. DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora. Genetics 2004; 168:1925-35. [PMID: 15611165 PMCID: PMC1448707 DOI: 10.1534/genetics.104.031526] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2004] [Accepted: 08/18/2004] [Indexed: 11/18/2022] Open
Abstract
During the early stages of meiosis in Neurospora, the symmetry of homologous chromosomal regions is carefully evaluated by actively trans-sensing their identity. If a DNA region cannot be detected on the opposite homologous chromosome, then this lack of "sensing" activates meiotic silencing, a post-transcriptional gene silencing-like mechanism that silences all genes in the genome with homology to the loop of unpaired DNA, whether they are paired or unpaired. In this work, we genetically dissected the meiotic trans-sensing step from meiotic silencing by demonstrating that DNA methylation affects sensing without interfering with silencing. We also determined that DNA sequence is an important parameter considered during meiotic trans-sensing. Altogether, these observations assign a previously undescribed role for DNA methylation in meiosis and, on the basis of studies in other systems, we speculate the existence of an intimate connection among meiotic trans-sensing, meiotic silencing, and meiotic recombination.
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Affiliation(s)
- Robert J Pratt
- Department of Biology, College of Science, Texas A&M University, College Station, Texas 77843-3258, USA
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Abstract
Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions.
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Affiliation(s)
- Charles Brenner
- Department of Genetics and the Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH 03756, USA.
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Gardiner DM, Howlett BJ. Negative selection using thymidine kinase increases the efficiency of recovery of transformants with targeted genes in the filamentous fungus Leptosphaeria maculans. Curr Genet 2004; 45:249-55. [PMID: 14749893 DOI: 10.1007/s00294-004-0488-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Revised: 12/09/2003] [Accepted: 01/05/2004] [Indexed: 11/27/2022]
Abstract
A vector system was constructed that is designed to decrease the number of transformants required to be screened when looking for gene disruption events in filamentous fungi. This vector was used to mutate two genes, an ATP-binding cassette transporter ( LmABCt4) and a two-component histidine kinase gene ( LmHK1) in the ascomycete Leptosphaeria maculans. The system uses the thymidine kinase gene from the herpes simplex virus as a negative selectable marker. Thymidine kinase expression is regulated by the TrpC regulatory elements from Aspergillus nidulans and should be applicable to other ascomycetous fungi. When thymidine kinase is expressed in the presence of particular thymidine analogues, these analogues are converted to toxic compounds which kill the cell. We also report the transformation of L. maculans using Agrobacterium tumefaciens-mediated DNA delivery.
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Affiliation(s)
- Donald M Gardiner
- School of Botany, The University of Melbourne, 3010, Melbourne, Victoria, Australia.
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Elliott CE, Howlett BJ. Approaches for identification of fungal genes essential for plant disease. GENETIC ENGINEERING 2004; 26:85-103. [PMID: 15387294 DOI: 10.1007/978-0-306-48573-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
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Kutil BL, Seong KY, Aramayo R. Unpaired genes do not silence their paired neighbors. Curr Genet 2003; 43:425-32. [PMID: 12802506 DOI: 10.1007/s00294-003-0412-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2002] [Revised: 04/23/2003] [Accepted: 05/08/2003] [Indexed: 11/25/2022]
Abstract
During meiotic chromosome pairing, a loop of unpaired DNA induces the silencing of all paired and unpaired homologous DNA via meiotic silencing, an RNA-mediated post-transcriptional gene-silencing mechanism. To test the effect of unpaired DNA on adjacent genes, we constructed strains containing the DNA of a transformation marker integrated immediately downstream of the Ascospore maturation-1 ( Asm-1) gene and tested whether this unpaired DNA silences asm-1(+). We conclude that unpaired downstream DNA has no effect on Asm-1 expression during meiosis or ascospore development, which suggests that the silencing signal produced by unpaired DNA does not propagate onto adjacent paired regions.
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Affiliation(s)
- Brandi L Kutil
- Department of Plant Pathology and Microbiology, College of Agriculture, Texas A&M University, Room 206, Peterson Building, TX 77843-2132, College Station, USA
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Lee DW, Haag JR, Aramayo R. Construction of strains for rapid homokaryon purification after integration of constructs at the histidine-3 ( his-3) locus of Neurospora crassa. Curr Genet 2003; 43:17-23. [PMID: 12684841 DOI: 10.1007/s00294-002-0366-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2002] [Revised: 11/25/2002] [Accepted: 12/12/2002] [Indexed: 11/30/2022]
Abstract
We report the construction of histidine-3 (his-3) strains of Neurospora crassa containing the hygromycin B phosphotransferase gene of Escherichia coli (hph(+)) fused in-frame to the herpes simplex virus thymidine kinase gene (tk(+); Lupton et al. 1991), integrated at the his-3 locus. We also report the construction of two ampicillin-resistant and two kanamycin-resistant his-3 gene-replacement vector plasmids. The combined use of these strains and plasmids for his-3-targeted gene integration allows for the rapid identification of homokaryotic transformants containing the expected gene replacement event.
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Affiliation(s)
- Dong W Lee
- Department of Biology, College of Science, Texas A&M University, Room 415, Building BSBW, College Station, TX 77843-3258, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003; 4:277-84. [PMID: 18629117 PMCID: PMC2447404 DOI: 10.1002/cfg.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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