201
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Reveal BS, Paietta JV. Analysis of the sulfur-regulated control of the cystathionine γ-lyase gene of Neurospora crassa. BMC Res Notes 2012; 5:339. [PMID: 22748183 PMCID: PMC3496659 DOI: 10.1186/1756-0500-5-339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 06/05/2012] [Indexed: 02/04/2023] Open
Abstract
Background Cystathionine γ-lyase plays a key role in the transsulfuration pathway through its primary reaction of catalyzing the formation of cysteine from cystathionine. The Neurospora crassa cystathionine γ-lyase gene (cys-16+) is of particular interest in dissecting the regulation and dynamics of transsulfuration. The aim of this study was to determine the regulatory connection of cys-16+ to the Neurospora sulfur regulatory network. In addition, the cys-16+ promoter was characterized with the goal of developing a strongly expressed and regulatable gene expression tool. Findings The cystathionine γ-lyase cys-16+ gene was cloned and characterized. The gene, which contains no introns, encodes a protein of 417 amino acids with conserved pyridoxal 5’-phosphate binding site and substrate-cofactor binding pocket. Northern blot analysis using wild type cells showed that cys-16+ transcript levels increased under sulfur limiting (derepressing) conditions and were present only at a low level under sulfur sufficient (repressing) conditions. In contrast, cys-16+ transcript levels in a Δcys-3 regulatory mutant were present at a low level under either derepressing or repressing conditions. Gel mobility shift analysis demonstrated the presence of four CYS3 transcriptional activator binding sites on the cys-16+ promoter, which were close matches to the CYS3 consensus binding sequence. Conclusions In this work, we confirm the control of cystathionine γ-lyase gene expression by the CYS3 transcriptional activator through the loss of cys-16+ expression in a Δcys-3 mutant and through the in vitro binding of CYS3 to the cys-16+ promoter at four sites. The highly regulated cys-16+ promoter should be a useful tool for gene expression studies in Neurospora
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Affiliation(s)
- Brad S Reveal
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH 45435, USA
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202
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McCluskey K. Variation in mitochondrial genome primary sequence among whole-genome-sequenced strains of Neurospora crassa. IMA Fungus 2012; 3:93-8. [PMID: 23155504 PMCID: PMC3399107 DOI: 10.5598/imafungus.2012.03.01.10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 06/06/2012] [Indexed: 01/19/2023] Open
Abstract
Eighteen classical mutant strains of Neurospora crassa were subject to whole genome sequence analysis and the mitochondrial genome is analyzed. Overall, the mitochondrial genomes of the classical mutant strains are 99.45 to 99.98 % identical to the reference genome. Two-thirds of the SNPs and three-fourths of indels identified in this analysis are shared among more than one strain. Most of the limited variability in mitochondrial genome sequence is neutral with regard to protein structure. Despite the fact that the mitochondrial genome is present in multiple copies per cell, many of the polymorphisms were homozygous within each strain. Conversely, some polymorphisms, especially those associated with large scale rearrangements are only present in a fraction of the reads covering each region. The impact of this variation is unknown and further studies will be necessary to ascertain if this level of polymorphism is common among fungi and whether it reflects the impact of ageing cultures.
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Affiliation(s)
- Kevin McCluskey
- Fungal Genetics Stock Center, University of Missouri-Kansas City, Kansas City, MO 64110, USA; e-mail:
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203
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Hamam A, Lew RR. Electrical phenotypes of calcium transport mutant strains of a filamentous fungus, Neurospora crassa. EUKARYOTIC CELL 2012; 11:694-702. [PMID: 22408225 PMCID: PMC3346425 DOI: 10.1128/ec.05329-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 02/28/2012] [Indexed: 12/27/2022]
Abstract
We characterized the electrical phenotypes of mutants with mutations in genes encoding calcium transporters-a mechanosensitive channel homolog (MscS), a Ca(2+)/H(+) exchange protein (cax), and Ca(2+)-ATPases (nca-1, nca-2, nca-3)-as well as those of double mutants (the nca-2 cax, nca-2 nca-3, and nca-3 cax mutants). The electrical characterization used dual impalements to obtain cable-corrected current-voltage measurements. Only two types of mutants (the MscS mutant; the nca-2 mutant and nca-2-containing double mutants) exhibited lower resting potentials. For the nca-2 mutant, on the basis of unchanged conductance and cyanide-induced depolarization of the potential, the cause is attenuated H(+)-ATPase activity. The growth of the nca-2 mutant-containing strains was inhibited by elevated extracellular Ca(2+) levels, indicative of lesions in Ca(2+) homeostasis. However, the net Ca(2+) effluxes of the nca-2 mutant, measured noninvasively with a self-referencing Ca(2+)-selective microelectrode, were similar to those of the wild type. All of the mutants exhibited osmosensitivity similar to that of the wild type (the turgor of the nca-2 mutant was also similar to that of the wild type), suggesting that Ca(2+) signaling does not play a role in osmoregulation. The hyphal tip morphology and tip-localized mitochondria of the nca-2 mutant were similar to those of the wild type, even when the external [Ca(2+)] was elevated. Thus, although Ca(2+) homeostasis is perturbed in the nca-2 mutant (B. J. Bowman et al., Eukaryot. Cell 10:654-661, 2011), the phenotype does not extend to tip growth or to osmoregulation but is revealed by lower H(+)-ATPase activity.
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Affiliation(s)
- Ahmed Hamam
- Biology Department, York University, Toronto, Ontario, Canada
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204
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Function of Cryptococcus neoformans KAR7 (SEC66) in karyogamy during unisexual and opposite-sex mating. EUKARYOTIC CELL 2012; 11:783-94. [PMID: 22544906 DOI: 10.1128/ec.00066-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The human basidiomycetous fungal pathogen Cryptococcus neoformans serves as a model fungus to study sexual development and produces infectious propagules, basidiospores, via the sexual cycle. Karyogamy is the process of nuclear fusion and an essential step to complete mating. Therefore, regulation of nuclear fusion is central to understanding sexual development of C. neoformans. However, our knowledge of karyogamy genes was limited. In this study, using a BLAST search with the Saccharomyces cerevisiae KAR genes, we identified five C. neoformans karyogamy gene orthologs: CnKAR2, CnKAR3, CnKAR4, CnKAR7 (or CnSEC66), and CnKAR8. There are no apparent orthologs of the S. cerevisiae genes ScKAR1, ScKAR5, and ScKar9 in C. neoformans. Karyogamy involves the congression of two nuclei followed by nuclear membrane fusion, which results in diploidization. ScKar7 (or ScSec66) is known to be involved in nuclear membrane fusion. In C. neoformans, kar7 mutants display significant defects in hyphal growth and basidiospore chain formation during both a-α opposite and α-α unisexual reproduction. Fluorescent nuclear imaging revealed that during kar7 × kar7 bilateral mutant matings, the nuclei congress but fail to fuse in the basidia. These results demonstrate that the KAR7 gene plays an integral role in both opposite-sex and unisexual mating, indicating that proper control of nuclear dynamics is important. CnKAR2 was found to be essential for viability, and its function in mating is not known. No apparent phenotypes were observed during mating of kar3, kar4, or kar8 mutants, suggesting that the role of these genes may be dispensable for C. neoformans mating, which demonstrates a different evolutionary trajectory for the KAR genes in C. neoformans compared to those in S. cerevisiae.
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205
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Heterochromatin protein 1 forms distinct complexes to direct histone deacetylation and DNA methylation. Nat Struct Mol Biol 2012; 19:471-7, S1. [PMID: 22504884 DOI: 10.1038/nsmb.2274] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 03/05/2012] [Indexed: 11/09/2022]
Abstract
DNA methylation, methylation of histone H3 at Lys9 (H3K9me3) and hypoacetylated histones are common molecular features of heterochromatin. Important details of their functions and inter-relationships remain unclear, however. In Neurospora crassa, H3K9me3 directs DNA methylation through a complex containing heterochromatin protein 1 (HP1) and the DNA methyltransferase DIM-2. We identified a distinct HP1 complex, HP1, CDP-2, HDA-1 and CHAP (HCHC), and found that it is responsible for silencing independently of DNA methylation. HCHC defects cause hyperacetylation of centromeric histones, greater accessibility of DIM-2 and hypermethylation of centromeric DNA. Loss of HCHC also causes mislocalization of the DIM-5 H3K9 methyltransferase at a subset of interstitial methylated regions, leading to selective DNA hypomethylation. We demonstrate that HP1 forms distinct DNA methylation and histone deacetylation complexes that work in parallel to assemble silent chromatin in N. crassa.
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206
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Genome-wide analysis of cell wall-related genes in Tuber melanosporum. Curr Genet 2012; 58:165-77. [PMID: 22481122 DOI: 10.1007/s00294-012-0374-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 03/15/2012] [Accepted: 03/20/2012] [Indexed: 10/28/2022]
Abstract
A genome-wide inventory of proteins involved in cell wall synthesis and remodeling has been obtained by taking advantage of the recently released genome sequence of the ectomycorrhizal Tuber melanosporum black truffle. Genes that encode cell wall biosynthetic enzymes, enzymes involved in cell wall polysaccharide synthesis or modification, GPI-anchored proteins and other cell wall proteins were identified in the black truffle genome. As a second step, array data were validated and the symbiotic stage was chosen as the main focus. Quantitative RT-PCR experiments were performed on 29 selected genes to verify their expression during ectomycorrhizal formation. The results confirmed the array data, and this suggests that cell wall-related genes are required for morphogenetic transition from mycelium growth to the ectomycorrhizal branched hyphae. Labeling experiments were also performed on T. melanosporum mycelium and ectomycorrhizae to localize cell wall components.
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207
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208
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Read ND, Goryachev AB, Lichius A. The mechanistic basis of self-fusion between conidial anastomosis tubes during fungal colony initiation. FUNGAL BIOL REV 2012. [DOI: 10.1016/j.fbr.2012.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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209
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Wang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genet Biol 2012; 49:405-13. [PMID: 22469835 DOI: 10.1016/j.fgb.2012.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/09/2012] [Accepted: 03/13/2012] [Indexed: 02/04/2023]
Abstract
Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of Neurospora crassa was induced on two different media, a chemically sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144 h after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi. Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi.
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Affiliation(s)
- Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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210
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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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211
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Jacob-Wilk D, Moretti M, Turina M, Kazmierczak P, Van Alfen NK. Differential expression of the putative Kex2 processed and secreted aspartic proteinase gene family of Cryphonectria parasitica. Fungal Biol 2012; 116:363-78. [DOI: 10.1016/j.funbio.2011.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 01/12/2023]
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212
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Pettersson N, Filipsson C, Becit E, Brive L, Hohmann S. Aquaporins in yeasts and filamentous fungi. Biol Cell 2012; 97:487-500. [PMID: 15966864 DOI: 10.1042/bc20040144] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, genome sequences from different fungi have become available. This information reveals that yeasts and filamentous fungi possess up to five aquaporins. Functional analyses have mainly been performed in budding yeast, Saccharomyces cerevisiae, which has two orthodox aquaporins and two aquaglyceroporins. Whereas Aqy1 is a spore-specific water channel, Aqy2 is only expressed in proliferating cells and controlled by osmotic signals. Fungal aquaglyceroporins often have long, poorly conserved terminal extensions and differ in the otherwise highly conserved NPA motifs, being NPX and NXA respectively. Three subgroups can be distinguished. Fps1-like proteins seem to be restricted to yeasts. Fps1, the osmogated glycerol export channel in S. cerevisiae, plays a central role in osmoregulation and determination of intracellular glycerol levels. Sequences important for gating have been identified within its termini. Another type of aquaglyceroporin, resembling S. cerevisiae Yfl054, has a long N-terminal extension and its physiological role is currently unknown. The third group of aquaglyceroporins, only found in filamentous fungi, have extensions of variable size. Taken together, yeasts and filamentous fungi are a fruitful resource to study the function, evolution, role and regulation of aquaporins, and the possibility to compare orthologous sequences from a large number of different organisms facilitates functional and structural studies.
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Affiliation(s)
- Nina Pettersson
- Department of Cell and Molecular Biology, Göteborg University, Box 462, S-40530 Göteborg, Sweden
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213
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Tisch D, Kubicek CP, Schmoll M. The phosducin-like protein PhLP1 impacts regulation of glycoside hydrolases and light response in Trichoderma reesei. BMC Genomics 2011; 12:613. [PMID: 22182583 PMCID: PMC3267782 DOI: 10.1186/1471-2164-12-613] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/19/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In the biotechnological workhorse Trichoderma reesei (Hypocrea jecorina) transcription of cellulase genes as well as efficiency of the secreted cellulase mixture are modulated by light. Components of the heterotrimeric G-protein pathway interact with light-dependent signals, rendering this pathway a key regulator of cellulase gene expression. RESULTS As regulators of heterotrimeric G-protein signaling, class I phosducin-like proteins, are assumed to act as co-chaperones for G-protein beta-gamma folding and exert their function in response to light in higher eukaryotes. Our results revealed light responsive transcription of the T. reesei class I phosducin-like protein gene phlp1 and indicate a light dependent function of PhLP1 also in fungi. We showed the functions of PhLP1, GNB1 and GNG1 in the same pathway, with one major output being the regulation of transcription of glycoside hydrolase genes including cellulase genes in T. reesei. We found no direct correlation between the growth rate and global regulation of glycoside hydrolases, which suggests that regulation of growth does not occur only at the level of substrate degradation efficiency.Additionally, PhLP1, GNB1 and GNG1 are all important for proper regulation of light responsiveness during long term exposure. In their absence, the amount of light regulated genes increased from 2.7% in wild type to 14% in Δphlp1. Besides from the regulation of degradative enzymes, PhLP1 was also found to impact on the transcription of genes involved in sexual development, which was in accordance with decreased efficiency of fruiting body formation in Δphlp1. The lack of GNB1 drastically diminished ascospore discharge in T. reesei. CONCLUSIONS The heterotrimeric G-protein pathway is crucial for the interconnection of nutrient signaling and light response of T. reesei, with the class I phosducin-like protein PhLP1, GNB1 and GNG1 acting as important nodes, which influence light responsiveness, glycoside hydrolase gene transcription and sexual development.
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Affiliation(s)
- Doris Tisch
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
| | - Christian P Kubicek
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
| | - Monika Schmoll
- Research Area of Gene Technology and Applied Biochemistry, Institute for Chemical Engineering, Vienna University of Technology, Gumpendorferstraße 1a, A-1060 Wien, Austria
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214
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Bardea A, Burshtein N, Rudich Y, Salame T, Ziv C, Yarden O, Naaman R. Sensitive Detection and Identification of DNA and RNA Using a Patterned Capillary Tube. Anal Chem 2011; 83:9418-23. [DOI: 10.1021/ac202480w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amos Bardea
- Department of Chemical Physics, The Weizmann Institute, Rehovot 76100, Israel
| | - Noa Burshtein
- Department of Environmental Sciences, The Weizmann Institute, Rehovot 76100, Israel
| | - Yinon Rudich
- Department of Environmental Sciences, The Weizmann Institute, Rehovot 76100, Israel
| | - Tomer Salame
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Carmit Ziv
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Ron Naaman
- Department of Chemical Physics, The Weizmann Institute, Rehovot 76100, Israel
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215
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Araujo-Palomares CL, Richthammer C, Seiler S, Castro-Longoria E. Functional characterization and cellular dynamics of the CDC-42 - RAC - CDC-24 module in Neurospora crassa. PLoS One 2011; 6:e27148. [PMID: 22087253 PMCID: PMC3210136 DOI: 10.1371/journal.pone.0027148] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022] Open
Abstract
Rho-type GTPases are key regulators that control eukaryotic cell polarity, but their role in fungal morphogenesis is only beginning to emerge. In this study, we investigate the role of the CDC-42 – RAC – CDC-24 module in Neurospora crassa. rac and cdc-42 deletion mutants are viable, but generate highly compact colonies with severe morphological defects. Double mutants carrying conditional and loss of function alleles of rac and cdc-42 are lethal, indicating that both GTPases share at least one common essential function. The defects of the GTPase mutants are phenocopied by deletion and conditional alleles of the guanine exchange factor (GEF) cdc-24, and in vitro GDP-GTP exchange assays identify CDC-24 as specific GEF for both CDC-42 and RAC. In vivo confocal microscopy shows that this module is organized as membrane-associated cap that covers the hyphal apex. However, the specific localization patterns of the three proteins are distinct, indicating different functions of RAC and CDC-42 within the hyphal tip. CDC-42 localized as confined apical membrane-associated crescent, while RAC labeled a membrane-associated ring excluding the region labeled by CDC42. The GEF CDC-24 occupied a strategic position, localizing as broad apical membrane-associated crescent and in the apical cytosol excluding the Spitzenkörper. RAC and CDC-42 also display distinct localization patterns during branch initiation and germ tube formation, with CDC-42 accumulating at the plasma membrane before RAC. Together with the distinct cellular defects of rac and cdc-42 mutants, these localizations suggest that CDC-42 is more important for polarity establishment, while the primary function of RAC may be maintaining polarity. In summary, this study identifies CDC-24 as essential regulator for RAC and CDC-42 that have common and distinct functions during polarity establishment and maintenance of cell polarity in N. crassa.
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Affiliation(s)
- Cynthia L. Araujo-Palomares
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada Baja California, México
| | - Corinna Richthammer
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
| | - Stephan Seiler
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Göttingen, Germany
- * E-mail: (SS); (EC-L)
| | - Ernestina Castro-Longoria
- Department of Microbiology, Center for Scientific Research and Higher Education of Ensenada (CICESE), Ensenada Baja California, México
- * E-mail: (SS); (EC-L)
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216
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The Neurospora crassa DCC-1 protein, a putative histidine kinase, is required for normal sexual and asexual development and carotenogenesis. EUKARYOTIC CELL 2011; 10:1733-9. [PMID: 22058142 DOI: 10.1128/ec.05223-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two-component signaling pathways based on phosphoryl group transfer between histidine kinase and response regulator proteins regulate environmental responses in bacteria, archaea, plants, slime molds, and fungi. Here we characterize a mutant form of DCC-1, a putative histidine kinase encoded by the NCU00939 gene of the filamentous fungus Neurospora crassa. We show that this protein participates in the regulation of processes such as conidiation, perithecial development, and, to a certain degree, carotenogenesis. Furthermore, DCC-1 is suggested to exert its effect by promoting cyclic AMP production, thereby placing this protein within the context of a signaling pathway.
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217
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Berepiki A, Lichius A, Read ND. Actin organization and dynamics in filamentous fungi. Nat Rev Microbiol 2011; 9:876-87. [PMID: 22048737 DOI: 10.1038/nrmicro2666] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Growth and morphogenesis of filamentous fungi is underpinned by dynamic reorganization and polarization of the actin cytoskeleton. Actin has crucial roles in exocytosis, endocytosis, organelle movement and cytokinesis in fungi, and these processes are coupled to the production of distinct higher-order structures (actin patches, cables and rings) that generate forces or serve as tracks for intracellular transport. New approaches for imaging actin in living cells are revealing important similarities and differences in actin architecture and organization within the fungal kingdom, and have yielded key insights into cell polarity, tip growth and long-distance intracellular transport. In this Review, we discuss the contribution that recent live-cell imaging and mutational studies have made to our understanding of the dynamics and regulation of actin in filamentous fungi.
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Affiliation(s)
- Adokiye Berepiki
- Fungal Cell Biology Group, Institute of Cell Biology, Rutherford Building, University of Edinburgh, Edinburgh, UK
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218
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Neurospora crassa Light Signal Transduction Is Affected by ROS. JOURNAL OF SIGNAL TRANSDUCTION 2011; 2012:791963. [PMID: 22046507 PMCID: PMC3199206 DOI: 10.1155/2012/791963] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 06/23/2011] [Indexed: 11/17/2022]
Abstract
In the ascomycete fungus Neurospora crassa blue-violet light controls the expression of genes responsible for differentiation of reproductive structures, synthesis of secondary metabolites, and the circadian oscillator activity. A major photoreceptor in Neurospora cells is WCC, a heterodimeric complex formed by the PAS-domain-containing polypeptides WC-1 and WC-2, the products of genes white collar-1 and white collar-2. The photosignal transduction is started by photochemical activity of an excited FAD molecule noncovalently bound by the LOV domain (a specialized variant of the PAS domain). The presence of zinc fingers (the GATA-recognizing sequences) in both WC-1 and WC-2 proteins suggests that they might function as transcription factors. However, a critical analysis of the phototransduction mechanism considers the existence of residual light responses upon absence of WCC or its homologs in fungi. The data presented
point at endogenous ROS generated by a photon stimulus as an alternative input to pass on light signals to downstream targets.
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Global analysis of serine-threonine protein kinase genes in Neurospora crassa. EUKARYOTIC CELL 2011; 10:1553-64. [PMID: 21965514 DOI: 10.1128/ec.05140-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Serine/threonine (S/T) protein kinases are crucial components of diverse signaling pathways in eukaryotes, including the model filamentous fungus Neurospora crassa. In order to assess the importance of S/T kinases to Neurospora biology, we embarked on a global analysis of 86 S/T kinase genes in Neurospora. We were able to isolate viable mutants for 77 of the 86 kinase genes. Of these, 57% exhibited at least one growth or developmental phenotype, with a relatively large fraction (40%) possessing a defect in more than one trait. S/T kinase knockouts were subjected to chemical screening using a panel of eight chemical treatments, with 25 mutants exhibiting sensitivity or resistance to at least one chemical. This brought the total percentage of S/T mutants with phenotypes in our study to 71%. Mutants lacking apg-1, an S/T kinase required for autophagy in other organisms, possessed the greatest number of phenotypes, with defects in asexual and sexual growth and development and in altered sensitivity to five chemical treatments. We showed that NCU02245/stk-19 is required for chemotropic interactions between female and male cells during mating. Finally, we demonstrated allelism between the S/T kinase gene NCU00406 and velvet (vel), encoding a p21-activated protein kinase (PAK) gene important for asexual and sexual growth and development in Neurospora.
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Zhang J, Yao X, Fischer L, Abenza JF, Peñalva MA, Xiang X. The p25 subunit of the dynactin complex is required for dynein-early endosome interaction. ACTA ACUST UNITED AC 2011; 193:1245-55. [PMID: 21708978 PMCID: PMC3216330 DOI: 10.1083/jcb.201011022] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The p25 subunit of the dynactin complex is required for the interaction between cytoplasmic dynein and early endosomes but is not required for dynein-mediated nuclear distribution. Cytoplasmic dynein transports various cellular cargoes including early endosomes, but how dynein is linked to early endosomes is unclear. We find that the Aspergillus nidulans orthologue of the p25 subunit of dynactin is critical for dynein-mediated early endosome movement but not for dynein-mediated nuclear distribution. In the absence of NUDF/LIS1, p25 deletion abolished the localization of dynein–dynactin to the hyphal tip where early endosomes abnormally accumulate but did not prevent dynein–dynactin localization to microtubule plus ends. Within the dynactin complex, p25 locates at the pointed end of the Arp1 filament with Arp11 and p62, and our data suggest that Arp11 but not p62 is important for p25–dynactin association. Loss of either Arp1 or p25 significantly weakened the physical interaction between dynein and early endosomes, although loss of p25 did not apparently affect the integrity of the Arp1 filament. These results indicate that p25, in conjunction with the rest of the dynactin complex, is important for dynein–early endosome interaction.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, the Uniformed Services University, Bethesda, MD 20814, USA
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Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa. G3-GENES GENOMES GENETICS 2011; 1:303-16. [PMID: 22384341 PMCID: PMC3276140 DOI: 10.1534/g3.111.000307] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 08/03/2011] [Indexed: 12/15/2022]
Abstract
Classical forward genetics has been foundational to modern biology, and has been the paradigm for characterizing the role of genes in shaping phenotypes for decades. In recent years, reverse genetics has been used to identify the functions of genes, via the intentional introduction of variation and subsequent evaluation in physiological, molecular, and even population contexts. These approaches are complementary and whole genome analysis serves as a bridge between the two. We report in this article the whole genome sequencing of eighteen classical mutant strains of Neurospora crassa and the putative identification of the mutations associated with corresponding mutant phenotypes. Although some strains carry multiple unique nonsynonymous, nonsense, or frameshift mutations, the combined power of limiting the scope of the search based on genetic markers and of using a comparative analysis among the eighteen genomes provides strong support for the association between mutation and phenotype. For ten of the mutants, the mutant phenotype is recapitulated in classical or gene deletion mutants in Neurospora or other filamentous fungi. From thirteen to 137 nonsense mutations are present in each strain and indel sizes are shown to be highly skewed in gene coding sequence. Significant additional genetic variation was found in the eighteen mutant strains, and this variability defines multiple alleles of many genes. These alleles may be useful in further genetic and molecular analysis of known and yet-to-be-discovered functions and they invite new interpretations of molecular and genetic interactions in classical mutant strains.
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222
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Goll MG, Halpern ME. DNA methylation in zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:193-218. [PMID: 21507352 DOI: 10.1016/b978-0-12-387685-0.00005-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methylation is crucial for normal development and cellular differentiation in many large-genome eukaryotes. The small tropical freshwater fish Danio rerio (zebrafish) has recently emerged as a powerful system for the study of DNA methylation, especially in the context of development. This review summarizes our current knowledge of DNA methylation in zebrafish and provides evidence for the general conservation of this system with mammals. In addition, emerging strategies are highlighted that use the fish model to address some of the key unanswered questions in DNA methylation research.
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Affiliation(s)
- Mary G Goll
- Developmental Biology Program, Sloan-Kettering Institute, New York, USA
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223
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Abstract
Circadian clocks organize our inner physiology with respect to the external world, providing life with the ability to anticipate and thereby better prepare for major fluctuations in its environment. Circadian systems are widely represented in nearly all major branches of life, except archaebacteria, and within the eukaryotes, the filamentous fungus Neurospora crassa has served for nearly half a century as a durable model organism for uncovering the basic circadian physiology and molecular biology. Studies using Neurospora have clarified our fundamental understanding of the clock as nested positive and negative feedback loops regulated through transcriptional and post-transcriptional processes. These feedback loops are centered on a limited number of proteins that form molecular complexes, and their regulation provides a physical explanation for nearly all clock properties. This review will introduce the basics of circadian rhythms, the model filamentous fungus N. crassa, and provide an overview of the molecular components and regulation of the circadian clock.
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224
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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Gonçalves RD, Cupertino FB, Freitas FZ, Luchessi AD, Bertolini MC. A genome-wide screen for Neurospora crassa transcription factors regulating glycogen metabolism. Mol Cell Proteomics 2011; 10:M111.007963. [PMID: 21768394 DOI: 10.1074/mcp.m111.007963] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transcription factors play a key role in transcription regulation as they recognize and directly bind to defined sites in promoter regions of target genes, and thus modulate differential expression. The overall process is extremely dynamic, as they have to move through the nucleus and transiently bind to chromatin in order to regulate gene transcription. To identify transcription factors that affect glycogen accumulation in Neurospora crassa, we performed a systematic screen of a deletion strains set generated by the Neurospora Knockout Project and available at the Fungal Genetics Stock Center. In a wild-type strain of N. crassa, glycogen content reaches a maximal level at the end of the exponential growth phase, but upon heat stress the glycogen content rapidly drops. The gene encoding glycogen synthase (gsn) is transcriptionally down-regulated when the mycelium is exposed to the same stress condition. We identified 17 deleted strains having glycogen accumulation profiles different from that of the wild-type strain under both normal growth and heat stress conditions. Most of the transcription factors identified were annotated as hypothetical protein, however some of them, such as the PacC, XlnR, and NIT2 proteins, were biochemically well-characterized either in N. crassa or in other fungi. The identification of some of the transcription factors was coincident with the presence of DNA-binding motifs specific for the transcription factors in the gsn 5'-flanking region, and some of these DNA-binding motifs were demonstrated to be functional by Electrophoretic Mobility Shift Assay (EMSA) experiments. Strains knocked-out in these transcription factors presented impairment in the regulation of gsn expression, suggesting that the transcription factors regulate glycogen accumulation by directly regulating gsn gene expression. Five selected mutant strains showed defects in cell cycle progression, and two transcription factors were light-regulated. The results indicate that there are connections linking different cellular processes, such as metabolism control, biological clock, and cell cycle progression.
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Affiliation(s)
- Rodrigo Duarte Gonçalves
- Instituto de Química, UNESP, Departamento de Bioquímica e Tecnologia Química, 14800-900, Araraquara, SP, Brazil
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226
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Deka R, Kumar R, Tamuli R. Neurospora crassa homologue of Neuronal Calcium Sensor-1 has a role in growth, calcium stress tolerance, and ultraviolet survival. Genetica 2011; 139:885-94. [DOI: 10.1007/s10709-011-9592-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
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227
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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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228
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Tang X, Dong W, Griffith J, Nilsen R, Matthes A, Cheng KB, Reeves J, Schuttler HB, Case ME, Arnold J, Logan DA. Systems biology of the qa gene cluster in Neurospora crassa. PLoS One 2011; 6:e20671. [PMID: 21695121 PMCID: PMC3114802 DOI: 10.1371/journal.pone.0020671] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 05/10/2011] [Indexed: 11/18/2022] Open
Abstract
An ensemble of genetic networks that describe how the model fungal system, Neurospora crassa, utilizes quinic acid (QA) as a sole carbon source has been identified previously. A genetic network for QA metabolism involves the genes, qa-1F and qa-1S, that encode a transcriptional activator and repressor, respectively and structural genes, qa-2, qa-3, qa-4, qa-x, and qa-y. By a series of 4 separate and independent, model-guided, microarray experiments a total of 50 genes are identified as QA-responsive and hypothesized to be under QA-1F control and/or the control of a second QA-responsive transcription factor (NCU03643) both in the fungal binuclear Zn(II)2Cys6 cluster family. QA-1F regulation is not sufficient to explain the quantitative variation in expression profiles of the 50 QA-responsive genes. QA-responsive genes include genes with products in 8 mutually connected metabolic pathways with 7 of them one step removed from the tricarboxylic (TCA) Cycle and with 7 of them one step removed from glycolysis: (1) starch and sucrose metabolism; (2) glycolysis/glucanogenesis; (3) TCA Cycle; (4) butanoate metabolism; (5) pyruvate metabolism; (6) aromatic amino acid and QA metabolism; (7) valine, leucine, and isoleucine degradation; and (8) transport of sugars and amino acids. Gene products both in aromatic amino acid and QA metabolism and transport show an immediate response to shift to QA, while genes with products in the remaining 7 metabolic modules generally show a delayed response to shift to QA. The additional QA-responsive cutinase transcription factor-1β (NCU03643) is found to have a delayed response to shift to QA. The series of microarray experiments are used to expand the previously identified genetic network describing the qa gene cluster to include all 50 QA-responsive genes including the second transcription factor (NCU03643). These studies illustrate new methodologies from systems biology to guide model-driven discoveries about a core metabolic network involving carbon and amino acid metabolism in N. crassa.
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Affiliation(s)
- Xiaojia Tang
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia, United States of America
- Statistics Department, University of Georgia, Athens, Georgia, United States of America
| | - Wubei Dong
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
| | - James Griffith
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
- College of Agricultural and Environmental Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Roger Nilsen
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
| | - Allison Matthes
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
| | - Kevin B. Cheng
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
| | - Jaxk Reeves
- Statistics Department, University of Georgia, Athens, Georgia, United States of America
| | - H.-Bernd Schuttler
- Department of Physics and Astronomy, University of Georgia, Athens, Georgia, United States of America
| | - Mary E. Case
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
| | - Jonathan Arnold
- Genetics Department, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - David A. Logan
- Department of Biological Sciences, Clark Atlanta University, Atlanta, Georgia, United States of America
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Amicucci A, Balestrini R, Kohler A, Barbieri E, Saltarelli R, Faccio A, Roberson RW, Bonfante P, Stocchi V. Hyphal and cytoskeleton polarization in Tuber melanosporum: A genomic and cellular analysis. Fungal Genet Biol 2011; 48:561-72. [DOI: 10.1016/j.fgb.2010.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 12/04/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
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Architecture and development of the Neurospora crassa hypha – a model cell for polarized growth. Fungal Biol 2011; 115:446-74. [PMID: 21640311 DOI: 10.1016/j.funbio.2011.02.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 11/20/2022]
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231
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Hane JK, Rouxel T, Howlett BJ, Kema GHJ, Goodwin SB, Oliver RP. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 2011; 12:R45. [PMID: 21605470 PMCID: PMC3219968 DOI: 10.1186/gb-2011-12-5-r45] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Revised: 04/27/2011] [Accepted: 05/24/2011] [Indexed: 12/20/2022] Open
Abstract
Background Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa. Results These analyses identified a novel form of evolution in which genes are conserved within homologous chromosomes, but with randomized orders and orientations. This mode of evolution is designated mesosynteny, to differentiate it from micro- and macrosynteny seen in other organisms. Mesosynteny is an alternative evolutionary pathway very different from macrosyntenic conservation. Surprisingly, mesosynteny was not found in all fungal groups. Instead, mesosynteny appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes. Conclusions The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis.
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Affiliation(s)
- James K Hane
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia
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232
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Wang TY, He F, Hu QW, Zhang Z. A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa. MOLECULAR BIOSYSTEMS 2011; 7:2278-85. [PMID: 21584303 DOI: 10.1039/c1mb05028a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The filamentous fungus Neurospora crassa is a leading model organism for circadian clock studies. Computational identification of a protein-protein interaction (PPI) network (also known as an interactome) in N. crassa can provide new insights into the cellular functions of proteins. Using two well-established bioinformatics methods (the interolog method and the domain interaction-based method), we predicted 27,588 PPIs among 3006 N. crassa proteins. To the best of our knowledge, this is the first identified interactome for N. crassa, although it remains problematic because of incomplete interactions and false positives. In particular, the established PPI network has provided clues to further decipher the molecular mechanism of circadian rhythmicity. For instance, we found that clock-controlled genes (ccgs) are more likely to act as bottlenecks in the established PPI network. We also identified an important module related to circadian oscillators, and some functional unknown proteins in this module may serve as potential candidates for new oscillators. Finally, all predicted PPIs were compiled into a user-friendly database server (NCPI), which is freely available at .
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Affiliation(s)
- Ting-You Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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233
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Costantino V, Mangoni A, Teta R, Kra-Oz G, Yarden O. Neurosporaside, a tetraglycosylated sphingolipid from Neurospora crassa. JOURNAL OF NATURAL PRODUCTS 2011; 74:554-558. [PMID: 21425845 DOI: 10.1021/np1009493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The new tetraglycosylceramide neurosporaside (1a) has been isolated from the fungus Neurospora crassa. Neurosporaside is a tetraglycosylated glycosphingolipid characterized by a sugar chain unprecedented among natural glycoconjugates. The structure of neurosporaside was elucidated by extensive spectroscopic analysis and microscale degradation analysis, which allowed full structure elucidation using less than 1 mg of compound.
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Affiliation(s)
- Valeria Costantino
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
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Heterochromatin is required for normal distribution of Neurospora crassa CenH3. Mol Cell Biol 2011; 31:2528-42. [PMID: 21505064 DOI: 10.1128/mcb.01285-10] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Centromeres serve as platforms for the assembly of kinetochores and are essential for nuclear division. Here we identified Neurospora crassa centromeric DNA by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) of DNA associated with tagged versions of the centromere foundation proteins CenH3 (CENP-A) and CEN-C (CENP-C) and the kinetochore protein CEN-T (CENP-T). On each chromosome we found an ∼150- to 300-kbp region of enrichment for all three proteins. These regions correspond to intervals predicted to be centromeric DNA by genetic mapping and DNA sequence analyses. By ChIP-seq we found extensive colocalization of CenH3, CEN-C, CEN-T, and histone H3K9 trimethylation (H3K9me3). In contrast, H3K4me2, which has been found at the cores of plant, fission yeast, Drosophila, and mammalian centromeres, was not enriched in Neurospora centromeric DNA. DNA methylation was most pronounced at the periphery of centromeric DNA. Mutation of dim-5, which encodes an H3K9 methyltransferase responsible for nearly all H3K9me3, resulted in altered distribution of CenH3-green fluorescent protein (GFP). Similarly, CenH3-GFP distribution was altered in the absence of HP1, the chromodomain protein that binds to H3K9me3. We conclude that eukaryotes with regional centromeres make use of different strategies for maintenance of CenH3 at centromeres, and we suggest a model in which centromere proteins nucleate at the core but require DIM-5 and HP1 for spreading.
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235
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Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biol 2011; 12:R40. [PMID: 21501500 PMCID: PMC3218866 DOI: 10.1186/gb-2011-12-4-r40] [Citation(s) in RCA: 379] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 03/28/2011] [Accepted: 04/18/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei. CONCLUSIONS The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
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Affiliation(s)
- Christian P Kubicek
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Verena Seidl-Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Diego A Martinez
- Broad Institute of MIT and Harvard, 301 Binney St, Cambridge, MA 02142, USA
| | - Irina S Druzhinina
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Michael Thon
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Susanne Zeilinger
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Sergio Casas-Flores
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Prasun K Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Mala Mukherjee
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Luis D Alcaraz
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Andrea Aerts
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Zsuzsanna Antal
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, Szeged, H-6726, Hungary
| | - Lea Atanasova
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Mayte G Cervantes-Badillo
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Jean Challacombe
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Olga Chertkov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Fanny Coulpier
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Nandan Deshpande
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Hans von Döhren
- TU Berlin, Institut für Chemie, FG Biochemie und Molekulare Biologie OE2, Franklinstr. 29, 10587 Berlin, Germany
| | - Daniel J Ebbole
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Edgardo U Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Michel Flipphi
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Apartado de Correos 73, Burjassot (Valencia) E-46100, Spain
| | - Fabian Glaser
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Elida Y Gómez-Rodríguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Sabine Gruber
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Cliff Han
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Rosa Hermosa
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Campus Guanajuato, Km. 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Mexico
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, Debrecen, H-4010, Hungary
| | - Idit Kosti
- Department of Biology, Technion - Israel Institute of Technology, Neve Shaanan Campus, Technion City, Haifa, 32000, Israel
| | - Stéphane Le Crom
- Institut de Biologie de l'École normale supérieure (IBENS), Institut National de la Santé et de la Recherche Médicale U1024, Centre National de la Recherche Scientifique UMR8197, 46, rue d'Ulm, Paris 75005, France
| | - Erika Lindquist
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mette Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Peter S Lübeck
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Lautrupvang 15, DK-2750 Ballerup, Denmark
| | - Antoine Margeot
- Biotechnology Department, IFP Energies nouvelles, 1-4 avenue de Bois Préau, Rueil-Malmaison, 92852, France
| | - Benjamin Metz
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Monica Misra
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Helena Nevalainen
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Markus Omann
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Nicolle Packer
- Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive Building F7B, North Ryde, Sydney, NSW 2109, Australia
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Edith E Uresti-Rivera
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José, No. 2055, Colonia Lomas 4a Sección, San Luis Potosí, SLP., 78216, México
| | - Asaf Salamov
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Monika Schmoll
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Bernhard Seiboth
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Harris Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Serenella Sukno
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Juan Antonio Tamayo-Ramos
- Wageningen University, Systems and Synthetic Biology, Fungal Systems Biology Group, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Doris Tisch
- Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria
| | - Aric Wiest
- School of Biological Sciences, University of Missouri- Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Heather H Wilkinson
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Michael Zhang
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de la Méditerranée, Case 932, 163 Avenue de Luminy, 13288 Marseille 13288, France
| | - Charles M Kenerley
- Department of Plant Pathology and Microbiology Building 0444, Nagle Street, Texas A&M University College Station, TX 77843, USA
| | - Enrique Monte
- Centro Hispanoluso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Calle Del Duero, 12, Villamayor 37185, Spain
| | - Scott E Baker
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Igor V Grigoriev
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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236
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Use of 1H nuclear magnetic resonance to measure intracellular metabolite levels during growth and asexual sporulation in Neurospora crassa. EUKARYOTIC CELL 2011; 10:820-31. [PMID: 21460191 DOI: 10.1128/ec.00231-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Conidiation is an asexual sporulation pathway that is a response to adverse conditions and is the main mode of dispersal utilized by filamentous fungal pathogens for reestablishment in a more favorable environment. Heterotrimeric G proteins (consisting of α, β, and γ subunits) have been shown to regulate conidiation in diverse fungi. Previous work has demonstrated that all three of the Gα subunits in the filamentous fungus Neurospora crassa affect the accumulation of mass on poor carbon sources and that loss of gna-3 leads to the most dramatic effects on conidiation. In this study, we used (1)H nuclear magnetic resonance (NMR) to profile the metabolome of N. crassa in extracts isolated from vegetative hyphae and conidia from cultures grown under conditions of high or low sucrose. We compared wild-type and Δgna-3 strains to determine whether lack of gna-3 causes a significant difference in the global metabolite profile. The results demonstrate that the global metabolome of wild-type hyphae is influenced by carbon availability. The metabolome of the Δgna-3 strain cultured on both high and low sucrose is similar to that of the wild type grown on high sucrose, suggesting an overall defect in nutrient sensing in the mutant. However, analysis of individual metabolites revealed differences in wild-type and Δgna-3 strains cultured under conditions of low and high sucrose.
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237
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Li X, Shen Y, Sun J, Wang B, He Q. A reporter for dsRNA response in Neurospora crassa. FEBS Lett 2011; 585:906-12. [PMID: 21354420 DOI: 10.1016/j.febslet.2011.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/12/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
In the filamentous fungus Neurospora, the production of dsRNA can elicit a dsRNA-induced transcriptional response similar to the interferon response in vertebrates. However, how fungi sense the expression of dsRNA and activate gene expression is unknown. In this study, we established a dsRNA response reporter system in Neurospora crassa. Using the dsRNA-activated RNA-dependent RNA polymerase gene rrp-3 promoter, we created an expression construct (pRRP-3::Myc-Al-1) and introduced it into al-1(KO) mutant. The test dsRNA efficiently induced pRRP-3::Myc-Al-1 expression in the al-1(KO) mutant, resulting in conidia color switching from white to yellow. These results confirm that the dsRNA response is regulated at the transcriptional level and this reporter system can be used for future studies in dsRNA response in filamentous fungi.
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Affiliation(s)
- Xiaolin Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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238
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Whittle CA, Sun Y, Johannesson H. Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta. Genome Biol Evol 2011; 3:332-43. [PMID: 21402862 PMCID: PMC3089379 DOI: 10.1093/gbe/evr018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.
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Affiliation(s)
- C A Whittle
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
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239
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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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Traffic of chitin synthase 1 (CHS-1) to the Spitzenkörper and developing septa in hyphae of Neurospora crassa: actin dependence and evidence of distinct microvesicle populations. EUKARYOTIC CELL 2011; 10:683-95. [PMID: 21296914 DOI: 10.1128/ec.00280-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe the subcellular location of chitin synthase 1 (CHS-1), one of seven chitin synthases in Neurospora crassa. Laser scanning confocal microscopy of growing hyphae showed CHS-1-green fluorescent protein (GFP) localized conspicuously in regions of active wall synthesis, namely, the core of the Spitzenkörper (Spk), the apical cell surface, and developing septa. It was also present in numerous fine particles throughout the cytoplasm plus some large vacuoles in distal hyphal regions. Although the same general subcellular distribution was observed previously for CHS-3 and CHS-6, they did not fully colocalize. Dual labeling showed that the three different chitin synthases were contained in different vesicular compartments, suggesting the existence of a different subpopulation of chitosomes for each CHS. CHS-1-GFP persisted in the Spk during hyphal elongation but disappeared from the septum after its development was completed. Wide-field fluorescence microscopy and total internal reflection fluorescence microscopy revealed subapical clouds of particles, suggestive of chitosomes moving continuously toward the Spk. Benomyl had no effect on CHS-1-GFP localization, indicating that microtubules are not strictly required for CHS trafficking to the hyphal apex. Conversely, actin inhibitors caused severe mislocalization of CHS-1-GFP, indicating that actin plays a major role in the orderly traffic and localization of CHS-1 at the apex.
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Ceccaroli P, Buffalini M, Saltarelli R, Barbieri E, Polidori E, Ottonello S, Kohler A, Tisserant E, Martin F, Stocchi V. Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum. THE NEW PHYTOLOGIST 2011; 189:751-764. [PMID: 21039570 DOI: 10.1111/j.1469-8137.2010.03520.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
• Primary carbohydrate metabolism plays a special role related to carbon/nitrogen exchange, as well as metabolic support of fruiting body development, in ectomycorrhizal macrofungi. In this study, we used information retrieved from the recently sequenced Tuber melanosporum genome, together with transcriptome analysis data and targeted validation experiments, to construct the first genome-wide catalogue of the proteins supporting carbohydrate metabolism in a plant-symbiotic ascomycete. • More than 100 genes coding for enzymes of the glycolysis, pentose phosphate, tricarboxylic acid, glyoxylate and methylcitrate pathways, glycogen, trehalose and mannitol metabolism and cell wall precursor were annotated. Transcriptional regulation of these pathways in different stages of the T. melanosporum lifecycle was investigated using whole-genome oligoarray expression data together with real-time reverse transcription-polymerase chain reaction analysis of selected genes. • The most significant results were the identification of methylcitrate cycle genes and of an acid invertase, the first enzyme of this kind to be described in a plant-symbiotic filamentous fungus. • A subset of transcripts coding for trehalose, glyoxylate and methylcitrate enzymes was up-regulated in fruiting bodies, whereas genes involved in mannitol and glycogen metabolism were preferentially expressed in mycelia and ectomycorrhizas, respectively. These data indicate a high degree of lifecycle stage specialization for particular branches of carbohydrate metabolism in T. melanosporum.
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Affiliation(s)
- P Ceccaroli
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - M Buffalini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - R Saltarelli
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - E Barbieri
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - E Polidori
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
| | - S Ottonello
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Parma, Viale G.P. Usberti 23/A, 43100 Parma, Italy
| | - A Kohler
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - E Tisserant
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - F Martin
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - V Stocchi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino 'Carlo Bo', via Saffi, 2, 61029 Urbino, Italy
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Montanini B, Levati E, Bolchi A, Kohler A, Morin E, Tisserant E, Martin F, Ottonello S. Genome-wide search and functional identification of transcription factors in the mycorrhizal fungus Tuber melanosporum. THE NEW PHYTOLOGIST 2011; 189:736-750. [PMID: 21058951 DOI: 10.1111/j.1469-8137.2010.03525.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
• Developmental transitions associated with the life cycle of plant-symbiotic fungi, such as the ascomycete Tuber melanosporum, are likely to require an extensive reprogramming of gene expression brought about by transcription factors (TFs). To date, little is known about the transcriptome alterations that accompany developmental shifts associated with symbiosis or fruiting body formation. • Taking advantage of the black truffle genome sequence, we used a bioinformatic approach, coupled with functional analysis in yeast and transcriptome profiling, to identify and catalogue T. melanosporum TFs, the so-called 'regulome'. • The T. melanosporum regulome contains 102 homologs of previously characterized TFs, 57 homologs of hypothetical TFs, and 42 putative TFs apparently unique to Tuber. The yeast screen allowed the functional discovery of four TFs and the validation of about one-fifth of the in silico predicted TFs. Truffle proteins apparently unrelated to transcription were also identified as potential transcriptional regulators, together with a number of plant TFs. • Twenty-nine TFs, some of which associated with particular developmental stages, were found to be up-regulated in ECMs or fruiting bodies. About one-quarter of these up-regulated TFs are expressed at surprisingly high levels, thus pointing to a striking functional specialization of the different stages of the Tuber life cycle.
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Affiliation(s)
- Barbara Montanini
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Elisabetta Levati
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Angelo Bolchi
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
| | - Annegret Kohler
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Emmanuelle Morin
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Emilie Tisserant
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Francis Martin
- Ecogenomics of Interactions Lab, UMR 'Interactions Arbres/Micro-Organismes', INRA-Nancy, 54280 Champenoux, France
| | - Simone Ottonello
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy
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244
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Watters MK, Boersma M, Johnson M, Reyes C, Westrick E, Lindamood E. A screen for Neurospora knockout mutants displaying growth rate dependent branch density. Fungal Biol 2011; 115:296-301. [PMID: 21354536 DOI: 10.1016/j.funbio.2010.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 12/21/2010] [Accepted: 12/27/2010] [Indexed: 11/18/2022]
Abstract
Branch density (the spatial distribution of branch initiation points along a growing hypha) in wild-type Neurospora has been shown to remain constant at different growth rates due to a hypothesized system which compensates for hyphal growth rate. Here we report the results of a survey of the Neurospora knockout library for mutants affecting this proposed growth rate compensation system. The mutants identified fail to maintain branching homeostasis at different growth rates, thus showing growth rate-dependent branch density. The gene functions highlighted by this screen are diverse with several emerging themes including: ubiquitin-binding proteins, kinases, metal binding/metal metabolism proteins, reactive oxygen species (ROS) control proteins, and clock-associated/clock-controlled proteins. Other than their common influence on branch density homeostasis, the relationships between these gene functions and how they interact to influence branching are unclear.
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Affiliation(s)
- Michael K Watters
- Department of Biology, Neils Science Centre, Valparaiso University, 1610 Campus Drive East, Valparaiso, IN 46383, USA.
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245
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Choi J, Kim KS, Rho HS, Lee YH. Differential roles of the phospholipase C genes in fungal development and pathogenicity of Magnaporthe oryzae. Fungal Genet Biol 2011; 48:445-55. [PMID: 21237279 DOI: 10.1016/j.fgb.2011.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/29/2010] [Accepted: 01/03/2011] [Indexed: 11/26/2022]
Abstract
Calcium plays a critical role in a variety of cellular processes in cells. However, relatively little is known about the biological effects of Ca²+ signaling on morphogenesis and pathogenesis in the rice blast fungus Magnaporthe oryzae compared to other signaling pathways. We have previously demonstrated that MoPLC1-mediated calcium regulation is important for infection-related development and pathogenicity in M. oryzae. In the present study, four genes encoding phospholipase C (PLC) isozymes (MoPLC2 to MoPLC5), which differ from MoPLC1 in their domain organization, were additionally identified. The C2 domain involved in Ca²+-dependent membrane binding is found only in MoPLC2 and MoPLC3. Detailed functional analysis using deletion mutants for MoPLC2 and MoPLC3 indicated that MoPLC2 and MoPLC3 play essential roles in development. The two deletion mutants for MoPLC2 and MoPLC3 showed reduced conidiation and a defect in appressorium-mediated penetration. Reintroduction of the genes restored defects of ΔMoplc2 and ΔMoplc3. Notably, ΔMoplc2 and ΔMoplc3 mutants developed multiple appressoria on separate germ tubes of a conidium, indicating that MoPLC2- and MoPLC3-regulated signaling suppresses a feedback loop of a pathway for appressorial development. The similarity in phenotypic defects between the two mutants indicates that both MoPLC2 and MoPLC3 are important for regulation of appropriate levels of signaling molecules in a similar manner. Comparative analysis indicated that the two MoPLCs-mediated signaling pathways have interrelated, but distinct, roles in the development of M. oryzae.
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Affiliation(s)
- Jinhee Choi
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Republic of Korea
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Abstract
In contrast to viruses of plants and animals, viruses of fungi, mycoviruses, uniformly lack an extracellular phase to their replication cycle. The persistent, intracellular nature of the mycovirus life cycle presents technical challenges to experimental design. However, these properties, coupled with the relative simplicity and evolutionary position of the fungal host, also provide opportunities for examining fundamental aspects of virus-host interactions from a perspective that is quite different from that pertaining for most plant and animal virus infections. This chapter presents support for this view by describing recent advances in the understanding of antiviral defense responses against one group of mycoviruses for which many of the technical experimental challenges have been overcome, the hypoviruses responsible for hypovirulence of the chestnut blight fungus Cryphonectria parasitica. The findings reveal new insights into the induction and suppression of RNA silencing as an antiviral defense response and an unexpected role for RNA silencing in viral RNA recombination.
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Affiliation(s)
- Donald L Nuss
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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Wang X, Hsueh YP, Li W, Floyd A, Skalsky R, Heitman J. Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 2010; 24:2566-82. [PMID: 21078820 DOI: 10.1101/gad.1970910] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cosuppression is a silencing phenomenon triggered by the introduction of homologous DNA sequences into the genomes of organisms as diverse as plants, fungi, flies, and nematodes. Here we report sex-induced silencing (SIS), which is triggered by tandem integration of a transgene array in the human fungal pathogen Cryptococcus neoformans. A SXI2a-URA5 transgene array was found to be post-transcriptionally silenced during sexual reproduction. More than half of the progeny that inherited the SXI2a-URA5 transgene became uracil-auxotrophic due to silencing of the URA5 gene. In vegetative mitotic growth, silencing of this transgene array occurred at an ∼250-fold lower frequency, indicating that silencing is induced during the sexual cycle. Central components of the RNAi pathway-including genes encoding Argonaute, Dicer, and an RNA-dependent RNA polymerase-are all required for both meiotic and mitotic transgene silencing. URA5-derived ∼22-nucleotide (nt) small RNAs accumulated in the silenced isolates, suggesting that SIS is mediated by RNAi via sequence-specific small RNAs. Through deep sequencing of the small RNA population in C. neoformans, we also identified abundant small RNAs mapping to repetitive transposable elements, and these small RNAs were absent in rdp1 mutant strains. Furthermore, a group of retrotransposons was highly expressed during mating of rdp1 mutant strains, and an increased transposition/mutation rate was detected in their progeny, indicating that the RNAi pathway squelches transposon activity during the sexual cycle. Interestingly, Ago1, Dcr1, Dcr2, and Rdp1 are translationally induced in mating cells, and Ago1, Dcr1, and Dcr2 localize to processing bodies (P bodies), whereas Rdp1 appears to be nuclear, providing mechanistic insights into the elevated silencing efficiency during sexual reproduction. We hypothesize that the SIS RNAi pathway operates to defend the genome during sexual development.
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Affiliation(s)
- Xuying Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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Frequent and efficient use of the sister chromatid for DNA double-strand break repair during budding yeast meiosis. PLoS Biol 2010; 8:e1000520. [PMID: 20976044 PMCID: PMC2957403 DOI: 10.1371/journal.pbio.1000520] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 09/02/2010] [Indexed: 01/07/2023] Open
Abstract
Studies of DNA double-strand break repair during meiosis reveal that a substantial fraction of recombination occurs between sister chromatids. Recombination between homologous chromosomes of different parental origin (homologs) is necessary for their accurate segregation during meiosis. It has been suggested that meiotic inter-homolog recombination is promoted by a barrier to inter-sister-chromatid recombination, imposed by meiosis-specific components of the chromosome axis. Consistent with this, measures of Holliday junction–containing recombination intermediates (joint molecules [JMs]) show a strong bias towards inter-homolog and against inter-sister JMs. However, recombination between sister chromatids also has an important role in meiosis. The genomes of diploid organisms in natural populations are highly polymorphic for insertions and deletions, and meiotic double-strand breaks (DSBs) that form within such polymorphic regions must be repaired by inter-sister recombination. Efforts to study inter-sister recombination during meiosis, in particular to determine recombination frequencies and mechanisms, have been constrained by the inability to monitor the products of inter-sister recombination. We present here molecular-level studies of inter-sister recombination during budding yeast meiosis. We examined events initiated by DSBs in regions that lack corresponding sequences on the homolog, and show that these DSBs are efficiently repaired by inter-sister recombination. This occurs with the same timing as inter-homolog recombination, but with reduced (2- to 3-fold) yields of JMs. Loss of the meiotic-chromosome-axis-associated kinase Mek1 accelerates inter-sister DSB repair and markedly increases inter-sister JM frequencies. Furthermore, inter-sister JMs formed in mek1Δ mutants are preferentially lost, while inter-homolog JMs are maintained. These findings indicate that inter-sister recombination occurs frequently during budding yeast meiosis, with the possibility that up to one-third of all recombination events occur between sister chromatids. We suggest that a Mek1-dependent reduction in the rate of inter-sister repair, combined with the destabilization of inter-sister JMs, promotes inter-homolog recombination while retaining the capacity for inter-sister recombination when inter-homolog recombination is not possible. In diploid organisms, which contain two parental sets of chromosomes, double-stranded breaks in DNA can be repaired by recombination, either with a copy of the chromosome produced by replication (the sister chromatid), or with either chromatid of the other parental chromosome (the homolog). During meiosis, recombination with the homolog ensures faithful segregation of chromosomes to gametes (sperm or egg). It has been suggested that use of the spatially distant homolog, as opposed to the nearby sister chromatid, results from a meiosis-specific barrier to recombination between sister chromatids. However, there are situations where meiotic recombination must occur between sister chromatids, such as when recombination initiates in sequences that are absent from the homolog. By studying such a situation, we show that meiotic recombination with the sister chromatid occurs with similar timing and efficiency as recombination with the homolog. Further analysis indicates that inter-sister recombination is more common than was previously thought, although still far less prevalent than in somatic cells, where inter-sister recombination predominates. We suggest that meiosis-specific factors act to roughly equalize repair from the sister and homolog, which both allows the establishment of physical connections between homologs and ensures timely repair of breaks incurred in regions lacking corresponding sequences on the homolog.
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Seiler S, Justa-Schuch D. Conserved components, but distinct mechanisms for the placement and assembly of the cell division machinery in unicellular and filamentous ascomycetes. Mol Microbiol 2010; 78:1058-76. [PMID: 21091496 DOI: 10.1111/j.1365-2958.2010.07392.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cytokinesis is essential for cell proliferation, yet its molecular description is challenging, because >100 conserved proteins must be spatially and temporally co-ordinated. Despite the high importance of a tight co-ordination of cytokinesis with chromosome and organelle segregation, the mechanism for determining the cell division plane is one of the least conserved aspects of cytokinesis in eukaryotic cells. Budding and fission yeast have developed fundamentally distinct mechanisms to ensure proper nuclear segregation. The extent to which these pathways are conserved in multicellular fungi remains unknown. Recent progress indicates common components, but different mechanisms that are required for proper selection of the septation site in the different groups of Ascomycota. Cortical cues are used in yeast- and filament-forming species of the Saccharomycotina clade that are established at the incipient bud site or the hyphal tip respectively. In contrast, septum formation in the filament-forming Pezizomycotina species Aspergillus nidulans and Neurospora crassa seems more closely related to the fission yeast programme in that they may combine mitotic signals with a cell end-based marker system and Rho GTPase signalling. Thus, significant differences in the use and connection of conserved signalling modules become apparent that reflect the phylogenetic relationship of the analysed models.
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Affiliation(s)
- Stephan Seiler
- Institut für Mikrobiologie und Genetik, Universität Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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H2B- and H3-specific histone deacetylases are required for DNA methylation in Neurospora crassa. Genetics 2010; 186:1207-16. [PMID: 20876559 DOI: 10.1534/genetics.110.123315] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neurospora crassa utilizes DNA methylation to inhibit transcription of heterochromatin. DNA methylation is controlled by the histone methyltransferase DIM-5, which trimethylates histone H3 lysine 9, leading to recruitment of the DNA methyltransferase DIM-2. Previous work demonstrated that the histone deacetylase (HDAC) inhibitor trichostatin A caused a reduction in DNA methylation, suggesting involvement of histone deacetylation in DNA methylation. We therefore created mutants of each of the four classical N. crassa HDAC genes and tested their effect on histone acetylation levels and DNA methylation. Global increases in H3 and H4 acetylation levels were observed in both the hda-3 and the hda-4 mutants. Mutation of two of the genes, hda-1 and hda-3, caused partial loss of DNA methylation. The site-specific loss of DNA methylation in hda-1 correlated with loss of H3 lysine 9 trimethylation and increased H3 acetylation. In addition, an increase in H2B acetylation was observed by two-dimensional gel electrophoresis of histones of the hda-1 mutant. We found a similar increase in the Schizosaccharomyces pombe Clr3 mutant, suggesting that this HDAC has a previously unrecognized substrate and raising the possibility that the acetylation state of H2B may play a role in the regulation of DNA methylation and heterochromatin formation.
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