The effect on gene expression in filamentous haploid of sugarcane smut fungus Sporisorium scitamineum
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ABSTRACT:
ORGANISM(S): Sporisorium scitamineum
PROVIDER: GSE238083 | GEO | 2024/09/01
REPOSITORIES: GEO
Similar Datasets
Project description:In filamentous strains of S. cerevisiae, nitrogen stress elicits a complex morphogenetic program resulting in the transition to a filamentous form of growth. The transcription factors Flo8p and Mss11p are both required for this filamentous growth transition, in that homozygous diploid flo8(delta/delta) and mss11(delta/delta) strains do not undergo filamentation under conditions of nitrogen stress. To identify genes that are regulated either directly or indirectly by the Flo8p and Mss11p transcription factors, we have implemented DNA microarray analysis to profile changes in mRNA levels in homozygous diploid strains of the filamentous (Sigma)1278b genetic background deleted for FLO8 and MSS11, respectively, under conditions of nitrogen stress. The transcriptional profiles will identify genes with altered transcriptional levels in the deletion mutants, serving as a means to identify cellular processes and signaling pathways regulated by Flo8p and Mss11p function.
2012-09-04 | GSE40530 | GEO
Project description:Candida albicans is an opportunistic fungal pathogen capable of causing superficial and systemic infections in humans. The ability of C. albicans to switch between various morphological forms depending on its host environment is thought to contribute to its virulence. Filamentous growth states are associated with tissue invasion, biofilm formation, evasion of innate host defences and mating. Although the mechanisms of activation of filamentous growth pathways are well understood, less is known about which factors control the negative regulation of filamentation. In this study, we have identified a previously uncharacterized Orf that shares sequence similarity with Saccharomyces cerevisiae Dig1p and Dig2p. Deletion of the gene encoding this Orf triggers invasive growth in C. albicans and so we have retained the yeast designation of Dig1 (for Down-regulation of Invasive Growth). Mutants lacking CaDIG1 form cultures of hyperpolarized cells, form robust biofilms, are highly invasive in vitro but not in vivo and are constitutively activated for the pheromone response. Deletion of key transcription factors that act downstream of Dig1p provide evidence to suggest that CaDig1 regulates filamentation and mating through multiple signalling pathways.
2015-08-31 | GSE70085 | GEO
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
2011-12-22 | GSE27297 | GEO
Project description:Candida albicans is an opportunistic fungal pathogen capable of causing superficial and systemic infections in humans. The ability of C. albicans to switch between various morphological forms depending on its host environment is thought to contribute to its virulence. Filamentous growth states are associated with tissue invasion, biofilm formation, evasion of innate host defences and mating. Although the mechanisms of activation of filamentous growth pathways are well understood, less is known about which factors control the negative regulation of filamentation. In this study, we have identified a previously uncharacterized Orf that shares sequence similarity with Saccharomyces cerevisiae Dig1p and Dig2p. Deletion of the gene encoding this Orf triggers invasive growth in C. albicans and so we have retained the yeast designation of Dig1 (for Down-regulation of Invasive Growth). Mutants lacking CaDIG1 form cultures of hyperpolarized cells, form robust biofilms, are highly invasive in vitro but not in vivo and are constitutively activated for the pheromone response. Deletion of key transcription factors that act downstream of Dig1p provide evidence to suggest that CaDig1 regulates filamentation and mating through multiple signalling pathways. Transcriptional analysis of the C. albicans dig1Δ/dig1Δ homozygous mutant versus the wild type (SN148) in the MTLa/alpha background. Four biological replicates of the mutant and the wild type were included in the analysis. Samples were grown at 30 °C in YPD medium plus uridine
2015-08-31 | E-GEOD-70085 | biostudies-arrayexpress
Project description:The goal of this experiment concerned the comparison of genes controling the mating and filamentation pathways in S. cerevisiae and the filamentous fungus A. gossypii. Even though the A. gossypii genome encodes homologous genes of all components of these two pathways, there are major differences in the modes of growth beween the two organisms, and the potential for mating is unknown in A. gossypii. To shed light on functional conservation the two pathway including transcriptional regulation, a bioinfomatics analysis that looked into transcription factor conservation was carried out. To experimentally investigate regulatory network conservation, the two transcription factors AgTec1. AgSte12 and the repressor AgDig1.2 that act at the end of the pathways were deleted. Subsequent comparisons of mRNA levels of the deletion mutants with wild type allowed the identification of genes and gene groups which are regulated by the transcription factors or the repressor.
2011-01-31 | E-MEXP-1954 | biostudies-arrayexpress
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating. With GPL10116 : 4 conditions each with four biological replicates :mat+, mat-, fpr1-, fmr1-; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5
2011-12-22 | E-GEOD-27297 | biostudies-arrayexpress
Project description:The opportunistic pathogenic fungus Candida albicans can cause devastating infections in severely compromised patients. Its ability to undergo a morphogenetic transition from yeast to filamentous forms allows it to penetrate tissues and cause damage, and the expression of a number of pathogenetic mechanisms are also coordinately regulated with this yeast-to-hyphae conversion. Therefore, it is widely considered that filamentation represents one of the main virulence factors of C. albicans. We have previously identified N-[3-(allyloxy)-phenyl]-4-methoxybenzamide (compound 9029936) as the lead compound in a series of small molecule inhibitors of C. albicans filamentation, and characterized its activity, both in vitro and in vivo, as a promising candidate for the development of alternative anti-virulence strategies for the treatment of C. albicans infections. Here we have performed RNA sequencing analysis of samples obtained from C. albicans cells grown under filament-inducing conditions in the presence or absence of this compound. Overall treatment with compound 9029936 resulted in 618 up-regulated and 702 down-regulated genes. Not surprisingly some of the top down-regulated genes included well characterized genes associated with filamentation and virulence such as SAP5, ECE1 (candidalysin), and ALS3, as well as genes that impact metal chelation and utilization. Gene ontology analysis revealed an over-representation of cell adhesion, iron transport, filamentation, biofilm formation, and pathogenesis processes among down-regulated genes as result of treatment with this leading compound. Interestingly, the top up-regulated genes pointed to an enhancement of vesicular transport pathways, and in particular SNARE interactions.
2019-08-22 | GSE136116 | GEO
Project description:We did transcription profiling on the effect of O-glycosylation inhibitor OGT2468 in Saccharomyces cerevisiae using strains SEY6210 (wild type). Yeast cells exposed to OGT2468 in YPD growth medium show a significant inhibition of mating, filamentation and induction of cell wall compensatory mechanism.
2010-09-30 | GSE12193 | GEO
Project description:We did transcription profiling on the effect of O-glycosylation inhibitor OGT2468 in Saccharomyces cerevisiae using strains SEY6210 (wild type). Yeast cells exposed to OGT2468 in YPD growth medium show a significant inhibition of mating, filamentation and induction of cell wall compensatory mechanism.
2010-09-30 | GSE12180 | GEO
Project description:In filamentous strains of S. cerevisiae, nitrogen stress elicits a complex morphogenetic program resulting in the transition to a filamentous form of growth. The transcription factors Flo8p and Mss11p are both required for this filamentous growth transition, in that homozygous diploid flo8(delta/delta) and mss11(delta/delta) strains do not undergo filamentation under conditions of nitrogen stress. To identify genes that are regulated either directly or indirectly by the Flo8p and Mss11p transcription factors, we have implemented DNA microarray analysis to profile changes in mRNA levels in homozygous diploid strains of the filamentous (Sigma)1278b genetic background deleted for FLO8 and MSS11, respectively, under conditions of nitrogen stress. The transcriptional profiles will identify genes with altered transcriptional levels in the deletion mutants, serving as a means to identify cellular processes and signaling pathways regulated by Flo8p and Mss11p function. Deletion mutants were constructed using a one-step polymerase chain reaction (PCR)-based gene disruption strategy with the G418 resistance cassette from plasmid pFA6a-KanMX6. After the haploid mutants were confirmed via PCR, the strains were allowed to mate on YPD+G418 plates for approximately 20 hours at 30 degrees Celsius. Mated cells were then streaked on SC-Trp-Leu plates to select for Y825 x HLY337 diploids. Yeast transformations were performed according to standard lithium acetate-mediated protocols with modifications. Yeast strains (wild-type and deletion mutants) were cultured under conditions of nitrogen stress (low ammonium media), and RNA was prepared using the Poly(A) Purist kit (Ambion, Austin, TX). RNA concentration and purity were determined spectrophotometrically and by gel electrophoresis. Microarray hybridization was performed with the Yeast Genome S98 Array using standard protocols (Affymetrix, Inc, Santa Clara, CA). Differentially expressed genes were identified by significance analysis of microarrays (SAM). SAM computed a nonparametric score for each gene by dividing the between-group difference of (normalized log) gene expression levels and the within-group difference of gene expression levels. The score was then compared with random permutation scores. The random permutation scores for a gene were computed in the same manner as the original score, but based on randomly sampled gene expressions. If the difference between the original score and the random permutation score was larger than a chosen threshold value, the corresponding change in gene expression was claimed to be significant. Each threshold value corresponded to a false discovery rate (the percentage of genes identified as being significant by chance alone). For all deletion comparisons in this study, we used SAM’s two-class unpaired analysis function, with significance thresholds selected so that the corresponding false discovery rate was 0.
2012-09-04 | E-GEOD-40530 | biostudies-arrayexpress