RNA-SEQ analysis of a C. albicans rim101-/- disrupted strain, a strain overexpressing RIM101 and a reference strain at both alkaline (7.6) and acidic (4) pH
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PROVIDER: PRJNA430363 | ENA |
REPOSITORIES: ENA
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Project description:The aim of the study was to compare the RNA-SEQ profiles of a wild type C. albicans strain (SC5314), a rim101-/- mutant strain (DAY25) and a strain overexpressing RIM101 (CGY1) at both alkaline (7.6) and acidic (4) pH, in order to identify Rim-dependent genes involved in tolerance to antifungals
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Project description:To investigate the function of Rfg1 in sensing acidic pH and regulating filamentation in C. albicans, we performed the global gene expression profile analysis of WT and rfg1/rfg1 mutant.We reveal that Rfg1 is an essential acidic pH sensor in C. albicans. Rfg1 regulates filamentous growth in acidic pH condition via co-regulation of Rim101-Phr1 pathway, cAMP signaling pathway,and the transcription factors Bcr1, Efg1, Flo8, and Hgc1.
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Project description:Alkaline pH triggers an adaptation mechanism in fungi that is mediated by Rim101/PacCp, a zinc finger transcription factor. To identify the genes under its control in Ustilago maydis, we performed microarray analyses, comparing gene expression in a wild type strain vs a rim101/pacC mutant of the fungus. In this study we obtained evidence of the large number of genes regulated mostly directly, but also indirectly (probably through regulation of other transcription factors) by Rim101/PacCp, including proteins involved in a large number of physiological activities of the fungus. Our analyses suggest that the response to alkaline conditions under the control of the Pal/Rim pathway involves changes in the cell wall and plasma membrane through alterations in their lipid, protein, and polysaccharide composition, changes in cell polarity, actin cytoskeleton organization, and budding patterns. Also as expected, adaptation involves regulation by Rim101/PacC of genes involved in the meiotic functions, such as recombination and segregation, and expression of genes involved in ion and nutrient transport, as well as general vacuole functions. The mutant analyzed in this study is described in PMID 15947192
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Project description:Alkaline pH triggers an adaptation mechanism in fungi that is mediated by Rim101/PacCp, a zinc finger transcription factor. To identify the genes under its control in Ustilago maydis, we performed microarray analyses, comparing gene expression in a wild type strain vs a rim101/pacC mutant of the fungus. In this study we obtained evidence of the large number of genes regulated mostly directly, but also indirectly (probably through regulation of other transcription factors) by Rim101/PacCp, including proteins involved in a large number of physiological activities of the fungus. Our analyses suggest that the response to alkaline conditions under the control of the Pal/Rim pathway involves changes in the cell wall and plasma membrane through alterations in their lipid, protein, and polysaccharide composition, changes in cell polarity, actin cytoskeleton organization, and budding patterns. Also as expected, adaptation involves regulation by Rim101/PacC of genes involved in the meiotic functions, such as recombination and segregation, and expression of genes involved in ion and nutrient transport, as well as general vacuole functions. The mutant analyzed in this study is described in PMID 15947192 Five different oligonucleotide probes per gene (60 nt in length) per duplicate represented each of the 6,883 genes of the U.maydis genome. Accordingly, the expressed data are equivalent to 10 different assays of the expression of each gene.
2014-07-21 | E-GEOD-53341 | biostudies-arrayexpress
Project description:As a successful commensal and pathogen of humans, Candida albicans encounters a wide range of environmental changes. Among them, ambient pH is an important factor, which changes frequently and affects many biological processes in this species. The ability to adapt to pH changes is tightly linked with pathogenesis and morphogenesis. In this study, we report that pH has a profound effect on white-opaque switching and sexual mating in C. albicans. Acidic pHs promote white-to-opaque switching but repress sexual mating of opaque cells. The cAMP signaling and Rim101-mediated pH sensing pathways are involved in the regulation of pH-regulated white-opaque switching. Interestingly, white and opaque cells of the cyr1/cyr1 mutant, which is defective in producing cAMP, show distinct growth defects under acidic and alkaline conditions. Phr2 could play a major role in acidic pHs-induced opaque cell formation. We further discover that acidic pH conditions repress sexual mating due to the failure of activation of the Ste2-mediated a-pheromone response pathway. The effects of pH changes on phenotypic switching and sexual mating could be a balance behavior between host adaptation and sexual reproduction.
2015-12-30 | GSE67101 | GEO
Project description:Elicidate the changes of the transcriptional program response of U. maydis WT strain (a2b2) when transfered from neutrality to acidic or alkaline medium The mutants strains CL211 and GP25 used as controls as well as the WT strain are described in Martínez-Espinoza et al., 1997; 2004;González-Prieto et al., 2014 and Banuett & Herskowitz, 1989 respectively.
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Project description:The purpose of this study was to examine how Mtb integrates acidic pH and available carbon sources as environmental cues to regulate its metabolism and growth rate. RNA-seq transcriptional profiling of M. tuberculosis growing at acidic or neutral pH, in pyruvate or glycerol, was examined. These studies identified carbon source-dependent and -independent pH-dependent adaptations. Mtb strain CDC1551 was grown in standing T-75 flasks in 40 mL of medium seeded an initial OD of 0.1. We examined medium in four conditions pH 7.0 10 mM glycerol, pH 5.7 10 mM glycerol, pH 7.0 10 mM pyruvate, pH 5.7 10 mM pyruvate. Following 3 days of incubation at 37C, RNA was isolated from the bacterial cultures and used for RNA-seq.
2014-07-07 | E-GEOD-52020 | biostudies-arrayexpress
Project description:During mammalian colonization and infection, microorganisms must be able to rapidly sense and adapt to changing environmental conditions including alterations in extracellular pH. The fungus-specific Rim/Pal signaling pathway is one process that supports microbial adaptation to alkaline pH. This cascading series of interacting proteins terminates in the proteolytic activation of the highly conserved Rim101/PacC protein, a transcription factor that mediates microbial responses that favor survival in neutral/alkaline pH growth conditions, including many mammalian tissues. We identified the putative Rim pathway proteins Rim101 and Rra1 in the human skin colonizing fungus Malassezia sympodialis. Targeted mutation of these proteins confirmed their role in M. sympodialis growth at higher pH. Additionally, comparative transcriptional analysis of the mutant strains compared to wild-type suggested mechanisms for fungal adaptation to alkaline conditions. These signaling proteins are required for optimal growth in a murine model of atopic dermatitis, a pathological condition associated with increased skin pH. Together these data elucidate both conserved and phylum-specific features of microbial adaptation to extracellular stresses.
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