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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ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE109291 | GEO | 2018/01/18
SECONDARY ACCESSION(S): PRJNA430363
REPOSITORIES: GEO
Similar Datasets
Project description:Cryptococcus neoformans is a prevalent human fungal pathogen that must survive within various tissues in order to establish a human infection. We have identified the C. neoformans Rim101 transcription factor, a highly conserved pH-response regulator in many fungal species. The rim101- mutant strain displays growth defects similar to other fungal species in the presence of alkaline pH, increased salt concentrations, and iron limitation. However, the rim101- strain is also characterized by a striking defect in capsule, an important virulence-associated phenotype. This capsular defect is likely due to alterations in polysaccharide attachment to the cell surface, not in polysaccharide biosynthesis. In contrast to many other C. neoformans capsule-defective strains, the rim101- mutant is hypervirulent in animal models of cryptococcosis. Whereas Rim101 activation in other fungal species occurs through the conserved Rim pathway, we demonstrate that C. neoformans Rim101 is also activated by the cAMP/PKA pathway. We report here that C. neoformans uses PKA and the Rim pathway to regulate the localization, activation, and processing of the Rim101 transcription factor. We also demonstrate specific host- relevant activating conditions for Rim101 cleavage, showing that C. neoformans has co-opted conserved signaling pathways to respond to the specific niche within the infected host. These results establish a novel mechanism for Rim101 activation and the integration of two conserved signaling cascades in response to host environmental conditions.
2010-09-04 | GSE23929 | GEO
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
2014-07-21 | GSE53341 | GEO
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: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
| PRJNA430363 | ENA
Project description:Purpose: To examine the comparative transcriptional profiles of WT and rim101 mutant cells in host-mimicking in vitro conditions to determine genes that are responsible for the increased virulence of the rim101 strain. The rim101 mutant is able to trigger an overactive inflammatory response, presumably by exposing an antigenic trigger. Using transcriptional profiling, we determined that many genes involved in cell wall processes were differentially transcribed between the wild type and the mutant strain.
2013-02-02 | GSE43189 | GEO
Project description:Purpose: To examine the comparative transcriptional profiles of WT and rim101 mutant cells in host-mimicking in vitro conditions to determine genes that are responsible for the increased virulence of the rim101 strain. The rim101 mutant is able to trigger an overactive inflammatory response, presumably by exposing an antigenic trigger. Using transcriptional profiling, we determined that many genes involved in cell wall processes were differentially transcribed between the wild type and the mutant strain. Whole mRNA profiles of WT and rim101 cells were generated by deep sequencing using Illumina GAII.
2013-02-02 | E-GEOD-43189 | biostudies-arrayexpress
Project description:Invasion of host tissue by the human fungal pathogen, Candida albicans is an important step during many forms of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. It is known for example that the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade into host tissue and to cause infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence as compared to SC5314. In this study we compare the in vitro transcriptional profiles and the genotypic profiles of these two widely used laboratory strains in order to determine the principal biological and genetic properties which may govern the different potential for invasiveness and virulence. Keywords: transcriptional profiling, comparative genomic hybridisation, invasive vs. non-invasive C. albicans strain
2008-03-11 | GSE10689 | GEO
Project description:Candida albicans is a diploid human fungal pathogen that displays significant genomic and phenotypic heterogeneity over a range of virulence traits and in the context of a variety of environmental niches. Here, we show that the effects of Rob1 on biofilm and filamentation virulence traits is dependent on both the specific environmental condition and the clinical strain of C. albicans. The C. albicans reference strain SC5314 is a ROB1 heterozygote with two alleles that differ by a single nucleotide polymorphism at position 946 resulting in a serine or proline containing isoform. An analysis of 224 sequenced C. albicans genomes indicates that SC5314 is the only ROB1 heterozygote documented to date and that the dominant allele contains a proline at position 946. Remarkably, the ROB1 alleles are functionally distinct and the rare ROB1946S allele supports increased filamentation in vitro and increased biofilm formation in vitro and in vivo, suggesting it is a phenotypic gain-of-function allele. SC5314 is amongst the most highly filamentous and invasive strains characterized to date. Introduction of the ROB1946S allele into a poorly filamenting clinical isolate increases filamentation and conversion of an SC5314 laboratory strain to a ROB1946S homozygote increases in vitro filamentation and biofilm formation. In a mouse model of oropharyngeal infection, the predominant ROB1946P allele establishes a commensal state while the ROB1946S phenocopies the parent strain and invades into the mucosae. These observations provide an explanation for the distinct phenotypes of SC5314 and highlight the role of heterozygosity as a driver of C. albicans phenotypic heterogeneity.
2023-07-29 | GSE238051 | GEO
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.
2024-02-01 | GSE254653 | GEO
Project description:Invasion of host tissue by the human fungal pathogen, Candida albicans is an important step during many forms of candidosis. However, not all C. albicans strains possess the same invasive and virulence properties. It is known for example that the two clinical isolates SC5314 and ATCC10231 differ in their ability to invade into host tissue and to cause infections. Strain SC5314 is invasive whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence as compared to SC5314. In this study we compare the in vitro transcriptional profiles and the genotypic profiles of these two widely used laboratory strains in order to determine the principal biological and genetic properties which may govern the different potential for invasiveness and virulence. Keywords: transcriptional profiling, comparative genomic hybridisation, invasive vs. non-invasive C. albicans strain Genomic DNA from C. albicans strains SC5314 and ATCC10231 hybridisations were done in duplicate including one dye swap. Total RNA from C. albicans strains SC5314 and ATCC10231 strains were compared in triplicate including one biological replicate and one dye swap.
2010-05-26 | E-GEOD-10689 | biostudies-arrayexpress