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Transcriptomic analysis of the role of Rim101 in the adaptation of Ustilago maydis to an alkaline environment

ABSTRACT: 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

ORGANISM(S): Mycosarcoma maydis

PROVIDER: GSE53341 | GEO | 2014/07/21

SECONDARY ACCESSION(S): PRJNA231750

REPOSITORIES: GEO

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Transcriptomic analysis of the role of Rim101 in the adaptation of Ustilago maydis to an alkaline environment

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

Malassezia responds to environmental pH signals through the conserved Rim/Pal pathway

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

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

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

2018-01-18 | GSE109291 | GEO

WT vs rim101 mutant gene expression under capsule inducing conditions

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

C. neoformans gene expression in DMEM of WT and rim101 mutant cells

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

C. neoformans gene expression in DMEM of WT and rim101 mutant cells

2013-02-02 | E-GEOD-43189 | biostudies-arrayexpress

Adaptation to pH and pH signaling in the phytopathogenic fungus Botrytis cinerea

Project description:The grey mould fungus Botrytis cinerea is capable of developing on a wide variety of host plants and different organs that differ greatly in their pH values. The strategy developed by this necrotrophic fungus is partly based on the acidification of the plant tissues via the secretion of several organic acids including oxalic acid. That’s why B.cinerea is considered as an “acidic” fungus. However, we have previously shown that it is also capable of alkalinizing its ambient environment during sunflower cotyledons or bean leaves infection and that the alkalinization is achieved by amino acids catabolism and ammonia secretion ( Billon-grand et al, 2012). This capacity to modulate the surrounding pH reveals also an ability to regulate the expression and the secretion of an arsenal of enzymes in order to produce virulence factors in accordance with the ambient pH and enzymes requirement for optimal activity. Expression of pH-regulated genes is controlled by the highly conserved signaling pathway Pal/Pac that leads to activation of the zinc finger transcription factor PACC under neutral or alkaline conditions. Investigations of the role of this pH regulator in the infectious process of B.cinerea are presented.

2021-09-13 | PXD004145 | Pride

Transcriptomic changes in the PacC transcription factor deletion mutant of the plant pathogenic fungus Botrytis cinerea

Project description:Botrytis cinerea, the causal agent of gray mold, is a necrotrophic fungus that can infect a wide variety of plant species and plant tissues. During infection, this pathogen modulates the pH of its environment by secreting organic acids or ammonia. Deletion of the gene encoding the pH-responsive transcription factor PacC revealed the importance of this regulator in different steps of the infection process and particularly in the secretion of organics acids, reactive oxygen species and plant cell wall degrading enzymes. This study aimed to identify the regulatory networks controlled by this fungus-specific transcription factor when the fungus is placed under acidic or alkaline conditions.

2024-08-20 | GSE265877 | GEO

Global transcriptome analysis of the pH regulator pacC in Colletotrichum gloeosporioides

Project description:Colletotrichum gloeosporioides, a widely distributed economically important agent in postharvest fruit disease thrives by massive secretion of ammonia to alkalize its environment and activate its pathogenicity genes. We sequenced the C. gloeosporioides transcriptomes of WT and a ∆pacC mutant, a major gene regulator under changing pH, under pH 7.0 in order to examine pacC regulation. Transcriptome analysis of the ∆pacC strain showed that 468 and 458 genes were up or down regulated, respectively. Both the up and down regulated genes were clustered into similar functions including: transporters to maintain cellular homeostasis, cell wall degrading enzymes to optimize pathogenicity and GATA-like transcription factors. Suggesting that activation of pacC under alkaline condition regulates genes expression to fit their optimal PKa. The transcript level predictions were verified by growth in different pH and fruit infection. Further analyses showed pacC binding sites were over-represented in the promoters of the pacC up-regulated genes but not in the promoters of the down-regulated genes, where instead, GATA-like binding sites were prominent. Evolutionary conservation of pacC control was sought by examining the gene orthologs in 5 fungal genomes whose members display contrasting alkaline or acidifying pathogenicity strategies. The results showed that irrespective of pathogen colonization strategy, only orthologs of up-regulated genes showed over-representation of pacC binding sites. Significantly, the down regulated orthologs revealed cross-genome over-representation of GATA transcription factor binding sites. Thus, pacC is a phylogenetically conserved fungal mechanism exerting dual pH control for maintaining homeostasis and pathogenicity in changing environments.

2013-11-21 | GSE41844 | GEO

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

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

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