A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen
Ontology highlight
ABSTRACT:
ORGANISM(S): Ajellomyces capsulatus
SUBMITTER: Mark Voorhies
PROVIDER: E-GEOD-47832 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi. This submission gives the expression profiling results. cDNA from each ryp mutants and wild-type controls was labeled with Cy5 and competitively hybridized against the Cy3-labeled pooled reference sample using H. capsulatum whole-genome 70-mer oligonucleotide microarray. For the experiments with ryp T-DNA mutants, there were 4 to 6 replicates for each strain and condition, and for the experiments with ryp knockdown strains, there were 3 to 12 replicates for each strain and condition. The T-DNA and knockdown experiments are being submitted as separate series, with samples further divided based on G217B platform version.
2013-06-14 | E-GEOD-46936 | biostudies-arrayexpress
Project description:The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi. This submission gives the expression profiling results. cDNA from each ryp mutants and wild-type controls was labeled with Cy5 and competitively hybridized against the Cy3-labeled pooled reference sample using H. capsulatum whole-genome 70-mer oligonucleotide microarray. For the experiments with ryp T-DNA mutants, there were 4 to 6 replicates for each strain and condition, and for the experiments with ryp knockdown strains, there were 3 to 12 replicates for each strain and condition. The T-DNA and knockdown experiments are being submitted as separate series, with samples further divided based on G217B platform version.
2013-06-14 | E-GEOD-46939 | biostudies-arrayexpress
Project description:The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi. This submission gives the expression profiling results. cDNA from each ryp mutants and wild-type controls was labeled with Cy5 and competitively hybridized against the Cy3-labeled pooled reference sample using H. capsulatum whole-genome 70-mer oligonucleotide microarray. For the experiments with ryp T-DNA mutants, there were 4 to 6 replicates for each strain and condition, and for the experiments with ryp knockdown strains, there were 3 to 12 replicates for each strain and condition. The T-DNA and knockdown experiments are being submitted as separate series, with samples further divided based on G217B platform version.
2013-06-14 | E-GEOD-46937 | biostudies-arrayexpress
Project description:The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi. This submission gives the expression profiling results. cDNA from each ryp mutants and wild-type controls was labeled with Cy5 and competitively hybridized against the Cy3-labeled pooled reference sample using H. capsulatum whole-genome 70-mer oligonucleotide microarray. For the experiments with ryp T-DNA mutants, there were 4 to 6 replicates for each strain and condition, and for the experiments with ryp knockdown strains, there were 3 to 12 replicates for each strain and condition. The T-DNA and knockdown experiments are being submitted as separate series, with samples further divided based on G217B platform version.
2013-06-14 | E-GEOD-46938 | biostudies-arrayexpress
Project description:Recent work has shown that small non-coding RNAs, including miRNAs, serve an important role in controlling gene expression during development and disease. However, little detailed information exists concerning the relative expression patterns of small RNAs during development of C. elegans. Here we use recent advances in high-throughput sequencing technology to show that expression of non-coding small RNAs, including miRNAs, changes dynamically during development and in the different sexes of C. elegans; approximately 16% of known miRNAs changed over 10 fold in expression during C. elegans development and about 12% of miRNAs showed major changes in expression between males and hermaphrodites of C. elegans. These results should lead to a better understanding of the expression and function of small RNAs in C. elegans development. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Examination of small RNA expression in six different developmental stages of hermaphrodites (Embryo, mid-L1, mid-L2, mid-L3, mid-L4, young adult), and young adult males (dpy-28;him-8) and spermatogenesis-defective young adult hermaphrodites (spe-9). The number of sequence reads for miRNA was assessed from the raw sequence data from Solexa sequencing using perfect sequence matching to known miRNAs (miRBase Release 11.0).
2008-12-01 | E-GEOD-13339 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-06-22 | E-GEOD-66893 | biostudies-arrayexpress
Project description:The ability to grow at host temperature is a critical trait for most pathogenic microbes of humans. Thermally dimorphic fungal pathogens, including Histoplasma capsulatum, are a class of soil fungi that undergo a dramatic change in cell shape and virulence gene expression in response to host temperature. Here we elucidate a complex temperature-responsive network in H. capsulatum, which switches from an environmental filamentous form to a pathogenic yeast form. We dissect the circuit driven by three regulators that control yeast-phase growth, and demonstrate that these factors, including two deeply conserved Velvet family proteins of unknown function, associate with DNA. We identify and characterize a fourth regulator of this pathway, and define cis-acting motifs that recruit these transcription factors to a tightly interwoven network of temperature-responsive target genes. Our results provide the first comprehensive analysis of the complex transcriptional network that links temperature to morphology and virulence in thermally dimorphic fungi. This submission gives the chromatin immunoprecipitation results. For each of the four Ryp proteins, ChIP vs. input hybridizations were performed for three replicate immunoprecipitations from the wild-type strain and two negative control replicates from the corresponding mutant strain.
2013-06-14 | E-GEOD-47341 | biostudies-arrayexpress
Project description:Like many microalgae unicellular green alga, Chlamydomonas reinhardtii also accumulates energy rich storage lipid and starch under nutrient-limited conditions, such as phosphorus (P) and nitrogen (N) limitation. To dissect the transcriptional regulation of lipid and starch biosynthesis in response to nutrient limitation, we have characterized the biological role of a candidate regulator: the MYB family transcription factor, PSR1 (phosphorus starvation response 1). Genetically modified (psr1 compromised) and wild-type lines were grown under P limiting and sufficient conditions and assayed at two time points by SOLiD RNA-seq.
2016-01-08 | E-MTAB-2556 | biostudies-arrayexpress
Project description:Transcriptomic analysis of Bacillus subtilis hfq mutant in exponential phase of growth. Wild-type strain and hfq mutant cells in exponentially growth phase were subjected to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. Hfq does not appear to influence B.subtilis RNA patterns during the exponential phase to any significant extent, at least in cells grown in rich medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined at OD ~0.5 in LB medium. Two biological replicates were analyzed.
2015-06-22 | E-GEOD-66891 | biostudies-arrayexpress
Project description:Transcriptomic analysis of Bacillus subtilis wild-type strain and hfq mutant in stationary phase of growth using to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. 97 transcription units (representing 134 genes) were found significantly different between the wild-type and the ?hfqBs strains in the stationary cultures performed in rich LB medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined 5 h after the onset of stationary phase in LB medium. Two biological replicates were analyzed.
2015-06-22 | E-GEOD-66892 | biostudies-arrayexpress