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Cryptococcus neoformans

ABSTRACT: RNA-Seq analysis of ada2Δ, nrg1Δ and cir1Δ and KN99α wildtype cells in capsule inducing and non-inducing conditions

PROVIDER: PRJNA155303 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR342865.fastq.gz	Fastqsanger.gz
	SRR342866.fastq.gz	Fastqsanger.gz
	SRR342867.fastq.gz	Fastqsanger.gz
	SRR342868.fastq.gz	Fastqsanger.gz
	SRR342869.fastq.gz	Fastqsanger.gz

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Toward an integrated model of capsule regulation in Cryptococcus neoformans

Project description:This SuperSeries is composed of the following subset Series: GSE31911: Cryptococcal H99 cells grown in 8 conditions for capsule induction GSE32049: RNA-Seq analysis of ada2?, nrg1? and cir1? and KN99? wildtype cells in capsule inducing and non-inducing conditions GSE32075: ChIP-Seq of H3K9 acetylation for wildtype and ada2? cells in Cryptococcus neoformans Refer to individual Series

2011-12-10 | E-GEOD-32228 | biostudies-arrayexpress

Unraveling capsule biosynthesis and signaling networks in Cryptococcus neoformans

Project description:Cryptococcus neoformans is an opportunistic basidiomycete pathogen that is a major etiological agent of fungal meningoencephalitis leading to more than 180,000 deaths worldwide annually. For this pathogen, the polysaccharide capsule is a key virulence factor, which interferes with the phagocytosis by host innate immune cells, but its complex signaling networks remain elusive. In this study, we systematically analyzed capsule biosynthesis and signaling networks by using C. neoformans transcription factor (TF) and kinase mutant libraries under diverse capsule-inducing conditions, such as Dulbecco’s Modified Eagle’s (DME), Littman’s medium (LIT) and fetal bovine serum (FBS) medium. We found that deletion of GAT201, YAP1, BZP4, and ADA2 consistently causes capsule production defects in all tested media, indicating that they are capsule-regulating core TFs. Epistatic and expression analysis showed that Yap1 and Ada2 control Gat201 upstream, whereas Bzp4 and Gat201 regulate capsule production independently. We next searched for potential upstream kinases and found that mutants deleted of PKA1, BUD32, POS5, IRE1 or CDC2801 showed reduced capsule production under all three capsule induction conditions, whereas mutants deleted of HOG1 and IRK5 displayed enhanced capsule production. Notably, Pka1 and Irk5 controls induction of GAT201 and BZP4, respectively, under capsule induction condition. Finally, we monitored transcriptome profiles governed by Bzp4, Gat201, and Ada2 under capsule-inducing condition and demonstrated that these TFs regulate redundant and unique sets of downstream target genes. In conclusion, this study provides further insight into the complex regulatory mechanism of capsule production related signaling pathways in C. neoformans.

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Cryptococcus neoformans var. grubii

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RNA-Seq analysis of ada2M-NM-^T, nrg1M-NM-^T and cir1M-NM-^T and KN99M-NM-1 wildtype cells in capsule inducing and non-inducing conditions

Project description:To contextualize the cryptococcal Spt-Ada-Gcn5 Acetyltransferase (SAGA) member Ada2 in the capsule regulatory network, RNA-Seq was performed on wildtype, ada2M-NM-^T and two other transcription factors, nrg1M-NM-^T and cir1M-NM-^T, which like ada2M-NM-^T are also defective for capsule formation, virulence and filamentation. Mutant and wildtype cells were grown in capsule inducing and non-inducing conditions for 90 minutes and transcriptional profiling was performed by RNA-Seq analysis.

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Transcriptome of ex vivo-sorted and in vitro-grown Cryptococcus neoformans cells

Project description:We compared the transcriptome of subpopulations of Cryptococcus neoformans cells within the lungs and C. neoformans cells cultured in capsule repressing medium, capsule inducing medium, and capsule inducing medium with the addition of 10% conditioned medium from cells grown in capsule repressing medium. The aim of the study was to identify genes that regulate C. neoformans cell body and capsule size reductions.

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Project description:Purpose: Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying TFs involved in a specific process and used it to map regulation of the key virulence factor of Cryptococcus neoformans, its capsule. Results: The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, mid-level, and “foreman” TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of 41 TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. Conclusions: These data resources and analyses provide the first integrated, systems level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to labs focused on specific physiological processes. A total of 288 expression profiles were generated by RNA-Seq analysis of Mutant and wildtype cells grown in capsule inducing conditions for 90 minutes. In addition, 3 replicate expression profiles were generated for wildtype cells grown in : a capsule non-inducing condition, a capsule inducing condition for 180 minutes, a capsule inducing condition for 480 minutes, and a capsule inducing condition for 1440 minutes. In addition, ChIP-seq of NRG1(CNAG_05222) in capsule inducing conditions, and USV101(CNAG_05420) in both capsule inducing and non-inducing conditions were generated.

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Project description:RNA-Seq of Cryptococcus neoformans var. grubii grown under all combinations of several capsule inducing conditions

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Project description:Cryptococcal H99 cells grown in 8 conditions for capsule induction

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How host-like signals drive gene expression and gene expression drives capsule growth in Cryptococcus neoformans [ep_wt]

Project description:Cryptococcus neoformans is a fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth in response to host-like conditions. To understand how individual host-like signals affect capsule size and gene expression, we grew cells with and without all combinations of 5 signals suspected of affecting capsule size: Tissue-culture medium (DMEM or RPMI), temperature (37°C), CO2 (5%), and the addition of HEPES buffer. For each combination of conditions, we grew cultures with or without exogenous cAMP, and sampled cells for RNA-Seq at 0, 30, 90, 180, 1440 minutes and for measurement of capsule thickness at 1440 min. We also took samples for RNA-Seq at 30, 90, 180, 1440 minutes and carried out RNA-Seq in quadruplicate.

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