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

ABSTRACT: To contextualize the cryptococcal Spt-Ada-Gcn5 Acetyltransferase (SAGA) member Ada2 in the capsule regulatory network, RNA-Seq was performed on wildtype, ada2Δ and two other transcription factors, nrg1Δ and cir1Δ, which like ada2Δ are also defective for capsule formation, virulence and filamentation.

ORGANISM(S): Cryptococcus neoformans

PROVIDER: GSE32049 | GEO | 2012/01/01

SECONDARY ACCESSION(S): PRJNA155303

REPOSITORIES: GEO

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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.

2012-01-01 | E-GEOD-32049 | biostudies-arrayexpress

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.

2022-10-18 | GSE208163 | GEO

WT vs gcn5 mutant gene expression under capsule inducing conditions

Project description:Cryptococcus neoformans is an environmental fungus and an opportunistic human pathogen. Previous studies have demonstrated major alterations in its transcriptional profile as this microorganism enters the hostile environment of the human host. To assess the role of chromatin remodeling in host-induced transcriptional responses, we identified the C. neoformans Gcn5 histone acetyltransferase and demonstrated its function by complementation studies of Saccharomyces cerevisiae. The C. neoformans gcn5Δ mutant strain has defects in high-temperature growth and capsule attachment to the cell surface, in addition to increased sensitivity to FK506 and oxidative stress. Treatment of wild-type cells with the histone acetyltransferase inhibitor garcinol mimics cellular effects of the gcn5Δ mutation. Gcn5 regulates the expression of many genes that are important in responding to the specific environmental conditions encountered by C. neoformans inside the host. Accordingly, the gcn5Δ mutant is avirulent in animal models of cryptococcosis. Our study demonstrates the importance of chromatin remodeling by the conserved histone acetyltransferase Gcn5 in regulating the expression of specific genes that allow C. neoformans to respond appropriately to the human host.

2010-09-04 | GSE23948 | GEO

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription

Project description:Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the non-acetyl histone lysine acylation modifications such as crotonylation, butyrylation and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.

2019-11-06 | PXD015488 | Pride

LC-MS/MS identification of Kbz sites on histones catalyzed by non-enzymatic and enzymatic ways.

Project description:Histone lysine benzoylation may occur by Gcn5-catalyzed and nonenzymatically ways in vivo. In this project, we identified several Kbz sites on Xenopus laevis octamer in the absence or presence Gcn5-Ada2 complex in vitro, respectively. The number 672 represents the data in the absence of Gcn5-Ada2, and the number 674 represents the data that in the presence of Gcn5-Ada2.

2022-05-19 | PXD030110 | Pride

The role of the central region of Ada2 in gene regulation

Project description:The SAGA complex of Saccharomyces cerevisiae contains greater than 20 components that acetylate and deubiquitylate nucleosomal histones. Its acetyltransferase, Gcn5 preferentially acetylates histones H3 and H2B and is regulated through interactions with Ada2 and Ngg1/Ada3. The N-terminal region of Ada2 contains a SANT domain that contacts Gcn5 near its catalytic site. Sequence alignments of Ada2 homologues indicate a conserved ~120 amino acid residue central region that interacts with Ngg1.To examine the function of this central region, we constructed ada2 alleles with mutations of clustered conserved residues. One of these alleles, ada2-RLR, resulted in a ~3-fold reduction in transcriptional activation of the PHO5 gene and growth changes that parallel deletion of ada2. Microarray analyses further revealed that ada2-RLR alters expression of a subset of those genes affected by deletion of ada2. Keywords: yeast, Ada2, SAGA complex, gene expression, genetic modification

2008-11-11 | GSE11377 | GEO

Inhibition of histone acetyltransferase GCN5 by a transcription factor FgPacC controls fungal adaption to host-derived iron stress

Project description:Fg infection induces host alkalinization, and the pH-dependent transcription factor FgPacC undergoes a proteolytic cleavage into the functional isoform named FgPacC30 under alkaline host environment. Subsequently FgPacC30 binds to a GCCAR(R=A/G)G element at the promoters of the genes involved in iron uptake and inhibits their expression, leading to adaption of Fg to high-iron stress. Mechanistically, FgPacC30 binds to FgGcn5 protein, a catalytic subunit of Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, leading to deregulation of histone acetylation at H3K18 and H2BK11, and repression of iron uptake genes.

2022-06-29 | GSE203093 | GEO

Genome wide expression profile of ada1 and gcn5 deletion strains in Saccharomycescerevisiae

Project description:Ada1, Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex component, was isolated as boundary factor that separated silenced chromatin and euchromatin by previous screening, and Ada1 maintains SAGA complex integrity. SAGA complex is one of a histone modification complex that has multiple functions contributing to transcriptional activation. In Saccharomyces cerevisiae, silencing is occurred by Sir protein complex, which deacetylates histones and form high-order chromatin structure. Gcn5, SAGA complex component, has histone acetyltransferase activity, which is considered that antagonize to silencing by the screening. Ada1 and Gcn5 might have different functions in SAGA complex, we performed microarray analysis to find different functions of gene regulations by using ada1Δ and gcn5Δ strains. As the results, Ada1-regulated genes include more than halves of Gcn5-regelated genes, which occupied only a part of Ada1 regulated genes. These suggest that the differences of contribution to SAGA functions. When SAGA complex have a loss of Ada1, almost function was lost. On the other hand, Gcn5 play a role only as acetyltransferase in SAGA complex.

2016-12-01 | GSE73998 | GEO

The ATAC and SAGA coactivator complexes assemble co-translationally, but their cellular localization properties and functions are distinct

Project description:To understand the precise mechanism that guide the formation of multisubunit complexes is of key importance. Nascent proteins can find and bind their interaction partners during their translation, leading to co-translational assembly. Here we demonstrate that the distinct modules of ATAC (ADA Two A Containing) and SAGA (SPT ADA GCN5 Acetyltransferase), two lysine acetyl transferase-containing transcription coactivator complexes, assemble co-translationally in the cytoplasm of mammalian cells. Fully assembled SAGA complex forms in the cytoplasm of mammalian cells and cytoplasmic SAGA acetylates non-histones proteins, before imported in the nucleus. In contrast, ATAC has no cytoplasmic functions as it cannot be detected in the cytoplasm of mammalian cells. However, fully assembled endogenous ATAC complex containing two functional modules forms and functions in the nucleus. Thus, the two related co-activators, ATAC and SAGA, assemble by using co-translational pathways, but their subcellular localization, cytoplasmic detectability and functions are distinct.

2023-09-27 | PXD038695 | Pride

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