Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Biofilm matrix regulation by Candida albicans Zap1

ABSTRACT: The Zap1 ChIP-chips were performed in a/alpha cell types using C-terminally Myc-tagged proteins and Myc antibodies. ChIPs were performed on 48 hour biofilm cells grown in Spider medium. Two biological replicates were performed, and normalized data is reported in matrix. Myc tagged strains were compared to untagged control strains.

ORGANISM(S): Candida albicans

SUBMITTER: Clarissa Nobile

PROVIDER: E-GEOD-29785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Biofilm matrix regulation by Candida albicans Zap1.

Nobile Clarissa J CJ Nett Jeniel E JE Hernday Aaron D AD Homann Oliver R OR Deneault Jean-Sebastien JS Nantel Andre A Andes David R DR Johnson Alexander D AD Mitchell Aaron P AP

PLoS biology 20090616 6

A biofilm is a surface-associated population of microorganisms embedded in a matrix of extracellular polymeric substances. Biofilms are a major natural growth form of microorganisms and the cause of pervasive device-associated infection. This report focuses on the biofilm matrix of Candida albicans, the major fungal pathogen of humans. We report here that the C. albicans zinc-response transcription factor Zap1 is a negative regulator of a major matrix component, soluble beta-1,3 glucan, in both ...[more]

PMID: 19529758

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Project description:Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C-terminus that recognizes Pol II CTD peptides phosphorylated on Ser2, Ser5 or Try1 in vitro. Deleting the tSH2 domain, however, only has a partial effect on Spt6 occupancy in vivo, suggesting that more complex mechanisms are involved in the Spt6 recruitment. Our results show that the Ser2 kinases Bur1 and Ctk1, but not the Ser5 kinase Kin28, cooperate in recruiting Spt6, genome-wide. Interestingly, the Ser2 kinases promote the association of Spt6 in early transcribed regions and not toward the 3' end of genes, where phosphorylated Ser2 reaches its maximum level. Additionally, our results uncover an unexpected role for histone deacetylases (Rpd3 and Hos2) in promoting Spt6 interaction with elongating Pol II. Finally, our data suggest that phosphorylation of the Pol II CTD on Tyr1 promotes the association of Spt6 with the 3' end of transcribed genes, independently of Ser2 phosphorylation. Collectively, our results show that a complex network of interactions, involving the Spt6 tSH2 domain, CTD phosphorylation and histone deacetylases, coordinate the recruitment of Spt6 to transcribed genes in vivo. We examined the genome-wide distribution (using ChIP-chip) of Spt6. Spt6 occupancy was also assayed in mutants for CTD Serine 2 and Serine 5 kinases and in mutants for histone deacetylases. ChIPs were performed with a Myc-tagged version of Spt6. Most ChIPs (in Cy5) were hybridyzed against a control ChIP sample from an isogenic non-tagged strain (in Cy3). In the ChIP experiments with the spt6-202del mutant, non immunoprecipitated DNA (input) was used as the control. In addition to Spt6 ChIPs, the project includes RNAPII (Rpb3) ChIP-chip datasets, where an anti-Rpb3 antibody was used to ChIP RNAPII and non immunoprecipitated DNA (input) was used as the control. All ChIP-chip experiments were done in duplicates. Each microarray was normalized using the Lima Loess and replicates were combined using a weighted average method as previously described (Pokholok et al., 2005).

Dataset Information

Biofilm matrix regulation by Candida albicans Zap1

Publications

Biofilm matrix regulation by Candida albicans Zap1.

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