Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Specific Roles for the Ccr4-Not Complex Subunits in Expression of the Genome

ABSTRACT: These Affymetrix data were used to determine the role of each non-essential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast S. cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene de-regulation were observed upon deletion of any given subunit, revealing the specificity of each subunit’s function. Consistently, the purification of the Ccr4-Not complex through Caf40p by tandem affinity purification from wild-type cells or cells lacking individual subunits of the Ccr4-Not complex revealed that each subunit had a particular impact on complex integrity. Furthermore, the micro-arrays revealed that the role of each subunit was specific to the growth conditions. From the study of only two different growth conditions, revealing an impact of the Ccr4-Not complex on more than 85% of all studied genes, we can infer that the Ccr4-Not complex is important for expression of most of the yeast genome. Keywords: genetic modification, stress response Wild-type and not2?, not3?, not4?, not5?, caf1?, caf130? and ccr4? null strains were grown in glucose rich medium to exponential phase and collected. Wild-type and not2?, not4?, caf1?, caf130? and ccr4? null strains were also grown in glucose rich medium to glucose depletion and collected 30 min after glucose depletion. Each sample was prepared twice independently. One array from the caf1? strain grown to glucose depletion, and one from the not5? and not4? strains growing exponentially were found to be problematic and discarded. A not5? sample was not prepared after glucose depletion, because it flocculates in that condition.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Martine Collart

PROVIDER: E-GEOD-10521 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Specific roles for the Ccr4-Not complex subunits in expression of the genome.

Azzouz Nowel N Panasenko Olesya O OO Deluen Cécile C Hsieh Julien J Theiler Grégory G Collart Martine A MA

RNA (New York, N.Y.) 20090120 3

In this work we used micro-array experiments to determine the role of each nonessential subunit of the conserved Ccr4-Not complex in the control of gene expression in the yeast Saccharomyces cerevisiae. The study was performed with cells growing exponentially in high glucose and with cells grown to glucose depletion. Specific patterns of gene deregulation were observed upon deletion of any given subunit, revealing the specificity of each subunit's function. Consistently, the purification of the ...[more]

PMID: 19155328

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Project description:The transmission of the malaria parasite between mosquitoes and mammals requires translational repression to ensure that only the proper proteins are expressed at the right time, while still allowing the parasite to prepare the mRNAs it will need for the next developmental stage. With relatively few known specific transcription factors (ApiAP2 family) that may specifically initiate gene transcription, Plasmodium parasites also regulate the stability and turnover of transcripts to provide more comprehensive gene regulation. The CAF1/CCR4/NOT complex has been shown in model organisms to be important for not only mRNA degradation, but also translational control through its deadenylases CAF1 and CCR4. However, few proteins that impose translational repression in Plasmodium sexual stages are known, and those that are characterized primarily affect female gametocytes. Therefore, we have characterized two deadenylases and have uncovered their roles in transmission. We have identified and characterized CCR4-1, which we show plays a role in activating male gametocytes, stabilizing transcripts in gametocytes, and regulating host-to-vector transmission. We find that when ccr4-1 is genetically deleted, there is a loss in the coordination of male gametocyte activation and a reduction in the ability of the parasite to productively infect the mosquito, which is independent of its effect upon male activation. Comparative RNA-seq shows that the deletion of ccr4-1 affects many transcripts that are translationally repressed in females, are related to male gamete function, and/or are important for early mosquito stage development. In contrast, we found that genetic deletion of the major deadenylase Caf1 is lethal. However, we observed that expression of only the N-terminal Caf1 domain is permissive, yet prevents proper complex assembly and phenocopies the ccr4-1 deletion. We therefore conclude that the general and transmission-specialized deadenylases of the CAF1/CCR4/NOT complex play critical and intertwined roles in parasite growth and transmission.

Dataset Information

Specific Roles for the Ccr4-Not Complex Subunits in Expression of the Genome

Publications

Specific roles for the Ccr4-Not complex subunits in expression of the genome.

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