Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae
Cells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase fa...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2017-07-01
|
| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.117.041814 |
| _version_ | 1819008908912492544 |
|---|---|
| author | Siwen Wang Zheng Xing Pete E. Pascuzzi Elizabeth J. Tran |
| author_facet | Siwen Wang Zheng Xing Pete E. Pascuzzi Elizabeth J. Tran |
| author_sort | Siwen Wang |
| collection | DOAJ |
| description | Cells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase family in Saccharomyces cerevisiae, has been proposed to integrate gene expression with cellular metabolism. Prior work from our laboratory has reported the necessity of DBP2 in proper gene expression, particularly for genes involved in glucose-dependent regulation. Here, by comparing differentially expressed genes in dbp2∆ to those of 700 other deletion strains from other studies, we find that CYC8 and TUP1, which form a complex and inhibit transcription of numerous genes, corepress a common set of genes with DBP2. Gene ontology (GO) annotations reveal that these corepressed genes are related to cellular metabolism, including respiration, gluconeogenesis, and alternative carbon-source utilization genes. Consistent with a direct role in metabolic gene regulation, loss of either DBP2 or CYC8 results in increased cellular respiration rates. Furthermore, we find that corepressed genes have a propensity to be associated with overlapping long noncoding RNAs and that upregulation of these genes in the absence of DBP2 correlates with decreased binding of Cyc8 to these gene promoters. Taken together, this suggests that Dbp2 integrates nutrient availability with energy homeostasis by maintaining repression of glucose-repressed, Cyc8-targeted genes across the genome. |
| first_indexed | 2024-12-21T00:47:57Z |
| format | Article |
| id | doaj.art-d6e55c4e54304ccb9c765ecc03c6c03a |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-21T00:47:57Z |
| publishDate | 2017-07-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-d6e55c4e54304ccb9c765ecc03c6c03a2022-12-21T19:21:28ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-07-01772235224710.1534/g3.117.04181421Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiaeSiwen WangZheng XingPete E. PascuzziElizabeth J. TranCells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase family in Saccharomyces cerevisiae, has been proposed to integrate gene expression with cellular metabolism. Prior work from our laboratory has reported the necessity of DBP2 in proper gene expression, particularly for genes involved in glucose-dependent regulation. Here, by comparing differentially expressed genes in dbp2∆ to those of 700 other deletion strains from other studies, we find that CYC8 and TUP1, which form a complex and inhibit transcription of numerous genes, corepress a common set of genes with DBP2. Gene ontology (GO) annotations reveal that these corepressed genes are related to cellular metabolism, including respiration, gluconeogenesis, and alternative carbon-source utilization genes. Consistent with a direct role in metabolic gene regulation, loss of either DBP2 or CYC8 results in increased cellular respiration rates. Furthermore, we find that corepressed genes have a propensity to be associated with overlapping long noncoding RNAs and that upregulation of these genes in the absence of DBP2 correlates with decreased binding of Cyc8 to these gene promoters. Taken together, this suggests that Dbp2 integrates nutrient availability with energy homeostasis by maintaining repression of glucose-repressed, Cyc8-targeted genes across the genome.http://g3journal.org/lookup/doi/10.1534/g3.117.041814helicaseDEAD-boxmetabolismCyc8Dbp2 |
| spellingShingle | Siwen Wang Zheng Xing Pete E. Pascuzzi Elizabeth J. Tran Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae G3: Genes, Genomes, Genetics helicase DEAD-box metabolism Cyc8 Dbp2 |
| title | Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae |
| title_full | Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae |
| title_fullStr | Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae |
| title_full_unstemmed | Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae |
| title_short | Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae |
| title_sort | metabolic adaptation to nutrients involves coregulation of gene expression by the rna helicase dbp2 and the cyc8 corepressor in saccharomyces cerevisiae |
| topic | helicase DEAD-box metabolism Cyc8 Dbp2 |
| url | http://g3journal.org/lookup/doi/10.1534/g3.117.041814 |
| work_keys_str_mv | AT siwenwang metabolicadaptationtonutrientsinvolvescoregulationofgeneexpressionbythernahelicasedbp2andthecyc8corepressorinsaccharomycescerevisiae AT zhengxing metabolicadaptationtonutrientsinvolvescoregulationofgeneexpressionbythernahelicasedbp2andthecyc8corepressorinsaccharomycescerevisiae AT peteepascuzzi metabolicadaptationtonutrientsinvolvescoregulationofgeneexpressionbythernahelicasedbp2andthecyc8corepressorinsaccharomycescerevisiae AT elizabethjtran metabolicadaptationtonutrientsinvolvescoregulationofgeneexpressionbythernahelicasedbp2andthecyc8corepressorinsaccharomycescerevisiae |