Reference: Pir P, et al. (2008) Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. cerevisiae. Yeast 25(9):661-72

Reference Help

Abstract


The transcriptional and metabolic impact of deleting one or both copies of a respiration-related gene has been studied in glucose-limited chemostats. Integration of literature information on phenotype with our exometabolome and transcriptome data enabled the identification of novel relationships between gene copy number, transcriptional regulation and phenotype. We found that the effect of complete respiratory deficiency on transcription was limited to downregulation of genes involved in oxidoreductase activity and iron assimilation. Partial respiratory deficiency had no significant impact on gene transcription. Changes in the copy number of two transcription-factor genes, HAP4 and MIG1, had a major impact on genes involved in mitochondrial function. Regulation of respiratory chain components encoded in the nucleus and mitochondria appears to be divided between Hap4p and Oxa1p, respectively. Similarly, repression of respiration may be imposed by the action of Mig1p and Mba1p on nuclear and mitochondrial gene expression, respectively. However, it is not clear whether Oxa1p and Mba1p regulate mitochondrial gene expression via their interaction with mitochondrial ribosomes or by some indirect means. The phenotype of nuclear petite mutants may not simply be due to the absence of respiration; e.g. Oxa1p or Bcs1p may play a role in the regulation of ribosome assembly in the nucleolus. Integration between respiration and cell growth may also result from the action of a single transcription factor. Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient-limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy. Copyright (c) 2008 John Wiley & Sons, Ltd.

Reference Type
Journal Article
Authors
Pir P, Kirdar B, Hayes A, Onsan ZI, Ulgen KO, Oliver SG
Primary Lit For
Additional Lit For
Review For

Interaction Annotations


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.

Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

Phenotype Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details.

Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Regulation Annotations


Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, SPELL, or YeastMine.

Regulator Target Experiment Assay Construct Conditions Strain Background Reference