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PMID:22696683

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Citation

McIsaac, RS, Petti, AA, Bussemaker, HJ and Botstein, D (2012) Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Mol. Biol. Cell 23:2993-3007

Abstract

In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also on many other physiological functions in the cell. Recently we characterized a gene induction system that, upon the addition of an inducer, results in near-immediate transcription of a gene of interest under physiological conditions. We used this to perturb levels of single transcription factors during steady-state growth in chemostats, which facilitated distinction of direct from indirect effects of individual factors dynamically through quantification of the subsequent changes in genome-wide patterns of gene expression. We were able to show directly that Cbf1p acts sometimes as a repressor and sometimes as an activator. We also found circumstances in which Met31p/Met32p function as repressors, as well as those in which they function as activators. We elucidated and numerically modeled feedback relationships among the regulators, notably feedforward regulation of Met32p (but not Met31p) by Met4p that generates dynamic differences in abundance that can account for the differences in function of these two proteins despite their identical binding sites.

Links

PubMed PMC3408425 Online version:10.1091/mbc.E12-03-0232

Keywords

5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/deficiency; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/physiology; Binding Sites; DNA-Binding Proteins/genetics; DNA-Binding Proteins/physiology; F-Box Proteins/genetics; F-Box Proteins/metabolism; Gene Expression Regulation, Fungal; Genome, Fungal; Methionine/biosynthesis; Methionine/genetics; Methionine/metabolism; Protein Binding; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae/metabolism; Saccharomyces cerevisiae Proteins/genetics; Saccharomyces cerevisiae Proteins/metabolism; Saccharomyces cerevisiae Proteins/physiology; Sulfur/metabolism; Sulfur/physiology; Transcription Factors/genetics; Transcription Factors/physiology; Transcription, Genetic; Ubiquitin/metabolism; Ubiquitin-Protein Ligase Complexes/genetics; Ubiquitin-Protein Ligase Complexes/metabolism

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

YEAST:CBF1

involved_in

GO:0000122: negative regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:CBF1

involved_in

GO:0045944: positive regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MET32

involved_in

GO:0000122: negative regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MET32

involved_in

GO:0045944: positive regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MET4

involved_in

GO:0045944: positive regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MET31

involved_in

GO:0000122: negative regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

YEAST:MET31

involved_in

GO:0045944: positive regulation of transcription by RNA polymerase II

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

Notes

See also

References

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