Dataset Information

A systems biology study in yeast

ABSTRACT: Not available

OTHER RELATED OMICS DATASETS IN: MTBLS8

INSTRUMENT(S): instrument model

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Jennifer Siepen

PROVIDER: PRD000086 | Pride | 2009-07-28

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_8761.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_8761.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_8761.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_8762.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_8762.pride.mztab.gz	Mztab

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Publications

Growth control of the eukaryote cell: a systems biology study in yeast.

Castrillo Juan I JI Zeef Leo A LA Hoyle David C DC Zhang Nianshu N Hayes Andrew A Gardner David Cj DC Cornell Michael J MJ Petty June J Hakes Luke L Wardleworth Leanne L Rash Bharat B Brown Marie M Dunn Warwick B WB Broadhurst David D O'Donoghue Kerry K Hester Svenja S SS Dunkley Tom Pj TP Hart Sarah R SR Swainston Neil N Li Peter P Gaskell Simon J SJ Paton Norman W NW Lilley Kathryn S KS Kell Douglas B DB Oliver Stephen G SG

Journal of biology 20070101 2

<h4>Background</h4>Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.<h4>Results</h4>Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rat ...[more]

PMID: 17439666

Similar Datasets

Project description:Control of growth rate is mediated by tight regulation mechanisms in all free-living organisms since long-term survival depends on adaptation to diverse environmental conditions. The yeast, Saccharomyces cerevisiae, when growing under nutrient-limited conditions, controls its growth rate via both nutrient-specific and nutrient-independent gene sets. At slow growth rates, at least, it has been found that the expression of the genes that exert significant control over growth rate (high flux control or HFC genes) is not necessarily regulated by growth rate itself. It has not been determined whether the set of HFC genes is the same at all growth rates or whether it is the same in conditions of nutrient limitation or excess.HFC genes were identified in competition experiments in which a population of hemizygous diploid yeast deletants were grown at, or close to, the maximum specific growth rate in either nutrient-limiting or nutrient-sufficient conditions. A hemizygous mutant is one in which one of any pair of homologous genes is deleted in a diploid, These HFC genes divided into two classes: a haploinsufficient (HI) set, where the hemizygous mutants grow slower than the wild type, and a haploproficient (HP) set, which comprises hemizygotes that grow faster than the wild type. The HI set was found to be enriched for genes involved in the processes of gene expression, while the HP set was enriched for genes concerned with the cell cycle and genome integrity.A subset of growth-regulated genes have HFC characteristics when grown in conditions where there are few, or no, external constraints on the rate of growth that cells may attain. This subset is enriched for genes that participate in the processes of gene expression, itself (i.e. transcription and translation). The fact that haploproficiency is exhibited by mutants grown at the previously determined maximum rate implies that the control of growth rate in this simple eukaryote represents a trade-off between the selective advantages of rapid growth and the need to maintain the integrity of the genome.

Project description:BackgroundCell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking.ResultsMetabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth.ConclusionThis work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell.