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A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

ABSTRACT: This paper presents a new method, steady-state regulatory flux balance analysis (SR-FBA), for predicting gene expression and metabolic fluxes in a large-scale integrated metabolic-regulatory model. Using SR-FBA to study the metabolism of Escherichia coli, we quantify the extent to which the different levels of metabolic and transcriptional regulatory constraints determine metabolic behavior: metabolic constraints determine the flux activity state of 45-51% of metabolic genes, depending on the growth media, whereas transcription regulation determines the flux activity state of 13-20% of the genes. A considerable number of 36 genes are redundantly expressed, that is, they are expressed even though the fluxes of their associated reactions are zero, indicating that they are not optimally tuned for cellular flux demands. The undetermined state of the remaining approximately 30% of the genes suggests that they may represent metabolic variability within a given growth medium. Overall, SR-FBA enables one to address a host of new questions concerning the interplay between regulation and metabolism.

SUBMITTER: Shlomi T

PROVIDER: S-EPMC1865583 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

Shlomi Tomer T Eisenberg Yariv Y Sharan Roded R Ruppin Eytan E

Molecular systems biology 20070417

This paper presents a new method, steady-state regulatory flux balance analysis (SR-FBA), for predicting gene expression and metabolic fluxes in a large-scale integrated metabolic-regulatory model. Using SR-FBA to study the metabolism of Escherichia coli, we quantify the extent to which the different levels of metabolic and transcriptional regulatory constraints determine metabolic behavior: metabolic constraints determine the flux activity state of 45-51% of metabolic genes, depending on the gr ...[more]

PMID: 17437026

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Project description:BackgroundDNA methylation in the 5' promoter regions of genes and microRNA (miRNA) regulation at the 3' untranslated regions (UTRs) are two major epigenetic regulation mechanisms in most eukaryotes. Both DNA methylation and miRNA regulation can suppress gene expression and their corresponding protein product; thus, they play critical roles in cellular processes. Although there have been numerous investigations of gene regulation by methylation changes and miRNAs, there is no systematic genome-wide examination of their coordinated effects in any organism.ResultsIn this study, we investigated the relationship between promoter methylation at the transcription level and miRNA regulation at the post-transcription level by taking advantage of recently released human methylome data and high quality miRNA and other gene annotation data. We found methylation level in the promoter regions and expression level was negatively correlated. Then, we showed that miRNAs tended to target the genes with a low DNA methylation level in their promoter regions. We further demonstrated that this observed pattern was not attributed to the gene expression level, expression broadness, or the number of transcription factor binding sites. Interestingly, we found miRNA target sites were significantly enriched in the genes located in differentially methylated regions or partially methylated domains. Finally, we explored the features of DNA methylation and miRNA regulation in cancer genes and found cancer genes tended to have low methylation level and more miRNA target sites.ConclusionThis is the first genome-wide investigation of the combined regulation of gene expression. Our results supported a complementary regulation between DNA methylation (transcriptional level) and miRNA function (post-transcriptional level) in the human genome. The results were helpful for our understanding of the evolutionary forces towards organisms' complexity beyond traditional sequence level investigation.

Project description:BackgroundGenome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in prokaryotes is one of the critical tasks of modern genomics. Bacteria from different taxonomic groups, whose lifestyles and natural environments are substantially different, possess highly diverged transcriptional regulatory networks. The comparative genomics approaches are useful for in silico reconstruction of bacterial regulons and networks operated by both transcription factors (TFs) and RNA regulatory elements (riboswitches).DescriptionRegPrecise (http://regprecise.lbl.gov) is a web resource for collection, visualization and analysis of transcriptional regulons reconstructed by comparative genomics. We significantly expanded a reference collection of manually curated regulons we introduced earlier. RegPrecise 3.0 provides access to inferred regulatory interactions organized by phylogenetic, structural and functional properties. Taxonomy-specific collections include 781 TF regulogs inferred in more than 160 genomes representing 14 taxonomic groups of Bacteria. TF-specific collections include regulogs for a selected subset of 40 TFs reconstructed across more than 30 taxonomic lineages. Novel collections of regulons operated by RNA regulatory elements (riboswitches) include near 400 regulogs inferred in 24 bacterial lineages. RegPrecise 3.0 provides four classifications of the reference regulons implemented as controlled vocabularies: 55 TF protein families; 43 RNA motif families; ~150 biological processes or metabolic pathways; and ~200 effectors or environmental signals. Genome-wide visualization of regulatory networks and metabolic pathways covered by the reference regulons are available for all studied genomes. A separate section of RegPrecise 3.0 contains draft regulatory networks in 640 genomes obtained by an conservative propagation of the reference regulons to closely related genomes.ConclusionsRegPrecise 3.0 gives access to the transcriptional regulons reconstructed in bacterial genomes. Analytical capabilities include exploration of: regulon content, structure and function; TF binding site motifs; conservation and variations in genome-wide regulatory networks across all taxonomic groups of Bacteria. RegPrecise 3.0 was selected as a core resource on transcriptional regulation of the Department of Energy Systems Biology Knowledgebase, an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses, and model interactions in microbes, plants, and their communities.

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A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

Publications

A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

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