RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Gama-Castro, Socorro; Jiménez-Jacinto, Verónica; Peralta-Gil, Martín; Santos-Zavaleta, Alberto; Peñaloza-Spínola, Mónica I; Contreras‐Moreira, Bruno; Segura-Salazar, Juan; Muñiz-Rascado, Luis; Martínez-Flores, Irma; Salgado, Heladia; Bonavides-Martínez, César; Abreu‐Goodger, Cei; Rodríguez-Penagos, Carlos; Miranda-Ríos, Juan; Morett, Enrique; Merino, Enrique; Huerta, A.; Treviño-Quintanilla, Luis Gerardo

doi:10.1093/nar/gkm994

Cited by 411 publications

(492 citation statements)

References 18 publications

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“…However, our analysis of the occurrence of the CCWGG motif across 2,558 experimentally verified transcription factor-binding sites in the RegulonDB database 37 showed that this motif occurs only 69 times in these sequences, which is not significantly different from the trend in the rest of the genome. Further, only two of these transcription factor-binding sequences contained more than one CCWGG motif.…”

Section: Resultsmentioning

confidence: 70%

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

et al. 2012

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DnA cytosine methylation regulates gene expression in mammals. In bacteria, its role in gene expression and genome architecture is less understood. Here we perform high-throughput sequencing of bisulfite-treated genomic DnA from Escherichia coli K12 to describe, for the first time, the extent of cytosine methylation of bacterial DnA at single-base resolution. Whereas most target sites (C m CWGG) are fully methylated in stationary phase cells, many sites with an extended CC m CWGG motif are only partially methylated in exponentially growing cells. We speculate that these partially methylated sites may be selected, as these are slightly correlated with the risk of spontaneous, non-synonymous conversion of methylated cytosines to thymines. microarray analysis in a cytosine methylation-deficient mutant of E. coli shows increased expression of the stress response sigma factor Rpos and many of its targets in stationary phase. Thus, DnA cytosine methylation is a regulator of stationary phase gene expression in E. coli.

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Section: Resultsmentioning

confidence: 70%

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

et al. 2012

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“…The -A-nucleotide of the translation initiation codon is designated +1. The predicted transcription start site (Gama-Castro et al, 2008;Rudd, 2000) occurs at nucleotide "84 relative to the translation start site. The upstream fusion site (not shown) was made at position "296 to ensure that all cycA regulatory elements would be contained in the cloned fragment.…”

Section: Resultsmentioning

confidence: 99%

Role of the sRNA GcvB in regulation of cycA in Escherichia coli

Pulvermacher

Stauffer

2009

Microbiology

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In Escherichia coli, the gcvB gene encodes a small non-translated RNA that regulates several genes involved in transport of amino acids and peptides (including sstT, oppA and dppA). Microarray analysis identified cycA as an additional regulatory target of GcvB. The cycA gene encodes a permease for the transport of glycine, d-alanine, d-serine and d-cycloserine. RT-PCR confirmed that GcvB and the Hfq protein negatively regulate cycA mRNA in cells grown in Luria–Bertani broth. In addition, deletion of the gcvB gene resulted in increased sensitivity to d-cycloserine, consistent with increased expression of cycA. A cycA : : lacZ translational fusion confirmed that GcvB negatively regulates cycA expression in Luria–Bertani broth and that Hfq is required for the GcvB effect. GcvB had no effect on cycA : : lacZ expression in glucose minimal medium supplemented with glycine. However, Hfq still negatively regulated the fusion in the absence of GcvB. A set of transcriptional fusions of cycA to lacZ identified a sequence in cycA necessary for regulation by GcvB. Analysis of GcvB identified a region complementary to this region of cycA mRNA. However, mutations predicted to disrupt base-pairing between cycA mRNA and GcvB did not alter expression of cycA : : lacZ. A model for GcvB function in cell physiology is discussed.

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“…Data about the order of E. coli genes in operons were downloaded from the work of Gama-Castro et al (27). The folding profile of groups of genes that are present in the end of operons, monocistronic genes, was compared with the folding profile of genes in the beginning or middle of an operon.…”

Section: Methodsmentioning

confidence: 99%

Translation efficiency is determined by both codon bias and folding energy

Tuller

Waldman²,

Kupiec³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

495

598

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Synonymous mutations do not alter the protein produced yet can have a significant effect on protein levels. The mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at the beginning of genes is the dominant factor via its effect on translation initiation. Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation efficiency. There is a significant association between codon bias and translation efficiency across all endogenous genes in E. coli and S. cerevisiae but no association between folding energy and translation efficiency, demonstrating the role of codon bias as an important determinant of translation efficiency. However, folding energy does modulate the strength of association between codon bias and translation efficiency, which is maximized at very weak mRNA folding (i.e., high folding energy) levels. We find a strong correlation between the genomic profiles of ribosomal density and genomic profiles of folding energy across mRNA, suggesting that lower folding energies slow down the ribosomes and decrease translation efficiency. Accordingly, we find that selection forces act near uniformly to decrease the folding energy at the beginning of genes. In summary, these findings testify that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels.mRNA folding | protein abundance | synonymous mutations | ribosome density | translation initiation

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RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Cited by 411 publications

References 18 publications

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

Role of the sRNA GcvB in regulation of cycA in Escherichia coli

Translation efficiency is determined by both codon bias and folding energy

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