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Superhelical destabilization in regulatory regions of stress response genes.

Wang H, Benham CJ - PLoS Comput. Biol. (2008)

Bottom Line: We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria.These results suggest that strong SIDD sites 5' to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity.We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes.

View Article: PubMed Central - PubMed

Affiliation: UC Davis Genome Center, University of California Davis, Davis, California, United States of America.

ABSTRACT
Stress-induced DNA duplex destabilization (SIDD) analysis exploits the known structural and energetic properties of DNA to predict sites that are susceptible to strand separation under negative superhelical stress. When this approach was used to calculate the SIDD profile of the entire Escherichia coli K12 genome, it was found that strongly destabilized sites occur preferentially in intergenic regions that are either known or inferred to contain promoters, but rarely occur in coding regions. Here, we investigate whether the genes grouped in different functional categories have characteristic SIDD properties in their upstream flanks. We report that strong SIDD sites in the E. coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding transcriptional regulators. In particular, the upstream regions of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. Moreover, if a pathway is controlled by a transcriptional regulator whose gene has a destabilized 5' flank, then the genes (operons) in that pathway also usually contain strongly destabilized SIDD sites in their 5' flanks. We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria. These results suggest that strong SIDD sites 5' to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity. We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes.

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Related in: MedlinePlus

Gene Sets Functioning in Transcriptions Assigned by GenProtEC and COGThe sizes of each set are indicated. The construction of the combined set is shown. (We note that the COG categories are not disjoint, so the same protein can appear in more than one COG group.) The statistical significances of the association of each set with SIDD0 sites are also given.
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pcbi-0040017-g003: Gene Sets Functioning in Transcriptions Assigned by GenProtEC and COGThe sizes of each set are indicated. The construction of the combined set is shown. (We note that the COG categories are not disjoint, so the same protein can appear in more than one COG group.) The statistical significances of the association of each set with SIDD0 sites are also given.

Mentions: Figure 3 shows a comparison of the compositions of these groups. The GenProtEC r group contains 395 genes, 62% of which fall into either COG group K (transcription) or group T (signal transduction mechanisms). Specifically, 207 of the 271 genes in COG group K (75%) and 92 of the 165 genes in COG group T (56%) are contained in the GenProtEC regulator group, r. (One important difference between the GenProtEC and the COG classifications is that in the former the groups are disjoint, whereas in the latter they may overlap; COG can assign a protein to more than one functional category.)


Superhelical destabilization in regulatory regions of stress response genes.

Wang H, Benham CJ - PLoS Comput. Biol. (2008)

Gene Sets Functioning in Transcriptions Assigned by GenProtEC and COGThe sizes of each set are indicated. The construction of the combined set is shown. (We note that the COG categories are not disjoint, so the same protein can appear in more than one COG group.) The statistical significances of the association of each set with SIDD0 sites are also given.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2211533&req=5

pcbi-0040017-g003: Gene Sets Functioning in Transcriptions Assigned by GenProtEC and COGThe sizes of each set are indicated. The construction of the combined set is shown. (We note that the COG categories are not disjoint, so the same protein can appear in more than one COG group.) The statistical significances of the association of each set with SIDD0 sites are also given.
Mentions: Figure 3 shows a comparison of the compositions of these groups. The GenProtEC r group contains 395 genes, 62% of which fall into either COG group K (transcription) or group T (signal transduction mechanisms). Specifically, 207 of the 271 genes in COG group K (75%) and 92 of the 165 genes in COG group T (56%) are contained in the GenProtEC regulator group, r. (One important difference between the GenProtEC and the COG classifications is that in the former the groups are disjoint, whereas in the latter they may overlap; COG can assign a protein to more than one functional category.)

Bottom Line: We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria.These results suggest that strong SIDD sites 5' to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity.We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes.

View Article: PubMed Central - PubMed

Affiliation: UC Davis Genome Center, University of California Davis, Davis, California, United States of America.

ABSTRACT
Stress-induced DNA duplex destabilization (SIDD) analysis exploits the known structural and energetic properties of DNA to predict sites that are susceptible to strand separation under negative superhelical stress. When this approach was used to calculate the SIDD profile of the entire Escherichia coli K12 genome, it was found that strongly destabilized sites occur preferentially in intergenic regions that are either known or inferred to contain promoters, but rarely occur in coding regions. Here, we investigate whether the genes grouped in different functional categories have characteristic SIDD properties in their upstream flanks. We report that strong SIDD sites in the E. coli K12 genome are statistically significantly overrepresented in the upstream regions of genes encoding transcriptional regulators. In particular, the upstream regions of genes that directly respond to physiological and environmental stimuli are more destabilized than are those regions of genes that are not involved in these responses. Moreover, if a pathway is controlled by a transcriptional regulator whose gene has a destabilized 5' flank, then the genes (operons) in that pathway also usually contain strongly destabilized SIDD sites in their 5' flanks. We observe this statistically significant association of SIDD sites with upstream regions of genes functioning in transcription in 38 of 43 genomes of free-living bacteria, but in only four of 18 genomes of endosymbionts or obligate parasitic bacteria. These results suggest that strong SIDD sites 5' to participating genes may be involved in transcriptional responses to environmental changes, which are known to transiently alter superhelicity. We propose that these SIDD sites are active and necessary participants in superhelically mediated regulatory mechanisms governing changes in the global pattern of gene expression in prokaryotes in response to physiological or environmental changes.

Show MeSH
Related in: MedlinePlus