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Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding.

Bonocora RP, Smith C, Lapierre P, Wade JT - PLoS Genet. (2015)

Bottom Line: Strikingly, the majority of σ54 binding sites are located inside genes.We conclude that many intragenic σ54 binding sites are likely to be functional.Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.

ABSTRACT
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.

No MeSH data available.


Related in: MedlinePlus

Distribution of σ54 binding sites relative to gene position.(A) (Top) Schematic representing the four possible classes of σ54 binding site relative to a gene. (Bottom) The distribution of each class of σ54 binding site in E. coli. (B) Cumulative frequency of the distance from intergenic (blue), intragenic (red) and all (purple) σ54 binding sites to the next available gene start. The cumulative frequency distribution of the distances between 4000 random positions and the next available gene start is also indicated (grey).
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pgen.1005552.g003: Distribution of σ54 binding sites relative to gene position.(A) (Top) Schematic representing the four possible classes of σ54 binding site relative to a gene. (Bottom) The distribution of each class of σ54 binding site in E. coli. (B) Cumulative frequency of the distance from intergenic (blue), intragenic (red) and all (purple) σ54 binding sites to the next available gene start. The cumulative frequency distribution of the distances between 4000 random positions and the next available gene start is also indicated (grey).

Mentions: With one exception [20], all previously described, experimentally confirmed σ54 binding sites in E. coli are located in intergenic regions. The distribution with respect to gene position of the 135 high stringency σ54 binding site locations we identified is shown in Fig 3A. As expected, σ54 binding sites as a group are closer to annotated gene starts than random genomic positions (Fig 3B). Surprisingly, 85 of the 135 σ54 binding sites (62%) are located inside genes (Fig 3A). Furthermore, of the 50 σ54 binding sites in intergenic regions, 8 are oriented away from the neighboring gene(s), indicating that they are not promoters for the immediately adjacent genes. Further analysis of the σ54 binding sites inside genes showed that 58 (68%) of these sites are positioned in the sense orientation with respect to the overlapping gene (Fig 3A). This is far more than expected by chance (Binomial test p = 5e-4, assuming a 50% random chance of sense/antisense orientation). We observed a similar, significant bias (79/129; 61%) for the low stringency sites (Binomial test p = 0.007; S2 Table). The distance of intragenic σ54 binding sites from the nearest appropriately oriented gene start is also non-random. Specifically, there are many more sites between 360 and 760 bp upstream of an available gene start than expected by chance (36.5% of all intragenic sites as compared to 14.3% of all intragenic coordinates genome-wide; Fig 3B).


Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding.

Bonocora RP, Smith C, Lapierre P, Wade JT - PLoS Genet. (2015)

Distribution of σ54 binding sites relative to gene position.(A) (Top) Schematic representing the four possible classes of σ54 binding site relative to a gene. (Bottom) The distribution of each class of σ54 binding site in E. coli. (B) Cumulative frequency of the distance from intergenic (blue), intragenic (red) and all (purple) σ54 binding sites to the next available gene start. The cumulative frequency distribution of the distances between 4000 random positions and the next available gene start is also indicated (grey).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591121&req=5

pgen.1005552.g003: Distribution of σ54 binding sites relative to gene position.(A) (Top) Schematic representing the four possible classes of σ54 binding site relative to a gene. (Bottom) The distribution of each class of σ54 binding site in E. coli. (B) Cumulative frequency of the distance from intergenic (blue), intragenic (red) and all (purple) σ54 binding sites to the next available gene start. The cumulative frequency distribution of the distances between 4000 random positions and the next available gene start is also indicated (grey).
Mentions: With one exception [20], all previously described, experimentally confirmed σ54 binding sites in E. coli are located in intergenic regions. The distribution with respect to gene position of the 135 high stringency σ54 binding site locations we identified is shown in Fig 3A. As expected, σ54 binding sites as a group are closer to annotated gene starts than random genomic positions (Fig 3B). Surprisingly, 85 of the 135 σ54 binding sites (62%) are located inside genes (Fig 3A). Furthermore, of the 50 σ54 binding sites in intergenic regions, 8 are oriented away from the neighboring gene(s), indicating that they are not promoters for the immediately adjacent genes. Further analysis of the σ54 binding sites inside genes showed that 58 (68%) of these sites are positioned in the sense orientation with respect to the overlapping gene (Fig 3A). This is far more than expected by chance (Binomial test p = 5e-4, assuming a 50% random chance of sense/antisense orientation). We observed a similar, significant bias (79/129; 61%) for the low stringency sites (Binomial test p = 0.007; S2 Table). The distance of intragenic σ54 binding sites from the nearest appropriately oriented gene start is also non-random. Specifically, there are many more sites between 360 and 760 bp upstream of an available gene start than expected by chance (36.5% of all intragenic sites as compared to 14.3% of all intragenic coordinates genome-wide; Fig 3B).

Bottom Line: Strikingly, the majority of σ54 binding sites are located inside genes.We conclude that many intragenic σ54 binding sites are likely to be functional.Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.

View Article: PubMed Central - PubMed

Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.

ABSTRACT
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70 family and the σ54 family. Members of the σ54 family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli σ54, the archetypal member of the σ54 family. Thus, we vastly expand the list of known σ54 binding sites to 135. Moreover, we estimate that there are more than 250 σ54 sites in total. Strikingly, the majority of σ54 binding sites are located inside genes. The location and orientation of intragenic σ54 binding sites is non-random, and many intragenic σ54 binding sites are conserved. We conclude that many intragenic σ54 binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54 promoters that drive transcription of mRNAs with unusually long 5' UTRs.

No MeSH data available.


Related in: MedlinePlus