Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals

Huerta, A.; Collado‐Vides, Julio

doi:10.1016/j.jmb.2003.07.017

Cited by 218 publications

(246 citation statements)

References 54 publications

(57 reference statements)

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“…The IP-dsRNAs located in the 5′/intergenic ends of genes are in operons or singularly transcribed. The msbA gene is predicted to be in an operon with the upstream and downstream genes ycaI, lpxK, and ycaZ (22). We identified an IP-dsRNA at the 5′ end of the msbA gene extending into the intergenic space.…”

Section: Resultsmentioning

confidence: 99%

The double-stranded transcriptome of Escherichia coli

Lybecker

Zimmermann

Bilusic

et al. 2014

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

104

146

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Advances in high-throughput transcriptome analyses have revealed hundreds of antisense RNAs (asRNAs) for many bacteria, although few have been characterized, and the number of functional asRNAs remains unknown. We have developed a genomewide high-throughput method to identify functional asRNAs in vivo. Most mechanisms of gene regulation via asRNAs require an RNA-RNA interaction with its target RNA, and we hypothesized that a functional asRNA would be found in a double strand (dsRNA), duplexed with its cognate RNA in a single cell. We developed a method of isolating dsRNAs from total RNA by immunoprecipitation with a ds-RNA specific antibody. Total RNA and immunoprecipitated dsRNA from Escherichia coli RNase III WT and mutant strains were deep-sequenced. A statistical model was applied to filter for biologically relevant dsRNA regions, which were subsequently categorized by location relative to annotated genes. A total of 316 potentially functional asRNAs were identified in the RNase III mutant strain and are encoded primarily opposite to the 5′ ends of transcripts, but are also found opposite ncRNAs, gene junctions, and the 3′ ends. A total of 21 sense/antisense RNA pairs identified in dsRNAs were confirmed by Northern blot analyses. Most of the RNA steady-state levels were higher or detectable only in the RNase III mutant strain. Taken together, our data indicate that a significant amount of dsRNA is formed in the cell, that RNase III degrades or processes these dsRNAs, and that dsRNA plays a major role in gene regulation in E. coli.T he advent and development of high-throughput sequencing technologies has uncovered the presence of widespread antisense transcription in many bacteria, with the number of annotated genes associated with antisense RNA (asRNA) differing greatly among bacterial species (1, 2). asRNAs are encoded on the DNA strand opposite an annotated gene and overlap a portion of a gene or the entire gene, or span multiple genes with perfect complementarity. asRNAs range in size from tens to thousands of nucleotides. Although numerous chromosomally encoded asRNAs have been identified, few have been confirmed by traditional methods or functionally characterized. Raghavan et al. (3) reported that few asRNAs are conserved between Escherichia coli and Salmonella enterica, and that the predicted promoter sequences of the asRNAs are not conserved between these species, suggesting that most asRNA transcripts are products of spurious transcription and are not biologically functional RNAs.The majority of functionally characterized asRNAs are found on plasmids, phages, and transposons (4, 5). The mode of regulation by asRNAs can be classified according to molecular mechanism as transcription interference, transcription attenuation, alteration of transcript stability, and translation inhibition (1, 2, 6). With the exception of transcription interference, a physical RNA-RNA interaction between the sense RNAs and asRNAs is necessary for all of these mechanisms, requiring that both RNAs be expressed in the same...

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Section: Resultsmentioning

confidence: 99%

The double-stranded transcriptome of Escherichia coli

Lybecker

Zimmermann

Bilusic

et al. 2014

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

104

146

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“…Their importance, however, is illustrated by the results of the computational analysis of bacterial genomic DNA, which reveals many falsepositive promoters, whereas the true promoters may not even have the highest computational scores (ref. 29 and references therein).…”

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confidence: 99%

Transcription regulatory elements are punctuation marks for DNA replication

Mirkin

Roa

Nudler

et al. 2006

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

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Collisions between DNA replication and transcription significantly affect genome organization, regulation, and stability. Previous studies have described collisions between replication forks and elongating RNA polymerases. Although replication collisions with the transcription-initiation or -termination complexes are potentially even more important because most genes are not actively transcribed during DNA replication, their existence and mechanisms remained unproven. To address this matter, we have designed a bacterial promoter that binds RNA polymerase and maintains it in the initiating mode by precluding the transition into the elongation mode. By using electrophoretic analysis of replication intermediates, we have found that this steadfast transcriptioninitiation complex inhibits replication fork progression in an orientation-dependent manner during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, codirectional orientation. Thus, transcription regulatory signals may serve as ''punctuation marks'' for DNA replication in vivo.collisions ͉ promoter ͉ terminator I mpairment of DNA replication is believed to be a major factor in genomic instability (1-13). Because transcription and replication share the same template, occasional collisions between the two machineries are inevitable and can interfere with replication fork progression. Collisions between the elongating RNA polymerase and the replication fork have been well documented in vitro (14-17) and in vivo in both Escherichia coli (18)(19)(20) and Saccharomyces cerevisiae (6,21,22). The consensus from those studies was that head-on collisions with elongating RNA polymerase are much more detrimental for replication fork progression than codirectional collisions. Although it was suggested that replication stalling during the head-on collisions with transcription was caused by topological stress in the DNA separating the two machineries (18,19,22,23), we have recently shown that it is caused by their direct, physical interaction (20). These results, combined with the data on preferred codirectional alignment of transcription units with the direction of replication in prokaryotes (23-27), have led to the suggestion that the main disadvantage of the head-on collisions could be their inhibitory effect on DNA replication.All of the experimental studies cited in the preceding paragraph evaluated the effects of elongating RNA polymerase on the progression of the replication fork. Is there an interplay between the replication machinery and the transcriptioninitiation complex? To the best of our knowledge, there have been few studies on this matter. One intriguing example was the detection of a polar replication fork pause site at the tRNA locus of S. cerevisiae, which depended on the functionality of both the promoter and the RNA polymerase III (pol III) (22). It was believed that the replication fork was attenuated during the encounter with the elongating RNA polymerase (22). A later study, however, suggest...

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“…All these factors make identification of functional promoter sequences a notoriously difficult task even in well studied model systems like E. coli, irrespective of the approach adopted [19; 28; 32; 66]. In fact, Huerta and Collado-Vides [28] show that several functional promoters are significantly different from the consensus [50]. In contrast, certain genomes with significant size reduction were found not to show this tendency, which was attributed to a process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations [29].…”

Section: Promoter Regionsmentioning

confidence: 99%

Structure and evolution of gene regulatory networks in microbial genomes

Janga¹,

Collado‐Vides²

2007

Research in Microbiology

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With the availability of genome sequences for hundreds of microbial genomes, it has become possible to address several questions from a comparative perspective to understand the structure and function of regulatory systems, at least in model organisms. Recent studies have focused on topological properties and the evolution of regulatory networks and their components. Our understanding of natural networks is paving the way to embedding synthetic regulatory systems into organisms, allowing us to expand the natural diversity of living systems to an extent we had never before anticipated.

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Sigma70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Overlapping Promoter-like Signals

Cited by 218 publications

References 54 publications

The double-stranded transcriptome of Escherichia coli

The double-stranded transcriptome of Escherichia coli

Transcription regulatory elements are punctuation marks for DNA replication

Structure and evolution of gene regulatory networks in microbial genomes

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