<b>Pervasive transcription: detecting functional RNAs in bacteria</b>

Lybecker, Meghan; Bilusic, Ivana; Raghavan, Rahul

doi:10.4161/21541272.2014.944039

Cited by 76 publications

(70 citation statements)

References 29 publications

(43 reference statements)

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“…Relatively little is known about the function of intraRNAs and they could encode non-coding regulatory RNAs or mRNAs for small peptides. Most intraRNAs have been identified through genome-wide transcriptional start site analyses or co-immunoprecipitation with Hfq and few have been functionally characterized [31, 55, 59, 62]. However, the only characterized sRNA in B. burgdorferi , DsrA Bb, is an intragenic RNA encoded from within bb0577 that post-transcriptionally regulates the alternative sigma factor RpoS [37].…”

Section: Resultsmentioning

confidence: 99%

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

et al. 2017

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BackgroundTransmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B. burgdorferi at both 23 °C and 37 °C, which mimics in vitro the transmission from the tick vector to the mammalian host.ResultsWe identified over 1000 sRNAs in B. burgdorferi revealing large amounts of antisense and intragenic sRNAs, as well as characteristic intergenic and 5′ UTR-associated sRNAs. A large fraction of the novel sRNAs (43%) are temperature-dependent and differentially expressed at the two temperatures, suggesting a role in gene regulation for adaptation during transmission. In addition, many genes important for maintenance of Borrelia during its enzootic cycle are associated with antisense RNAs or 5′ UTR sRNAs. RNA-seq data were validated for twenty-two of the sRNAs via Northern blot analyses.ConclusionsOur study demonstrates that sRNAs are abundant and differentially expressed by environmental conditions suggesting that gene regulation via sRNAs is a common mechanism utilized in B. burgdorferi. In addition, the identification of antisense and intragenic sRNAs impacts the broadly used loss-of-function genetic approach used to study gene function and increases the coding potential of a small genome. To facilitate access to the analyzed RNA-seq data we have set-up a website at http://www.cibiv.at/~niko/bbdb/ that includes a UCSC browser track hub. By clicking on the respective link, researchers can interactively inspect the data in the UCSC genome browser (Kent et al., Genome Res 12:996-1006, 2002).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3398-3) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

et al. 2017

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“…Thus RNAP could be the most efficient DNA damage detector that continuously patrols the genome and initiates the TCR process at lesion sites. Indeed, it has become evident in recent years that pervasive transcription is conserved in all the three domains of life [55,56]. Although eukaryotic genomes contain only 1-2% protein-coding regions, more than 80% of the genome is transcribed.…”

Section: Rna Polymerase As a Global Sensor Of Dna Damagementioning

confidence: 99%

“…In prokaryotes, it was assumed that pervasive transcription is very limited because ~80% of the genome is protein-coding DNA. However, recent advances in next generation sequencing have revealed the presence of abundant ncRNA in prokaryotes as well, including substantial amounts of antisense RNA [56,57]. It is, thus, tempting to speculate that seemingly wasteful pervasive transcription provides the beneficial means to achieve global surveillance of the genome for DNA damage and to enable robust NER.…”

Section: Rna Polymerase As a Global Sensor Of Dna Damagementioning

confidence: 99%

Rethinking transcription coupled DNA repair

Kamarthapu

Nudler

2015

Current Opinion in Microbiology

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Nucleotide excision repair (NER) is an evolutionarily conserved, multistep process that can detect a wide variety of DNA lesions. Transcription coupled repair (TCR) is a sub-pathway of NER that repairs the transcribed DNA strand faster than the rest of the genome. RNA polymerase (RNAP) stalled at DNA lesions mediates the recruitment of NER enzymes to the damage site. In this review we focus on a newly identified bacterial TCR pathway in which the NER enzyme UvrD, in conjunction with NusA, plays a major role in initiating the repair process. We discuss the tradeoff between the new and conventional models of TCR, how and when each pathway operates to repair DNA damage, and the necessity of pervasive transcription in maintaining genome integrity.

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“…Additionally, when it comes to sequence diversity, we would expect the evolution of dual-encoded sRNAs to be more restricted as compared to regions that encode a single RNA, but this question has yet to be systematically investigated. These dynamics regarding conservation and retention would also apply to sRNAs that are the product of mRNA processing of 3′ untranslated regions (UTRs) and the so-called intraRNAs whose promoters are found within protein-coding genes (65–67). …”

Section: Modes and Consequences Of Srna Lossmentioning

confidence: 99%

Origin, Evolution, and Loss of Bacterial Small RNAs

Dutcher

Raghavan

2018

Microbiol Spectr

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Despite the central role of bacterial non-coding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here, we compile what has been studied to date and trace a life cycle of sRNAs—from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from pre-existing genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently-emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss, and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.

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Pervasive transcription: detecting functional RNAs in bacteria

Cited by 76 publications

References 29 publications

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete

Rethinking transcription coupled DNA repair

Origin, Evolution, and Loss of Bacterial Small RNAs

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