Riboswitch distribution, structure, and function in bacteria

Pavlova, Nikolet; Kaloudas, Dimitrios; Penchovsky, Robert

doi:10.1016/j.gene.2019.05.036

Cited by 88 publications

(90 citation statements)

References 87 publications

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“…More likely, these leader RNAs may serve as cis-acting regulatory components, like riboswitches, which are co-transcribed with the downstream protein-coding gene and harbor regulatory stem-loops that influence translation of the respective transcript [55]. Determining whether the identified leader sRNAs are cis-and/or trans-acting elements would require further experiments such as Northern blots and 5' RACE experiments to see if there is read-through into the downstream gene.…”

Section: Discussionmentioning

confidence: 99%

Novel small RNAs expressed byBartonella bacilliformisunder multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host

Wachter

Hicks

Raghavan

et al. 2020

Preprint

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Bartonella bacilliformis , the etiological agent of Carrión’s disease, is a Gram-negative, facultative intracellular alphaproteobacterium. Carrión’s disease is an emerging but neglected tropical illness endemic to Peru, Colombia, and Ecuador. B. bacilliformis is spread between humans through the bite of female phlebotomine sand flies. As a result, the pathogen encounters significant and repeated environmental shifts during its life cycle, including changes in pH and temperature. In most bacteria, small non-coding RNAs (sRNAs) serve as effectors that may post-transcriptionally regulate the stress response to such changes. However, sRNAs have not been characterized in B. bacilliformis , to date. We therefore performed total RNA-sequencing analyses on B. bacilliformis grown in vitro then shifted to one of ten distinct conditions that simulate various environments encountered by the pathogen during its life cycle. From this, we identified 160 sRNAs significantly expressed under at least one of the conditions tested. sRNAs included the highly-conserved tmRNA, 6S RNA, RNase P RNA component, SRP RNA component, ffH leader RNA, and the alphaproteobacterial sRNAs αr45 and speF leader RNA. In addition, 153 other potential sRNAs of unknown function were discovered. Northern blot analysis was used to confirm the expression of eight novel sRNAs. We also characterized a B artonella b acilliformis g rou p I intron (BbgpI) that disrupts an un-annotated tRNA CCU Arg gene and determined that the intron splices in vivo and self-splices in vitro. Furthermore, we demonstrated the molecular targeting of B artonella b acilliformis s mall R NA 9 (BbsR9) to transcripts of the ftsH , nuoF , and gcvT genes, in vitro .

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Section: Discussionmentioning

confidence: 99%

Novel small RNAs expressed byBartonella bacilliformisunder multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host

Wachter

Hicks

Raghavan

et al. 2020

Preprint

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“…To date, riboswitches that respond to nearly fourty distinct small ligands have been discovered and experimentally validated. 76,77 For most of them, X-ray crystallography has revealed the three-dimensional structures of their ligand-binding aptamer domains, shedding light on the enormous diversity of RNA folds and RNA recognition patterns. [78][79][80] The first riboswitch validation reports date back to 2002 [81][82][83][84] and covered riboswitches that are very common and are present in bacteria from nearly all lineages.…”

Section: Riboswitch Rnasmentioning

confidence: 99%

“…They predict that there are potentially many thousands of distinct bacterial riboswitches remaining to be discovered. 76 Recent articles on riboswitch diversity and distribution cover biocomputational aspects, 76,77 several reviews summarize their structural concepts, [78][79][80] and some focus on latest developments to use riboswitches as sensor tools in biotechnological and biomedical applications. 10,14,[85][86][87][88][89][90] Here, we concisely focus on the most recent additions to riboswitches ( Fig.…”

Section: Riboswitch Rnasmentioning

confidence: 99%

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

2020

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“…The glmS riboswitch controls the fructose‐6‐phosphate amidotransferase gene (also called GlcN6P synthase) and can bind to its natural coenzyme GlcN6P, which leads to its own self‐cleavage, and eventually causes a decrease in gene expression and production of GlcN6P . Since GlcN6P is of vital importance in the metabolic pathway of bacterial cell wall synthesis and the glmS riboswitch is not found in the human genome, the glmS riboswitch is a promising target for antibacterial agents.…”

Section: Conclusion and Prospectivementioning

confidence: 99%

Recent Development of Glucosamine‐6‐phosphate Derivatives as Potential Antibacterial Agents

Liu

2020

ChemistrySelect

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The glmS riboswitch (glucosamine-6-phosphate activated riboswitch) is located at the 5'-untranslated region of the glmS mRNA, which carries the gene of glucosamine-6-phosphate (GlcN6P) synthetase named amidotransferase. The glmS riboswitch can bind to its natural coenzyme GlcN6P and lead to its own self-cleavage, causing the decrease in the expression of the glmS RNA and the synthesis of amidotransferase, and finally, reducing the production of GlcN6P. Since GlcN6P is of vital importance in the metabolic pathway of the bacterial cell wall synthesis, the glmS riboswitch gradually becomes a promising target of antibiotic drugs. In this review, an overview of the development of the glmS riboswitch activators as novel and potent antibacterial agents is described, which involves the structure of the glmS riboswitch and its self-cleavage mechanism, various the glmS riboswitch activators and their structure-activity relationships. In particular, the analogs of GlcN6P that can induce self-cleavage of the glmS riboswitch are highlighted. The most promising compound 9 (Carba-GlcN6P) exhibited not only excellent activity in inducing the selfcleavage of the glmS riboswitch, but also great efficacy (k obs = 0.153 min À 1 ) at 200 μM compared to GlcN6P (k obs = 0.177 min À 1 ).

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Riboswitch distribution, structure, and function in bacteria

Cited by 88 publications

References 87 publications

Novel small RNAs expressed byBartonella bacilliformisunder multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host

Novel small RNAs expressed byBartonella bacilliformisunder multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Recent Development of Glucosamine‐6‐phosphate Derivatives as Potential Antibacterial Agents

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