Experimental tools to identify RNA-protein interactions in<i>Helicobacter pylori</i>

Rieder, Renate; Reinhardt, Richard; Sharma, Cynthia M; Vogel, Jörg

doi:10.4161/rna.20331

Cited by 23 publications

(27 citation statements)

References 44 publications

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“…One of these methods is the in vitro or in vivo assembly of RNA and RBPs, followed by mass spectrometry (Tsai et al, 2011). This method has already been optimized for Helicobacter pylori , E. coli , Salmonella Typhimurium and P. aeruginosa (Windbichler et al, 2008; Said et al, 2009; Rieder et al, 2012; Osborne et al, 2014). …”

Section: Discussionmentioning

confidence: 99%

RNA-binding proteins involved in post-transcriptional regulation in bacteria

et al. 2015

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Post-transcriptional regulation is a very important mechanism to control gene expression in changing environments. In the past decade, a lot of interest has been directed toward the role of small RNAs (sRNAs) in bacterial post-transcriptional regulation. However, sRNAs are not the only molecules controlling gene expression at this level, RNA-binding proteins (RBPs) play an important role as well. CsrA and Hfq are the two best studied bacterial proteins of this type, but recently, additional proteins involved in post-transcriptional control have been identified. This review focuses on the general working mechanisms of post-transcriptionally active RBPs, which include (i) adaptation of the susceptibility of mRNAs and sRNAs to RNases, (ii) modulating the accessibility of the ribosome binding site of mRNAs, (iii) recruiting and assisting in the interaction of mRNAs with other molecules and (iv) regulating transcription terminator/antiterminator formation, and gives an overview of both the well-studied and the newly identified proteins that are involved in post-transcriptional regulatory processes. Additionally, the post-transcriptional mechanisms by which the expression or the activity of these proteins is regulated, are described. For many of the newly identified proteins, however, mechanistic questions remain. Most likely, more post-transcriptionally active proteins will be identified in the future.

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Section: Discussionmentioning

confidence: 99%

RNA-binding proteins involved in post-transcriptional regulation in bacteria

et al. 2015

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“…As of now, it is not clear if trans-acting sRNAs identified in this study would function in a chaperone-dependent or –independent manner. Hypothetical proteins such as HP1334 in H. pylori and several other RNA binding proteins such as YbeY in Sinorhizobium meliloti have been implicated with chaperone activity5758. More recently, a ProQ/FinO domain containing protein Lpp0148 has been reported to function as a RNA chaperone in Legionella pneumophila 59.…”

Section: Discussionmentioning

confidence: 99%

Small Regulatory RNAs of Rickettsia conorii

Narra

Schroeder

Sahni

et al. 2016

Sci Rep

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Small regulatory RNAs comprise critically important modulators of gene expression in bacteria, yet very little is known about their prevalence and functions in Rickettsia species. R. conorii, the causative agent of Mediterranean spotted fever, is a tick-borne pathogen that primarily infects microvascular endothelium in humans. We have determined the transcriptional landscape of R. conorii during infection of Human Microvascular Endothelial Cells (HMECs) by strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-acting (antisense) small RNAs (termed ‘Rc_sR’s). Independent expression of four novel trans-acting sRNAs (Rc_sR31, Rc_sR33, Rc_sR35, and Rc_sR42) and known bacterial sRNAs (6S, RNaseP_bact_a, ffs, and α-tmRNA) was next confirmed by Northern hybridization. Comparative analysis during infection of HMECs vis-à-vis tick AAE2 cells revealed significantly higher expression of Rc_sR35 and Rc_sR42 in HMECs, whereas Rc_sR31 and Rc_sR33 were expressed at similar levels in both cell types. We further predicted a total of 502 genes involved in all important biological processes as potential targets of Rc_sRs and validated the interaction of Rc_sR42 with cydA (cytochrome d ubiquinol oxidase subunit I). Our findings constitute the first evidence of the existence of post-transcriptional riboregulatory mechanisms in R. conorii and interactions between a novel Rc_sR and its target mRNA.

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“…New developments that help target identification on a global scale involve ribosome profiling (Guo, Updegrove, et al, 2014;Ingolia, 2014) and the use of protein cofactors as baits to purify regulatory complexes. Immunoprecipitation followed by RNA-sequencing (RIPseq) has identified RNA targets of Helicobacter pylori ribosomal protein S1 (Rieder, Reinhardt, Sharma, & Vogel, 2012) and S. aureus RNase III , and UV-induced RNAeHfq cross-linking followed by RNA deep-seq revealed new sRNAs that target regulatory RNAs in enterohemorrhagic E. coli (Tree et al, 2014). Alternative approaches use in vivo-generated tagged sRNAs to affinity-purify regulatory complexes, followed by RNA-seq and MS Lalaouna et al, 2015).…”

Section: Experimental Strategiesmentioning

confidence: 99%