RNA-binding proteins in bacteria

Holmqvist, Erik; Vogel, Jörg

doi:10.1038/s41579-018-0049-5

Cited by 195 publications

(159 citation statements)

References 202 publications

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“…Many lncRNAs can regulate the expression of downstream target genes by forming complexes with RNA‐binding proteins, then acts as an oncogene or a suppressor oncogene . In this study, we found that knockdown of MAPKAPK5‐AS1 in CRC cells could lead to changes in related downstream genes, including p15 , p21 , p27 , p57 , KLF2 , and Trail .…”

Section: Discussionmentioning

confidence: 64%

“…26 Therefore, the discovery of new CRC-related lncRNAs is of great significance for further understanding the molecular mechanisms of CRC progression and providing clinical therapeutic targets. In this study, we analyzed 2 sources Many lncRNAs can regulate the expression of downstream target genes by forming complexes with RNA-binding proteins, [27][28][29][30] then acts as an oncogene or a suppressor oncogene. [31][32][33][34][35] In this study, we found that knockdown of MAPKAPK5-AS1 in CRC cells could lead to changes in related downstream genes, including p15, p21, p27, p57, KLF2, and Trail.…”

Section: Discussionmentioning

confidence: 99%

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Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression

Hui

Wang

et al. 2018

Cancer Science

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Colorectal cancer (CRC) is the third most common malignancy in the world, and long noncoding RNA (lncRNA) plays a critical role in carcinogenesis. Here, we report a novel lncRNA, MAPKAPK5‐AS1, that acts as a critical oncogene in CRC. In addition, we attempted to explore the functions of MAPKAPK5‐AS1 on tumor progression in vitro and in vivo. Quantitative RT‐PCR was used to examine the expression of MAPKAPK5‐AS1 in CRC tissues and cells. Expression of MAPKAPK5‐AS1 was significantly upregulated in 50 CRC tissues, and increased expression of MAPKAPK5‐AS1 was found to be associated with greater tumor size and advanced pathological stage in CRC patients. Knockdown of MAPKAPK5‐AS1 significantly inhibited proliferation and caused apoptosis in CRC cells. We also found that p21 is a target of MAPKAPK5‐AS1. In addition, we are the first to report that MAPKAPK5‐AS1 plays a carcinogenic role in CRC. MAPKAPK5‐AS1 is a novel prognostic biomarker and a potential therapeutic candidate for CRC cancer.

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Section: Discussionmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 99%

Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression

Hui

Wang

et al. 2018

Cancer Science

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“…In many but not all bacteria, trans-encoded sRNAs require the RNA chaperone Hfq for efficient regulation (Vogel & Luisi, 2011;Holmqvist & Vogel, 2018;Woodson et al, 2018). Hfq is a ring-like homohexamer with at least three distinct RNA-binding surfaces (Updegrove et al, 2016;.…”

Section: Introductionmentioning

confidence: 99%

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

et al. 2019

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Small RNAs post‐transcriptionally regulate many processes in bacteria. Base‐pairing of sRNAs near ribosome‐binding sites in mRNAs inhibits translation, often requiring the RNA chaperone Hfq. In the canonical model, Hfq simultaneously binds sRNAs and mRNA targets to accelerate pairing. Here, we show that the Escherichia coli sRNAs OmrA and OmrB inhibit translation of the diguanylate cyclase DgcM (previously: YdaM), a player in biofilm regulation. In OmrA/B repression of dgcM, Hfq is not required as an RNA interaction platform, but rather unfolds an inhibitory RNA structure that impedes OmrA/B binding. This restructuring involves distal face binding of Hfq and is supported by RNA structure mapping. A corresponding mutant protein cannot support inhibition in vitro and in vivo; proximal and rim mutations have negligible effects. Strikingly, OmrA/B‐dependent translational inhibition in vitro is restored, in complete absence of Hfq, by a deoxyoligoribonucleotide that base‐pairs to the biochemically mapped Hfq site in dgcM mRNA. We suggest that Hfq‐dependent RNA structure remodeling can promote sRNA access, which represents a mechanism distinct from an interaction platform model.

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“…To complicate things further, these RNA sequence elements involve usually short (between 8 and less than 50 nts) and noncontinuous base pairings, and can be involved in alternative intramolecular secondary structures competing with the intermolecular interaction. Moreover, interacting proteins such as the RNA chaperones Hfq (Dos Santos, Arraiano, & Andrade, ) and ProQ (Smirnov et al, ) frequently mediate these interactions in Enterobacteriaceae (Holmqvist & Vogel, ). All these factors make the simple bioinformatic search for complementary segments in a given sRNA versus the pool of coding sequences inadequate (Backofen & Hess, ).…”

Section: The Challenge Of Identifying the Regulatory Targets Of Bactementioning

confidence: 99%

The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs

Georg

Lalaouna

Hou

et al. 2019

Molecular Microbiology

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Trans‐acting small regulatory RNAs (sRNAs) are key players in the regulation of gene expression in bacteria. There are hundreds of different sRNAs in a typical bacterium, which in contrast to eukaryotic microRNAs are more heterogeneous in length, sequence composition, and secondary structure. The vast majority of sRNAs function post‐transcriptionally by binding to other RNAs (mRNAs, sRNAs) through rather short regions of imperfect sequence complementarity. Besides, every single sRNA may interact with dozens of different target RNAs and impact gene expression either negatively or positively. These facts contributed to the view that the entirety of the regulatory targets of a given sRNA, its targetome, is challenging to identify. However, recent developments show that a more comprehensive sRNAs targetome can be achieved through the combination of experimental and computational approaches. Here, we give a short introduction into these methods followed by a description of two sRNAs, RyhB, and RsaA, to illustrate the particular strengths and weaknesses of these approaches in more details. RyhB is an sRNA involved in iron homeostasis in Enterobacteriaceae, while RsaA is a modulator of virulence in Staphylococcus aureus. Using such a combined strategy, a better appreciation of the sRNA‐dependent regulatory networks is now attainable.

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RNA-binding proteins in bacteria

Cited by 195 publications

References 202 publications

Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression

Long noncoding RNA MAPKAPK5‐AS1 promotes colorectal cancer proliferation by partly silencing p21 expression

Hfq‐dependent mRNA unfolding promotes sRNA ‐based inhibition of translation

The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs

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