Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

Stein, Ewa M; Kwiatkowska, J.; Basczok, Maciej M; Gravel, Chandra M; Berry, Katie; Olejniczak, Mikołaj

doi:10.1093/nar/gkaa497

Cited by 31 publications

(99 citation statements)

References 55 publications

(159 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5B). Interestingly, Inc and STnc700 both end with a 4U stretch, the latter of which is a recently proposed 3 ′ end-located recognition element for binding by the FinO-domain (Stein et al 2020). As previously observed with ProQ , the targets of FopA share no obvious primary sequence or structural motif as none could be predicated that fits all the main targets (Supplemental Fig.…”

Section: Fopa Is a Plasmid-encoded Rbp With A Unique Target Suitementioning

confidence: 58%

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Gerovac

Mouali

Kuper

et al. 2020

RNA

View full text Add to dashboard Cite

RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq, and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinOdomain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalog of microbial RBPs.

show abstract

Section: Fopa Is a Plasmid-encoded Rbp With A Unique Target Suitementioning

confidence: 58%

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Gerovac

Mouali

Kuper

et al. 2020

RNA

View full text Add to dashboard Cite

show abstract

“…ProQ recognizes structural features present in sRNAs and 3'-UTRs of mRNAs and increases their stability upon binding ( Smirnov et al, 2016 ; Holmqvist et al, 2018 ; Bauriedl et al, 2020 ; Stein et al, 2020 ). Specifically, ProQ was shown to stabilize cspE mRNA by binding its 3'-UTR and preventing RNase II-mediated exoribonucleolytic attack ( Holmqvist et al, 2018 ).…”

Section: Mechanisms Potentially Enabling Uttmentioning

confidence: 99%

Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

Irastortza-Olaziregi

Amster‐Choder

2021

Front. Microbiol.

View full text Add to dashboard Cite

Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming “RNAP.mRNA.ribosome” complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.

show abstract

“…Their role as new RNA matchmakers, mechanistically distinct from Hfq, is being intensively studied, but the molecular details of the interplay between ProQ and its natural RNA ligands only begin to emerge ( Melamed et al, 2020 ). Structural and functional studies highlighted the importance of the conserved N-terminal FinO-like domain, which harbors most of the RNA-binding activity and places ProQ into a larger family of FinO-like RNA chaperones ( Chaulk et al, 2010 , 2011 ; Glover et al, 2015 ; Gonzalez et al, 2017b ; Eidelpes et al, 2020 ; Gerovac et al, 2020 , 2021 ; Immer et al, 2020 ; Pandey et al, 2020 ; Stein et al, 2020 ). However, the role of the C-terminal “Tudor-like” domain ( Figure 6 ), that contributes to the RNA chaperone activities of ProQ ( Chaulk et al, 2011 ; Gonzalez et al, 2017b ), does not cease to intrigue researchers.…”

Section: Profiling Stable Rnps With Grad-seqmentioning

confidence: 99%

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Gerovac

Vogel

Smirnov

2021

Front. Mol. Biosci.

View full text Add to dashboard Cite

Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.

show abstract

Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ protein

Cited by 31 publications

References 55 publications

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Contact Info

Product

Resources

About