Mapping interactions between the RNA chaperone FinO and its RNA targets

Arthur, David C.; Edwards, Ross A.; Tsutakawa, Susan E.; Tainer, John A.; Frost, Laura S.; Glover, J. N. Mark

doi:10.1093/nar/gkr025

Cited by 41 publications

(67 citation statements)

References 49 publications

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“…RNA cross linking experiments have previously shown the residue corresponding to R58 as being implicated in RNA binding by FinO. Other residues implicated in RNA binding from this study of FinO clustered toward the N-and C-terminal helical extensions of this protein (Ghetu et al 2002;Arthur et al 2011).…”

Section: Discussionmentioning

confidence: 53%

Structure of the Escherichia coli ProQ RNA-binding protein

Gonzalez

Hardwick

Maslen

et al. 2017

RNA

123

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The protein ProQ has recently been identified as a global small noncoding RNA-binding protein in Salmonella, and a similar role is anticipated for its numerous homologs in divergent bacterial species. We report the solution structure of Escherichia coli ProQ, revealing an N-terminal FinO-like domain, a C-terminal domain that unexpectedly has a Tudor domain fold commonly found in eukaryotes, and an elongated bridging intradomain linker that is flexible but nonetheless incompressible. Structure-based sequence analysis suggests that the Tudor domain was acquired through horizontal gene transfer and gene fusion to the ancestral FinO-like domain. Through a combination of biochemical and biophysical approaches, we have mapped putative RNA-binding surfaces on all three domains of ProQ and modeled the protein's conformation in the apo and RNA-bound forms. Taken together, these data suggest how the FinO, Tudor, and linker domains of ProQ cooperate to recognize complex RNA structures and serve to promote RNA-mediated regulation.

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Section: Discussionmentioning

confidence: 53%

Structure of the Escherichia coli ProQ RNA-binding protein

Gonzalez

Hardwick

Maslen

et al. 2017

RNA

123

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“…). One early study showed that the 3′‐U 4 tail of FinP stem loop II was necessary for its efficient binding to FinO (Jerome and Frost, ), and later work showed that FinO protected lower parts of the stems and the 3′ single‐stranded regions of FinP (Arthur et al ., ). These observations are consistent with the better binding of L. pneumophila RocC protein to the 3′‐terminal stem loop of RocR sRNA with an adjacent U 3 CU tail than to a fragment composed of stem loops 1 and 2 devoid of the 3′ terminal extension (Attaiech et al ., ).…”

Section: Rnas Bound By Fino‐domain Proteinsmentioning

confidence: 97%

ProQ/FinO‐domain proteins: another ubiquitous family of RNA matchmakers?

Olejniczak

Storz

2017

Molecular Microbiology

131

124

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Summary Small RNAs (sRNAs), particularly those that act by limited base pairing with mRNAs, are part of most regulatory networks in bacteria. In many cases, the base-pairing interaction is facilitated by the RNA chaperone Hfq. However, not all bacteria encode Hfq and some base-pairing sRNAs do not require Hfq raising the possibility of other RNA chaperones. Candidates are proteins with homology to FinO, a factor that promotes base pairing between the FinP antisense sRNA and the traJ mRNA to control F plasmid transfer. Recent papers have shown that the Salmonella enterica FinO-domain protein ProQ binds a large suite of sRNAs, including the RaiZ sRNA, which represses translation of the hupA mRNA, and the Legionella pneumophila protein RocC binds the RocR sRNA, which blocks expression of competence genes. Here we discuss what is known about FinO-domain structures, including the recently solved Escherichia coli ProQ structure, as well as the RNA binding properties of this family of proteins and evidence they act as chaperones. We compare these properties with those of Hfq. We further summarize what is known about the physiological roles of FinO-domain proteins and enumerate outstanding questions whose answers will establish whether they constitute a second major class of RNA chaperones.

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“…Horizontal gene transfer, especially conjugative transfer of plasmids that carry resistance genes, is the primary cause of bacterial antibiotic resistance and—on the larger scale—bacterial evolution (Zatyka and Thomas, 1998; Arthur et al, 2011). The self-transmissible plasmids, such as the well-studied fertility F-plasmids and IncP plasmid RP4 (also known as RK2), generally present a mobilization (MOB) region which includes the origin of transfer (oriT) and the relaxase gene.…”

Section: Introductionmentioning

confidence: 99%

Quorum Sensing N-acyl Homoserine Lactones-SdiA Suppresses Escherichia coli-Pseudomonas aeruginosa Conjugation through Inhibiting traI Expression

Lü

Zeng

et al. 2017

Front. Cell. Infect. Microbiol.

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Conjugation is a key mechanism for horizontal gene transfer and plays an important role in bacterial evolution, especially with respect to antibiotic resistance. However, little is known about the role of donor and recipient cells in regulation of conjugation. Here, using an Escherichia coli (SM10λπ)-Pseudomonas aeruginosa (PAO1) conjugation model, we demonstrated that deficiency of lasI/rhlI, genes associated with generation of the quorum sensing signals N-acyl homoserine lactones (AHLs) in PAO1, or deletion of the AHLs receptor SdiA in the donor SM10λπ both facilitated conjugation. When using another AHLs-non-producing E. coli strain EC600 as recipient cells, deficiency of sdiA in donor SM10λπ hardly affect the conjugation. More importantly, in the presence of exogenous AHLs, the conjugation efficiency between SM10λπ and EC600 was dramatically decreased, while deficiency of sdiA in SM10λπ attenuated AHLs-inhibited conjugation. These data suggest the conjugation suppression function of AHLs-SdiA chemical signaling. Further bioinformatics analysis, β-galactosidase reporter system and electrophoretic mobility shift assays characterized the binding site of SdiA on the promoter region of traI gene. Furthermore, deletion of lasI/rhlI or sdiA promoted traI mRNA expression in SM10λπ and PAO1 co-culture system, which was abrogated by AHLs. Collectively, our results provide new insight into an important contribution of quorum sensing system AHLs-SdiA to the networks that regulate conjugation.

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Mapping interactions between the RNA chaperone FinO and its RNA targets

Cited by 41 publications

References 49 publications

Structure of the Escherichia coli ProQ RNA-binding protein

Structure of the Escherichia coli ProQ RNA-binding protein

ProQ/FinO‐domain proteins: another ubiquitous family of RNA matchmakers?

Quorum Sensing N-acyl Homoserine Lactones-SdiA Suppresses Escherichia coli-Pseudomonas aeruginosa Conjugation through Inhibiting traI Expression

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