FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism

Mukherjee, Sampriti; Oshiro, Reid T.; Yakhnin, Helen; Babitzke, Paul; Kearns, Daniel B.

doi:10.1073/pnas.1602455113

Cited by 31 publications

(54 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, hag is the only published target of CsrA in B. subtilis [22,23,31]. While hag mRNA is present under most conditions in high intracellular amounts [32] , SR1 is only present in significant intracellular amounts under gluconeogenic conditions with 200-225 molecules/cell [8] and under conditions of sporulation [32].…”

Section: Csra Does Not Influence the Translation Of Ahrc Mrna Directlymentioning

confidence: 99%

See 1 more Smart Citation

A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis

et al. 2019

View full text Add to dashboard Cite

show abstract

Section: Csra Does Not Influence the Translation Of Ahrc Mrna Directlymentioning

confidence: 99%

“…In B. subtilis, CsrA has so far only been found to regulate one target, hag mRNA, and is not sequestered by an sRNA, but by a protein (FliW) [22]. Thereby, FliW interacts with a C-terminal extension of CsrA and allosterically antagonizes CsrA in a non-competitive manner thus preventing CsrA binding to hag mRNA [23].…”

Section: Introductionmentioning

confidence: 99%

A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Most other bacteria however, antagonize the RNA-binding activity of CsrA by expressing a protein, FliW Sze et al, 2011;Mukherjee et al, 2011;Dugar et al, 2016;Radomska et al, 2016;Li et al, 2018). Genetic and structural analysis supports the notion that FliW functions differently than the sRNA such that CsrA is antagonized non-competitively (Altegoer et al, 2016;Mukherjee et al, 2016). Despite having a high-resolution structure of the inhibited complex, the mechanism of FliW-mediated CsrA-inhibition remains unclear.…”

Section: Discussionmentioning

confidence: 99%

“…The flagellin transcript is the most abundant transcript in the cell when expressed, and thus would be difficult to outcompete if CsrA was regulated by a competitive mechanism (Mondal et al, 2016). Instead, CsrA is antagonized non-competitively by a stoichiometric ratio of the protein FliW (Mukherjee et al, 2011;Mukherjee et al, 2016;Altegoer et al, 2016;Oshiro et al, 2019). FliW seems to be the ancestral form of CsrA regulation and is conserved in spirochaetes like Borrelia burgdorferi and epsilon-proteobacteria like Campylobacter jejuni Sze et al, 2011;Dugar et al, 2016;Radomska et al, 2016;Li et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Contact with the CsrA core is required for allosteric inhibition by FliW inBacillus subtilis

Kearns

Oshiro

2020

Preprint

Self Cite

View full text Add to dashboard Cite

AbstractThe RNA-binding protein CsrA is a post-transcriptional regulator that is encoded in genomes throughout the bacterial phylogeny. In the gamma-proteobacteria, the activity of CsrA is inhibited by small RNAs that competitively sequester CsrA binding. In contrast, the firmicute Bacillus subtilis encodes a protein inhibitor of CsrA called FliW, that non-competitively inhibits CsrA activity but the precise mechanism of antagonism is unclear. Here we take an unbiased genetic approach to identify residues of FliW important for CsrA inhibition that fall into two distinct spatial and functional classes. Most loss-of-function alleles mutated FliW residues that surround the critical regulatory CsrA residue N55 and abolished CsrA interaction. Two loss-of-function alleles however mutated FliW residues near the CsrA core dimerization domain and maintained interaction with CsrA. One of these two alleles reversed charge at what appeared to be a salt bridge with the CsrA core region, charge reversal of the CsrA partner residue phenocopied the FliW allele, and charge reversal of both residues simultaneously restored antagonism. We propose a model in which initial interaction between FliW and CsrA is necessary but not sufficient for antagonism which also requires salt bridge formation with, and deformation of, the CsrA core domain to allosterically abolish RNA binding activity.SummaryCsrA is a small dimeric protein that binds RNA and is one of the few known examples of transcript-specific translational regulators in bacteria. A protein called FliW binds to and antagonizes CsrA; despite having a high-resolution three-dimensional structure of the FliW-CsrA complex, the mechanism of non-competitive inhibition remains unresolved. Here we identify FliW residues required for antagonism and we find that the residues make a linear connection in the complex from initial binding interaction with CsrA to a critical salt bridge near the core of the CsrA dimer. We propose that the salt bridge represents an allosteric contact that distorts the CsrA core to prevent RNA binding.

show abstract

“…FliW does not bind to the same residues of CsrA required for hag mRNA binding. Some csrA mutants abolished CsrA-FliW binding, but others did not, indicating that FliW and RNA interaction is not mutually exclusive (79). Structural analysis of the CsrA-FliW complex from G. thermodenitrificans indicates that each CsrA subunit binds to a FliW monomer (47).…”

Section: Protein Antagonists Of Csramentioning

confidence: 99%

Global Regulation by CsrA and Its RNA Antagonists

Romeo

Babitzke

2018

Regulating With RNA in Bacteria and Archaea

Self Cite

View full text Add to dashboard Cite

The sequence-specific RNA binding protein CsrA is employed by diverse bacteria in the posttranscriptional regulation of gene expression. Its binding interactions with RNA have been documented at atomic resolution and shown to alter RNA secondary structure, RNA stability, translation and/or Rho-mediated transcription termination through a growing number of molecular mechanisms. In Gammaproteobacteria, small regulatory RNAs that contain multiple CsrA binding sites compete with mRNA for binding to CsrA, thereby sequestering and antagonizing this protein.Both the synthesis and turnover of these sRNAs are regulated, allowing CsrA activity to be rapidly and efficiently adjusted in response to nutritional conditions and stresses. Feedback loops between the Csr regulatory components improve the dynamics of signal response by the Csr system. The Csr system of E. coli is intimately interconnected with other global regulatory systems, permitting it to contribute to regulation by those systems. In some species, a protein antagonist of CsrA functions as part of a checkpoint for flagellum biosynthesis. In other species, a protein antagonist participates in a mechanism in which a type III secretion system is used for sensing interactions with host cells. Recent transcriptomics studies reveal vast effects of CsrA on gene expression through direct binding to hundreds of mRNAs, and indirectly through its effects on the expression of dozens of transcription factors. CsrA binding to basepairing sRNAs and novel mRNA segments, such as the 3′ UTR and deep within coding regions, predict its participation in yet to be discovered regulatory mechanisms. INRODUCTIONThe Csr (carbon storage regulator) or Rsm (repressor of stationary phase metabolites) system is among the most extensively studied bacterial RNA-based regulatory systems. Its central component, the RNA binding protein CsrA (RsmA), was uncovered by a transposon mutagenesis screen designed to identify regulators of gene expression in the stationary phase of growth, using glycogen biosynthesis and glgC'-'lacZ expression as reporters (1).

show abstract

FliW antagonizes CsrA RNA binding by a noncompetitive allosteric mechanism

Cited by 31 publications

References 53 publications

A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis

A new role for CsrA: promotion of complex formation between an sRNA and its mRNA target in Bacillus subtilis

Contact with the CsrA core is required for allosteric inhibition by FliW inBacillus subtilis

Global Regulation by CsrA and Its RNA Antagonists

Contact Info

Product

Resources

About