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

Assche, Elke Van; Puyvelde, Sandra Van; Vanderleyden, Jos; Steenackers, Hans

doi:10.3389/fmicb.2015.00141

Cited by 128 publications

(120 citation statements)

References 165 publications

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“…These findings hint at the possibility that the regulatory principle implemented by bicoid protein and caudal mRNA in Drosophila may be at work also in other developmental systems. While translational regulation has also been reported in bacteria [61][62][63][64][65][66][67], here typical mRNA numbers are of order ~1 [99], such that in prokaryotes translational regulation may serve a different purpose than averaging the input to enhance information transmission. In summary, our results suggest that the dual role of proteins as both transcriptional and translational regulators is not just an accident of history, but a solution to a fundamental physics problem faced by the cell.…”

Section: Discussionmentioning

confidence: 99%

“…Since these regulatory proteins bind to DNA, it is plausible that they could also bind to mRNA, thereby regulating translation; this is known to happen in the large class of homeodomain proteins [45][46][47] and for the Argonaute family proteins [48,49], for several other proteins that fulfill important functions in the Drosophila embryo and oocyte [50][51][52][53][54][55][56][57], but also in other eukaryotic species [58][59][60] and in prokaryotes [61][62][63][64][65][66][67]. Intuitively, each mRNA molecule could act as an independent sensor of the input concentration, and averaging over these multiple sensors could reduce the input noise and thereby allow for more effective information transmission at low input concentrations.…”

Section: Introductionmentioning

confidence: 99%

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Extending the dynamic range of transcription factor action by translational regulation

Sokolowski¹,

Walczak²,

Bialek³

et al. 2016

Phys. Rev. E

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A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Extending the dynamic range of transcription factor action by translational regulation

Sokolowski¹,

Walczak²,

Bialek³

et al. 2016

Phys. Rev. E

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“…The regulation of gene expression at the RNA level relies on the binding of numerous RNA binding proteins (RBPs) to a variety of functional RNA classes (Iadevaia and Gerber, 2015; Mitchell and Parker; Shi and Barna, 2015; Singh et al, 2015; Van Assche et al, 2015). To delineate and understand the functions of RBPs it is critical to understand their specificity, that is, how they discriminate between alternative RNA binding sites.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity

Lin

Zhao

Niland

et al. 2016

Cell Chemical Biology

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Summary RNA-binding proteins (RBPs) are typically involved in non-equilibrium cellular processes, and specificity can arise from differences in ground state, transition state or product states of the binding reactions for alternative RNAs. Here, we use high throughput methods to measure and analyze the RNA association kinetics and equilibrium binding affinity for all possible sequence combinations in precursor tRNA binding site of C5, the essential protein subunit of Escherichia coli ribonuclease P. The results show that the RNA sequence specificity of C5 arises due to favorable RNA-protein interactions that stabilize the transition state for association and bound ES complex. Specificity is further impacted by unfavorable RNA structure involving the C5 binding site in the ground state. The results illustrate a comprehensive quantitative approach for analysis of RNA binding specificity, and show how both RNA structure and sequence preferences of an essential protein subunit direct the specificity of a ribonucleoprotein enzyme.

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“…hnRNP A1 | protein-RNA specificity | RNA structure | thermodynamics | binding kinetics G ene expression is regulated by an ensemble of protein-RNA complexes that assemble and disassemble throughout the lifetime of a transcript (1)(2)(3)(4)(5). Knowledge of the determinants of RNA-binding protein (RBP) specificity is therefore essential to understanding the relative affinity for sites of association within the transcriptome.…”

mentioning

confidence: 99%

Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution

Jain

Lin

Morgan

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5′-YAG-3′ and shows how its copy number, position in the loop, and loop structure modulate affinity. For a subset of ESS3 variants, we show that specificity is determined by association rate constants and that variants lacking the minimal sequence motif bind competitively with consensus RNA. Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding how it discriminates between alternative competing RNA ligands in vivo.hnRNP A1 | protein-RNA specificity | RNA structure | thermodynamics | binding kinetics G ene expression is regulated by an ensemble of protein-RNA complexes that assemble and disassemble throughout the lifetime of a transcript (1-5). Knowledge of the determinants of RNA-binding protein (RBP) specificity is therefore essential to understanding the relative affinity for sites of association within the transcriptome. A characteristic feature of many RBPs is their ability to elicit biological function by binding at sites in RNAs that vary significantly in sequence and local structure. This broad specificity of RBPs challenges the simplistic description of RNA binding as either specific or nonspecific. Global profiling methods provide consensus sequence motifs that represent preferential binding sites by RBPs in the transcriptome (6-11). Although powerful, such approaches are usually nonquantitative. Moreover, they do not readily provide information on how surrounding sequence identity or positioning of preferred sequences within higher order structure alters affinity. Methods such as high-throughput sequencing kinetics (HTS-KIN), RNA Bind-n-Seq, and RNA MaP have recently been developed that allow the affinities and reaction kinetics of thousands of RNAs to be measured simultaneously (6,(12)(13)(14)(15). These methods can potentially provide global information on the surrounding context of a given sequence motif; however, they have yet to see wide application for structure/function studies of RNA specificity.Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a diverse family of RBPs that are implicated at most stages of posttranscriptional gene regulation (16,17). The prototypical member of this family, hnRNP A1, regulates alternative splicing, nuclear export, translation, and other RNA processing events (17). HnRNP A1 has a modular domain organization consisting of tandem RNA recognition motifs (RRMs), collectively referred to as unwinding protein 1 (UP1), and an intrinsically di...

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

Cited by 128 publications

References 165 publications

Extending the dynamic range of transcription factor action by translational regulation

Extending the dynamic range of transcription factor action by translational regulation

Analysis of the RNA Binding Specificity Landscape of C5 Protein Reveals Structure and Sequence Preferences that Direct RNase P Specificity

Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution

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