Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria

Bobrovskyy, Maksym; Vanderpool, Carin K.; Richards, Gregory R.

doi:10.1128/microbiolspec.mbp-0009-2014

Cited by 26 publications

(17 citation statements)

References 281 publications

(414 reference statements)

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“…We selected the RNA chaperone Hfq as another possible candidate interactor based on several studies that showed YbeY to play a role in sRNA regulation in bacteria (2, 7–9). Hfq is the general sRNA chaperone in bacteria and is part of the RNase E degradosome that includes RNase E, PNPase, and the DEAD box RNA helicase RhlB (36–38).…”

Section: Resultsmentioning

confidence: 99%

“…To date, studies have shown that YbeY is crucial in 16S rRNA maturation, 70S ribosomal assembly, late-stage 70S ribosome quality control, and stress regulation in Escherichia coli , Vibrio cholerae , Sinorhizobium meliloti and chloroplasts of Arabidopsis thaliana (1–5). In addition to a general role in mRNA regulation (6), YbeY is also implicated in the bacterial small RNA (sRNA) regulatory network, acting alongside key proteins such as Hfq, RNase E, or PNPase (2, 7–9). It is, therefore, not surprising that YbeY has an important role in host-microbe interactions.…”

Section: Introductionmentioning

confidence: 99%

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Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

Vercruysse

Köhrer

Shen³

et al. 2016

mBio

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YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY’s involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3′ end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY—and not amino acids known to be important for YbeY’s RNase activity—functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

Vercruysse

Köhrer

Shen³

et al. 2016

mBio

View full text Add to dashboard Cite

show abstract

“…Although classically identified as important players in bacterial stress response, sRNAs also play general roles regulating the genes involved in cell growth, nutrient acquisition, social behavior, and virulence (1,2). sRNAs often act through translational repression, in which a given sRNA base pairs with the leader sequence of a target mRNA, obscuring the site that would otherwise form contacts with the ribosomal 30S subunit (3).…”

mentioning

confidence: 99%

The Phosphorolytic Exoribonucleases Polynucleotide Phosphorylase and RNase PH Stabilize sRNAs and Facilitate Regulation of Their mRNA Targets

Cameron¹,

Lay

2016

J Bacteriol

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Gene regulation by base pairing between small noncoding RNAs (sRNAs) and their mRNA targets is an important mechanism that allows bacteria to maintain homeostasis and respond to dynamic environments. In Gram-negative bacteria, sRNA pairing and regulation are mediated by several RNA-binding proteins, including the sRNA chaperone Hfq and polynucleotide phosphorylase (PNPase). PNPase and its homolog RNase PH together represent the two 3= to 5= phosphorolytic exoribonucleases found in Escherichia coli; however, the role of RNase PH in sRNA regulation has not yet been explored and reported. Here, we have examined in detail how PNPase and RNase PH interact to support sRNA stability, activity, and base pairing in exponential and stationary growth conditions. Our results indicate that these proteins facilitate the stability and regulatory function of the sRNAs RyhB, CyaR, and MicA during exponential growth. PNPase further appears to contribute to pairing between RyhB and its mRNA targets. During stationary growth, each sRNA responded differently to the absence or presence of PNPase and RNase PH. Finally, our results suggest that PNPase and RNase PH stabilize only Hfq-bound sRNAs. Taken together, these results confirm and extend previous findings that PNPase participates in sRNA regulation and reveal that RNase PH serves a similar, albeit more limited, role as well. These proteins may, therefore, act to protect sRNAs from spurious degradation while also facilitating regulatory pairing with their targets. IMPORTANCEIn many bacteria, Hfq-dependent base-pairing sRNAs facilitate rapid changes in gene expression that are critical for maintaining homeostasis and responding to stress and environmental changes. While a role for Hfq in this process was identified more than 2 decades ago, the identity and function of the other proteins required for Hfq-dependent regulation by sRNAs have not been resolved. Here, we demonstrate that PNPase and RNase PH, the two phosphorolytic RNases in E. coli, stabilize sRNAs against premature degradation and, in the case of PNPase, also accelerate regulation by sRNA-mRNA pairings for certain sRNAs. These findings are the first to demonstrate that RNase PH influences and supports sRNA regulation and suggest shared and distinct roles for these phosphorolytic RNases in this process. Bacteria rapidly alter gene expression through small noncoding RNAs (sRNAs) that act by base pairing with target mRNAs. Although classically identified as important players in bacterial stress response, sRNAs also play general roles regulating the genes involved in cell growth, nutrient acquisition, social behavior, and virulence (1, 2). sRNAs often act through translational repression, in which a given sRNA base pairs with the leader sequence of a target mRNA, obscuring the site that would otherwise form contacts with the ribosomal 30S subunit (3). This pairing can also lead to subsequent RNase E-mediated decay of the mRNA (4). In other cases, pairing with an mRNA leader sequence promotes gene expression by revea...

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“…In contrast, a growing number of examples of translational activation and mRNA stabilization by sRNAs have now been documented. A given sRNA often employs a conserved region to interact with and regulate both repressed and activated targets (6,7).…”

mentioning

confidence: 99%

Iron Homeostasis Regulates the Genotoxicity of Escherichia coli That Produces Colibactin

et al. 2016

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eThe genotoxin colibactin is a secondary metabolite produced by a variety of pathogenic enterobacteria. Its biosynthesis requires the enzymatic activity of the phosphopantetheinyl transferase (PPTase) ClbA. We previously showed that ClbA can also contribute to the production of siderophores. Because the biosynthesis of siderophores is regulated by iron availability, we hypothesized that iron could also modulate the production of colibactin through the transcriptional regulation of clbA. This study revealed an increased transcription of clbA under iron-limiting conditions and a decrease of clbA expression in iron-rich media. We demonstrate that clbA transcription is regulated by both the ferric uptake regulator (Fur) and the small regulatory noncoding RNA RyhB. We evidenced that the regulation of the transcription of clbA by Fur and RyhB leads to the regulation of colibactin production. This work highlights the complex mechanism of regulation of an important virulence factor by the two major regulators of bacterial iron homeostasis, making iron a key environmental factor contributing to bacterial virulence and carcinogenesis.

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Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria

Cited by 26 publications

References 281 publications

Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

The Phosphorolytic Exoribonucleases Polynucleotide Phosphorylase and RNase PH Stabilize sRNAs and Facilitate Regulation of Their mRNA Targets

Iron Homeostasis Regulates the Genotoxicity of Escherichia coli That Produces Colibactin

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