Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators

Reyer, Matthew A.; Chennakesavalu, Shriram; Heideman, Emily M; Ma, Xiangqian; Bujnowska, Magda; Li, Hong; Dinner, Aaron R.; Vanderpool, Carin K.; Fei, Jingyi

doi:10.1016/j.celrep.2021.109764

Cited by 11 publications

(5 citation statements)

References 84 publications

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“…Gel retardation assays showed in vitro that RsaG recognized a high number of RNAs with various binding affinities, which illustrates a possible hierarchical regulation. However, binding affinities in vivo might be different as the sRNA is expected to bind the mRNA cotranscriptionally and transacting factors might also modulate the mRNA structure and facilitate the pairings (Reyer et al, 2021). Among the target RNAs, none of them are directly linked to the G6P catabolism per se but some of them are involved in carbohydrate-dependent metabolic pathways (ccpA, ldh1) and to redox homeostasis (rex).…”

Section: Rsag Expands the Regulon Of Hptrsmentioning

confidence: 99%

The 3′UTR‐derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose‐6‐phosphate uptake in Staphylococcus aureus

Desgranges

Barrientos

Herrgott

et al. 2021

Molecular Microbiology

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Staphylococcus aureus is usually described as an extracellular opportunistic pathogen, infecting a wide range of organs and tissues.However, it also invades and replicates in various phagocytic or nonphagocytic host cells (Hamza & Li, 2014). To be successful as a pathogen, this bacterium needs to adapt to the hostile environment of the host and must acquire imposed nutriments for its survival.Consequently, the staphylococcal genome encodes several transporters for metabolites (sugars, metals, amino acids, etc.), which are

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Section: Rsag Expands the Regulon Of Hptrsmentioning

confidence: 99%

The 3′UTR‐derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose‐6‐phosphate uptake in Staphylococcus aureus

Desgranges

Barrientos

Herrgott

et al. 2021

Molecular Microbiology

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“…Repressed translation of galK leads to increased Rho-dependent termination within galK (Wang et al , 2015). Our recent work added to these translation-dependent examples of regulation by demonstrating that sRNAs including SgrS and RyhB that were previously described as post-transcriptional regulators because of their demonstrated ability to repress translation of mRNA targets can also act on some (but not all) targets co-transcriptionally to promote Rho-dependent termination (Reyer et al , 2021).…”

Section: Discussionmentioning

confidence: 99%

Multiple Small RNAs Modulate Rho-Dependent Termination in the Cyclopropane Fatty Acid Synthase mRNA 5’ Untranslated Region

Farley,

Bianco,

Vanderpool

2024

Preprint

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Bacterial small RNAs (sRNAs) have been commonly characterized as regulators of post-transcriptional steps of gene expression including translation and stability of mRNA targets. Previous work revealed that the Escherichia coli cyclopropane fatty acid synthase (cfa) mRNA is regulated by at least five different sRNAs by a proposed mechanism involving regulated cfa mRNA turnover by the RNase E degradosome. However, recent work identified the long 5' untranslated region (UTR) of cfa mRNA as a potential target for Rho-dependent transcription termination, leading us to question whether sRNAs might regulate cfa gene expression at the level of transcription elongation. In this study we report evidence for premature Rho-dependent termination within the long 5' UTR of cfa, and demonstrate that a pyrimidine-only tract within the 5' UTR is required for efficient Rho-dependent regulation of cfa. Our data suggest that all of the sequence determinants required for efficient Rho-mediated termination are harbored within the cfa long mRNA 5' UTR. Finally, we discovered that both the activating sRNA RydC and repressing sRNA CpxQ regulate cfa primarily by modulating Rho-dependent termination of cfa transcription, with only a minor effect on RNase E degradosome-dependent turnover of cfa mRNA. These results illustrate the versatile mechanisms sRNAs use to regulate target gene expression at transcriptional and post-transcriptional levels and suggest that regulation by sRNAs in long UTRs can involve modulation of transcription elongation.

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“…While most studies performed in the last decades have led to the idea that sRNAs regulate gene expression at the post-transcriptional level ( 58–60 ), it has recently been shown that sRNAs can also operate cotranscriptionally by controlling Rho transcription termination ( 61–63 ). For ChiX, Rho transcription termination is indirectly controlled through the modulation of translation initiation in Salmonella enterica ( 64 ).…”

Section: Discussionmentioning

confidence: 99%

Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms

Bastet,

Korepanov,

Jagodnik

et al. 2024

Nucleic Acids Research

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Small RNAs (sRNAs) and riboswitches represent distinct classes of RNA regulators that control gene expression upon sensing metabolic or environmental variations. While sRNAs and riboswitches regulate gene expression by affecting mRNA and protein levels, existing studies have been limited to the characterization of each regulatory system in isolation, suggesting that sRNAs and riboswitches target distinct mRNA populations. We report that the expression of btuB in Escherichia coli, which is regulated by an adenosylcobalamin (AdoCbl) riboswitch, is also controlled by the small RNAs OmrA and, to a lesser extent, OmrB. Strikingly, we find that the riboswitch and sRNAs reduce mRNA levels through distinct pathways. Our data show that while the riboswitch triggers Rho-dependent transcription termination, sRNAs rely on the degradosome to modulate mRNA levels. Importantly, OmrA pairs with the btuB mRNA through its central region, which is not conserved in OmrB, indicating that these two sRNAs may have specific targets in addition to their common regulon. In contrast to canonical sRNA regulation, we find that OmrA repression of btuB is lost using an mRNA binding-deficient Hfq variant. Together, our study demonstrates that riboswitch and sRNAs modulate btuB expression, providing an example of cis- and trans-acting RNA-based regulatory systems maintaining cellular homeostasis.

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Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators

Cited by 11 publications

References 84 publications

The 3′UTR‐derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose‐6‐phosphate uptake in Staphylococcus aureus

The 3′UTR‐derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose‐6‐phosphate uptake in Staphylococcus aureus

Multiple Small RNAs Modulate Rho-Dependent Termination in the Cyclopropane Fatty Acid Synthase mRNA 5’ Untranslated Region

Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms

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