RNA polyadenylation and its consequences in prokaryotes

Hajnsdorf, Eliane; Kaberdin, Vladimir R.

doi:10.1098/rstb.2018.0166

Cited by 37 publications

(28 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The doublet sizes of P 1 -Vc2 transcripts and the pattern of their degradation we observed in our rifampin stability assay are consistent with distinct populations of 3=-tailed and nontailed transcripts, which is a hallmark of the 3=-end degradative processes described for many regulatory RNAs in bacteria (Fig. 6A) (47). We hypothesize that closure of the P1 stem of the Vc2 aptamer during a c-di-GMP binding event increases the stability of P 1 -Vc2 by making the nucleotides at the 3= end of the riboswitch transcript inaccessible to 3= to 5= exonucleases.…”

Section: Figsupporting

confidence: 84%

The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability

et al. 2019

View full text Add to dashboard Cite

Cyclic di-GMP (c-di-GMP) is a bacterial second messenger molecule that is important in the biology of Vibrio cholerae, but the molecular mechanisms by which this molecule regulates downstream phenotypes have not been fully characterized. We have previously shown that the Vc2 c-di-GMP-binding riboswitch, encoded upstream of the gene tfoY, functions as an off switch in response to c-di-GMP. However, the mechanism by which c-di-GMP controls expression of tfoY has not been fully elucidated. During our studies of this mechanism, we determined that c-di-GMP binding to Vc2 also controls the abundance and stability of upstream noncoding RNAs with 3′ ends located immediately downstream of the Vc2 riboswitch. Our results suggest these putative small RNAs (sRNAs) are not generated by transcriptional termination but rather by preventing degradation of the upstream untranslated RNA when c-di-GMP is bound to Vc2. IMPORTANCE Riboswitches are typically RNA elements located in the 5′ untranslated region of mRNAs. They are highly structured and specifically recognize and respond to a given chemical cue to alter transcription termination or translation initiation. In this work, we report a novel mechanism of riboswitch-mediated gene regulation in Vibrio cholerae whereby a 3′ riboswitch, named Vc2, controls the stability of upstream untranslated RNA upon binding to its cognate ligand, the second messenger cyclic di-GMP, leading to the accumulation of previously undescribed putative sRNAs. We further demonstrate that binding of the ligand to the riboswitch prevents RNA degradation. As binding of riboswitches to their ligands often produces compactly structured RNA, we hypothesize this mechanism of gene regulation is widespread.

show abstract

Section: Figsupporting

confidence: 84%

The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability

et al. 2019

View full text Add to dashboard Cite

show abstract

“…mitochondria | gene expression | PPR proteins | protein-RNA complex | PAR-CLIP R NA 3′ polyadenylation is ubiquitous in cells. Polyadenylation can stabilize RNA or aid in its decay, it enables nuclear mRNA export, and facilitates translation (1)(2)(3)(4)(5)(6)(7). In organelles, poly(A) tails are generally known to alter the stability of mRNA; however, the mitochondria of the yeast Saccharomyces cerevisiae lack polyadenylation machinery (8,9).…”

mentioning

confidence: 99%

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs

Hillen

Markov

Wojtas

et al. 2021

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

View full text Add to dashboard Cite

Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5′ capping and 3′ polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3′-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3′-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.

show abstract

“…In contrast to the mostly stabilizing role of poly(A) tails at the 3' ends of cytoplasmic RNAs in eukaryotes, polyadenylation in eubacteria, chloroplasts, and mitochondria as well as in nuclei of diverse eukaryotes promotes the rapid exonucleolytic degradation of RNAs [94]. Several enzymes such as nucleotidyltransferase (CCA-NTR), poly(A) polymerase I (PAP I), which produce homopolymeric poly(A)-tails and is lacking in Bacillus subtilis and polynucleotide phosphorylase (PNPase) were shown to be responsible for RNA 3'-tail synthesis in bacteria.…”

Section: Polyadenylationmentioning

confidence: 95%

“…The RNA chaperone Hfq stimulates initiated polyadenylation, thereby increasing the processivity of PAP. RNA degradation involves a large set of exo-and endonucleases as well as the action of the eubacterial degradosome [94].…”

Section: Polyadenylationmentioning

confidence: 99%

The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods

Manavski

Vicente

Chi

et al. 2021

Genes

View full text Add to dashboard Cite

Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.

show abstract

RNA polyadenylation and its consequences in prokaryotes

Cited by 37 publications

References 83 publications

The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability

The Vc2 Cyclic di-GMP-Dependent Riboswitch of Vibrio cholerae Regulates Expression of an Upstream Putative Small RNA by Controlling RNA Stability

The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs

The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods

Contact Info

Product

Resources

About