Prevalence of Small Base-pairing RNAs Derived from Diverse Genomic Loci

Overview

Journal Biochim Biophys Acta Gene Regul Mech

Publisher Elsevier

Specialties Biochemistry
Biophysics
Genetics
Molecular Biology

Date 2020 Mar 10

PMID 32147527

Citations 44

Authors

Philip P Adams

Gisela Storz

Affiliations

Soon will be listed here.

Abstract

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.

Citing Articles

The pathogenicity island 1-encoded small RNA InvR mediates post-transcriptional feedback control of the activator HilA in .

Hou Y, Kim K, Cakar F, Golubeva Y, Slauch J, Vanderpool C bioRxiv. 2024; .

PMID: 39605656 PMC: 11601589. DOI: 10.1101/2024.11.21.624761.

Biological Insights from RNA-RNA Interactomes in Bacteria, as Revealed by RIL-seq.

Silverman A, Melamed S Methods Mol Biol. 2024; 2866:189-206.

PMID: 39546204 DOI: 10.1007/978-1-0716-4192-7_11.

Assessing the transcriptional landscape of Pseudomonas phage 201ϕ2-1: Uncovering the small regulatory details of a giant phage.

Poppeliers J, Focquet M, Boon M, De Mey M, Thomas J, Lavigne R Microb Biotechnol. 2024; 17(10):e70037.

PMID: 39460739 PMC: 11512511. DOI: 10.1111/1751-7915.70037.

ChimericFragments: computation, analysis and visualization of global RNA networks.

Siemers M, Lippegaus A, Papenfort K NAR Genom Bioinform. 2024; 6(2):lqae035.

PMID: 38633425 PMC: 11023125. DOI: 10.1093/nargab/lqae035.

In vivo RNA interactome profiling reveals 3'UTR-processed small RNA targeting a central regulatory hub.

Liu F, Chen Z, Zhang S, Wu K, Bei C, Wang C Nat Commun. 2023; 14(1):8106.

PMID: 38062076 PMC: 10703908. DOI: 10.1038/s41467-023-43632-1.

References

Iosub I, van Nues R, McKellar S, Nieken K, Marchioretto M, Sy B . Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. Elife. 2020; 9. PMC: 7213987. DOI: 10.7554/eLife.54655. View

Carroll R, Weiss A, Broach W, Wiemels R, Mogen A, Rice K . Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus. mBio. 2016; 7(1):e01990-15. PMC: 4752604. DOI: 10.1128/mBio.01990-15. View

Hao Y, Updegrove T, Livingston N, Storz G . Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA. Nucleic Acids Res. 2016; 44(14):6935-48. PMC: 5001591. DOI: 10.1093/nar/gkw404. View

Mader U, Nicolas P, Depke M, Pane-Farre J, Debarbouille M, van der Kooi-Pol M . Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions. PLoS Genet. 2016; 12(4):e1005962. PMC: 4818034. DOI: 10.1371/journal.pgen.1005962. View

Marinho C, Dos Santos P, Kallipolitis B, Johansson J, Ignatov D, Guerreiro D . The σ-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in through a direct interaction with the transcript. RNA Biol. 2019; 16(10):1424-1437. PMC: 6779388. DOI: 10.1080/15476286.2019.1632776. View

Le Pabic H, Germain-Amiot N, Bordeau V, Felden B . A bacterial regulatory RNA attenuates virulence, spread and human host cell phagocytosis. Nucleic Acids Res. 2015; 43(19):9232-48. PMC: 4627067. DOI: 10.1093/nar/gkv783. View

Landt S, Lesley J, Britos L, Shapiro L . CrfA, a small noncoding RNA regulator of adaptation to carbon starvation in Caulobacter crescentus. J Bacteriol. 2010; 192(18):4763-75. PMC: 2937403. DOI: 10.1128/JB.00343-10. View

Pagliuso A, Tham T, Allemand E, Robertin S, Dupuy B, Bertrand Q . An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling. Cell Host Microbe. 2019; 26(6):823-835.e11. PMC: 6907008. DOI: 10.1016/j.chom.2019.10.004. View

Chao Y, Li L, Girodat D, Forstner K, Said N, Corcoran C . In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Mol Cell. 2017; 65(1):39-51. PMC: 5222698. DOI: 10.1016/j.molcel.2016.11.002. View

10.

Brophy J, Voigt C . Antisense transcription as a tool to tune gene expression. Mol Syst Biol. 2016; 12(1):854. PMC: 4731013. DOI: 10.15252/msb.20156540. View

11.

Shearwin K, Callen B, Barry Egan J . Transcriptional interference--a crash course. Trends Genet. 2005; 21(6):339-45. PMC: 2941638. DOI: 10.1016/j.tig.2005.04.009. View

12.

Munishkin A, Wool I . The ribosome-in-pieces: binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin/ricin and thiostrepton domains of 23S ribosomal RNA. Proc Natl Acad Sci U S A. 1997; 94(23):12280-4. PMC: 24907. DOI: 10.1073/pnas.94.23.12280. View

13.

Andersen J, Forst S, Zhao K, Inouye M, Delihas N . The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli. J Biol Chem. 1989; 264(30):17961-70. View

14.

Perez N, Trevino J, Liu Z, Ho S, Babitzke P, Sumby P . A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus. PLoS One. 2009; 4(11):e7668. PMC: 2765633. DOI: 10.1371/journal.pone.0007668. View

15.

Melamed S, Faigenbaum-Romm R, Peer A, Reiss N, Shechter O, Bar A . Mapping the small RNA interactome in bacteria using RIL-seq. Nat Protoc. 2017; 13(1):1-33. DOI: 10.1038/nprot.2017.115. View

16.

Gogol E, Rhodius V, Papenfort K, Vogel J, Gross C . Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon. Proc Natl Acad Sci U S A. 2011; 108(31):12875-80. PMC: 3150882. DOI: 10.1073/pnas.1109379108. View

17.

Chen J, Morita T, Gottesman S . Regulation of Transcription Termination of Small RNAs and by Small RNAs: Molecular Mechanisms and Biological Functions. Front Cell Infect Microbiol. 2019; 9:201. PMC: 6582626. DOI: 10.3389/fcimb.2019.00201. View

18.

Rivas E, Eddy S . Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics. 2002; 2:8. PMC: 64605. DOI: 10.1186/1471-2105-2-8. View

19.

Liu J, Camilli A . Discovery of bacterial sRNAs by high-throughput sequencing. Methods Mol Biol. 2011; 733:63-79. PMC: 3564964. DOI: 10.1007/978-1-61779-089-8_5. View

20.

Sharma C, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A . The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010; 464(7286):250-5. DOI: 10.1038/nature08756. View