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Noncoding RNA

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  • Authors: E. Desgranges1, S. Marzi2, K. Moreau3, P. Romby4, I. Caldelari5
  • Editors: Vincent A. Fischetti6, Richard P. Novick7, Joseph J. Ferretti8, Daniel A. Portnoy9, Miriam Braunstein10, Julian I. Rood11
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, F-67000 Strasbourg, France; 2: Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, F-67000 Strasbourg, France; 3: CIRI, International Center for Infectiology Research, Inserm, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France; 4: Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, F-67000 Strasbourg, France; 5: Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, F-67000 Strasbourg, France; 6: The Rockefeller University, New York, NY; 7: Skirball Institute for Molecular Medicine, NYU Medical Center, New York, NY; 8: Department of Microbiology & Immunology, University of Oklahoma Health Science Center, Oklahoma City, OK; 9: Department of Molecular and Cellular Microbiology, University of California, Berkeley, Berkeley, CA; 10: Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, Chapel Hill, NC; 11: Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
  • Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.GPP3-0038-2018
  • Received 07 August 2018 Accepted 25 October 2018 Published 19 April 2019
  • Isabelle Caldelari, [email protected]
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  • Abstract:

    Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as , control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5′ or 3′ untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.

  • Citation: Desgranges E, Marzi S, Moreau K, Romby P, Caldelari I. 2019. Noncoding RNA. Microbiol Spectrum 7(2):GPP3-0038-2018. doi:10.1128/microbiolspec.GPP3-0038-2018.

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/content/journal/microbiolspec/10.1128/microbiolspec.GPP3-0038-2018
2019-04-19
2019-08-25

Abstract:

Regulatory RNAs, present in many bacterial genomes and particularly in pathogenic bacteria such as , control the expression of genes encoding virulence factors or metabolic proteins. They are extremely diverse and include noncoding RNAs (sRNA), antisense RNAs, and some 5′ or 3′ untranslated regions of messenger RNAs that act as sensors for metabolites, tRNAs, or environmental conditions (e.g., temperature, pH). In this review we focus on specific examples of sRNAs of that illustrate how numerous sRNAs and associated proteins are embedded in complex networks of regulation. In addition, we discuss the CRISPR-Cas systems defined as an RNA-interference-like mechanism, which also exist in staphylococcal strains.

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Image of FIGURE 1
FIGURE 1

Several mechanisms of RNA regulation in . Schematic drawing of the flavin mononucleotide riboswitch. The 5′ UTR adopts a particular structure recognized by the flavin mononucleotide, which in turn leads to the stabilization of a stem-loop structure sequestrating the SD sequence to inhibit translation. 30S is for the small ribosomal subunit. An example of a T-box motif as found in the 5′ UTR of many mRNAs encoding aminoacyl-tRNA synthetases. Nonaminoacylated tRNA binds to the leader region at two sites and stabilizes an antiterminator structure, allowing transcription of the downstream gene. The drawing is adapted from reference 4. The 3′ UTR of the biofilm repressor IcaR possesses a cytosine-rich motif, which binds to the SD sequence and hinders ribosomes from its binding site on the mRNA (see text for details). Overlapping 5′ UTRs of G and H mRNAs are processed by the endoribonuclease III (Rnase III). Shorter 5′ ends might facilitate ribosome recruitment. The antitoxin RNA SprF1 interacts at the 3′ end of the toxin encoded by sprG1 and triggers its degradation. A cluster of five sRNAs was sequenced in the Newman strain that encodes a putative toxin-antitoxin system (see text for details). sRNAs act by an antisense mechanism. Binding of the 5′ UTR of RNAIII to the 5′ UTR of mRNA liberates its SD and activated translation (g), whereas the 3′ domain of RNAIII acts as a repressor domain, which contains C-rich motifs for base-pairing with the SD sequence of mRNA as mRNA depicted in the figure (h). Green bar, SD sequence; black circle, RNase III (for references and more details, see text).

Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.GPP3-0038-2018
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Image of FIGURE 2
FIGURE 2

Examples of the complex network between sRNAs and transcriptional factors in in response to stress. Arrows show activation and bars show repression. Blue, transcriptional regulators; green, two-component systems; red, regulatory sRNAs. Red lines corresponded to posttranscriptional regulation, and black lines, to transcriptional regulation. Dotted lines are for the target mRNAs that were not experimentally validated. Only sRNA-dependent mRNA targets encoding transcriptional factors are depicted in the figure.

Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.GPP3-0038-2018
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Image of FIGURE 3
FIGURE 3

Genomic organization of the loci for the type III-A CRISPR system of strain 08BA02176. Type III is the typical CRISPR organization. The scheme was obtained using CRISPRone ( 72 ), and the genome sequence was deposited in GenBank (accession number 08BA02176; RefSeq accession number GCF_000296595.1). Genomic organization of the loci for the type II-C CRISPR system of strain M06/0171. The CRISPR-Cas genes were found on an SCC inserted into the 3′ end of the chromosomally located gene. The scheme was obtained using CRISPRone ( 72 ), and the SCCmec sequence was deposited in GenBank (GenBank accession number HE980450.1). Cartoon (RNA and DNA) and surface (Cas9) representations of the SaCas9-sgRNA-target DNA complex (pdb file 5AXW) ( 80 ). The SaCas9 sgRNA consists of the crRNA guide region (crGUIDE represented in pale yellow) forming a heteroduplex with the target DNA strand (tDNA in magenta) and the repeat/antirepeat helix (blue, the repeat crRNA-derived strand, green, the antirepeat trascrRNA-derived strand). The protospacer adjacent region-containing DNA duplex is red. Cas9 domains are colored as follows: cyan, WED domain; pale orange, REC domain; gray, NUC domain. Molecular graphics images were prepared using PyMol.

Source: microbiolspec April 2019 vol. 7 no. 2 doi:10.1128/microbiolspec.GPP3-0038-2018
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