1
|
Papenfort K, Storz G. Insights into bacterial metabolism from small RNAs. Cell Chem Biol 2024:S2451-9456(24)00304-0. [PMID: 39094580 DOI: 10.1016/j.chembiol.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/08/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Abstract
The study of small, regulatory RNAs (sRNA) that act by base-pairing with target RNAs in bacteria has been steadily advancing, particularly with the availability of more and more transcriptome and RNA-RNA interactome datasets. While the characterization of multiple sRNAs has helped to elucidate their mechanisms of action, these studies also are providing insights into protein function, control of metabolic flux, and connections between metabolic pathways as we will discuss here. In describing several examples of the metabolic insights gained, we will summarize the different types of base-pairing sRNAs including mRNA-derived sRNAs, sponge RNAs, RNA mimics, and dual-function RNAs as well as suggest how information about sRNAs could be exploited in the future.
Collapse
Affiliation(s)
- Kai Papenfort
- Friedrich Schiller University Jena, Institute of Microbiology, 07745 Jena, Germany; Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-4417, USA.
| |
Collapse
|
2
|
Raden M, Miladi M. How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA. Methods Mol Biol 2024; 2726:209-234. [PMID: 38780733 DOI: 10.1007/978-1-0716-3519-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Computational prediction of RNA-RNA interactions (RRI) is a central methodology for the specific investigation of inter-molecular RNA interactions and regulatory effects of non-coding RNAs like eukaryotic microRNAs or prokaryotic small RNAs. Available methods can be classified according to their underlying prediction strategies, each implicating specific capabilities and restrictions often not transparent to the non-expert user. Within this work, we review seven classes of RRI prediction strategies and discuss the advantages and limitations of respective tools, since such knowledge is essential for selecting the right tool in the first place.Among the RRI prediction strategies, accessibility-based approaches have been shown to provide the most reliable predictions. Here, we describe how IntaRNA, as one of the state-of-the-art accessibility-based tools, can be applied in various use cases for the task of computational RRI prediction. Detailed hands-on examples for individual RRI predictions as well as large-scale target prediction scenarios are provided. We illustrate the flexibility and capabilities of IntaRNA through the examples. Each example is designed using real-life data from the literature and is accompanied by instructions on interpreting the respective results from IntaRNA output. Our use-case driven instructions enable non-expert users to comprehensively understand and utilize IntaRNA's features for effective RRI predictions.
Collapse
Affiliation(s)
- Martin Raden
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany.
| | - Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| |
Collapse
|
3
|
Watkins D, Arya D. Models of Hfq interactions with small non-coding RNA in Gram-negative and Gram-positive bacteria. Front Cell Infect Microbiol 2023; 13:1282258. [PMID: 37942477 PMCID: PMC10628458 DOI: 10.3389/fcimb.2023.1282258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
Hfq is required by many Gram-negative bacteria to chaperone the interaction between small non-coding RNA (sRNA) and mRNA to facilitate annealing. Conversely and despite the presence of Hfq in many Gram-positive bacteria, sRNAs in Gram-positive bacteria bind the mRNA target independent of Hfq. Details provided by the Hfq structures from both Gram-negative and Gram-positive bacteria have demonstrated that despite a conserved global structure of the protein, variations of residues on the binding surfaces of Hfq results in the recognition of different RNA sequences as well as the ability of Hfq to facilitate the annealing of the sRNA to the mRNA target. Additionally, a subset of Gram-negative bacteria has an extended C-terminal Domain (CTD) that has been shown to affect the stability of the Hfq hexamer and increase the rate of release of the annealed sRNA-mRNA product. Here we review the structures of Hfq and biochemical data that have defined the interactions of the Gram-negative and Gram-positive homologues to highlight the similarities and differences in the interactions with RNA. These interactions provided a deeper understanding of the how Hfq functions to facilitate the annealing of sRNA-mRNA, the selectivity of the interactions with RNA, and the role of the CTD of Hfq in the interactions with sRNA.
Collapse
Affiliation(s)
- Derrick Watkins
- Department of Math and Science, University of Tennessee Southern, Pulaski, TN, United States
| | - Dev Arya
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
| |
Collapse
|
4
|
Abstract
Small regulatory RNA (sRNAs) are key mediators of posttranscriptional gene control in bacteria. Assisted by RNA-binding proteins, a single sRNA often modulates the expression of dozens of genes, and thus sRNAs frequently adopt central roles in regulatory networks. Posttranscriptional regulation by sRNAs comes with several unique features that cannot be achieved by transcriptional regulators. However, for optimal network performance, transcriptional and posttranscriptional control mechanisms typically go hand-in-hand. This view is reflected by the ever-growing class of mixed network motifs involving sRNAs and transcription factors, which are ubiquitous in biology and whose regulatory properties we are beginning to understand. In addition, sRNA activity can be antagonized by base-pairing with sponge RNAs, adding yet another layer of complexity to these networks. In this article, we summarize the regulatory concepts underlying sRNA-mediated gene control in bacteria and discuss how sRNAs shape the output of a network, focusing on several key examples.
Collapse
Affiliation(s)
- Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany;
- Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
| | - Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel;
| |
Collapse
|
5
|
Chihara K, Gerovac M, Hör J, Vogel J. Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq). RNA (NEW YORK, N.Y.) 2022; 29:rna.079439.122. [PMID: 36328526 PMCID: PMC9808575 DOI: 10.1261/rna.079439.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. New RNA-protein complexes are predicted based on the similarity of their elution profiles. In SEC-seq, we have replaced the glycerol gradient with separation by size exclusion chromatography, which shortens operation times and offers greater potential for automation. Applying SEC-seq to Escherichia coli, we find that the method provides a higher resolution than Grad-seq in the lower molecular weight range up to ~500 kDa. This is illustrated by the ability of SEC-seq to resolve two distinct, but similarly sized complexes of the global translational repressor CsrA with either of its antagonistic small RNAs, CsrB and CsrC. We also characterized changes in the SEC-seq profiles of the small RNA MicA upon deletion of its RNA chaperones Hfq and ProQ and investigated the redistribution of these two proteins upon RNase treatment. Overall, we demonstrate that SEC-seq is a tractable and reproducible method for the global profiling of bacterial RNA-protein complexes that offers the potential to discover yet-unrecognized associations between bacterial RNAs and proteins.
Collapse
Affiliation(s)
- Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
| | | | - Jens Hör
- Weizmann Institute, Rehovot, Israel
| | | |
Collapse
|
6
|
Roca J, Santiago-Frangos A, Woodson SA. Diversity of bacterial small RNAs drives competitive strategies for a mutual chaperone. Nat Commun 2022; 13:2449. [PMID: 35508531 PMCID: PMC9068810 DOI: 10.1038/s41467-022-30211-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/06/2022] [Indexed: 12/17/2022] Open
Abstract
Hundreds of bacterial small RNAs (sRNAs) require the Hfq chaperone to regulate mRNA expression. Hfq is limiting, thus competition among sRNAs for binding to Hfq shapes the proteomes of individual cells. To understand how sRNAs compete for a common partner, we present a single-molecule fluorescence platform to simultaneously visualize binding and release of multiple sRNAs with Hfq. We show that RNA residents rarely dissociate on their own. Instead, clashes between residents and challengers on the same face of Hfq cause rapid exchange, whereas RNAs that recognize different surfaces may cohabit Hfq for several minutes before one RNA departs. The prevalence of these pathways depends on the structure of each RNA and how it interacts with Hfq. We propose that sRNA diversity creates many pairwise interactions with Hfq that allow for distinct biological outcomes: active exchange favors fast regulation whereas co-residence of dissimilar RNAs favors target co-recognition or target exclusion.
Collapse
Affiliation(s)
- Jorjethe Roca
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA
| | - Andrew Santiago-Frangos
- CMDB Program, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.,Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.
| |
Collapse
|
7
|
Yeom J, Park JS, Jeon YM, Song BS, Yoo SM. Synthetic fused sRNA for the simultaneous repression of multiple genes. Appl Microbiol Biotechnol 2022; 106:2517-2527. [PMID: 35291022 DOI: 10.1007/s00253-022-11867-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/02/2022]
Abstract
Efficient control over multiple gene expression still presents a major challenge. Synthetic sRNA enables targeted gene expression control in trans without directly modifying the chromosome, but its use to simultaneously target multiple genes can often cause cell growth defects because of the need for additional energy for transcription and lowering of their repression efficiency by limiting the amount of Hfq protein. To address these limitations, we present fusion sRNA (fsRNA) that simultaneously regulates the translation of multiple genes efficiently. It is constructed by linking the mRNA-binding modules for multiple targeted genes in one sRNA scaffold via one-pot generation using overlap extension PCR. The repression capacity of fsRNA was demonstrated by the construction of sRNAs to target four endogenous genes: caiF, hybG, ytfR and minD in Escherichia coli. Their cross-reactivity and the effect on cell growth were also investigated. As practical applications, we applied fsRNA to violacein- and protocatechuic acid-producing strains, resulting in increases of 13% violacein and 81% protocatechuic acid, respectively. The developed fsRNA-mediated multiple gene expression regulation system thus enables rapid and efficient development of optimised cell factories for valuable chemicals without cell growth defects and limiting cellular resources.Key points• Synthetic fusion sRNA (fsRNA)-based system was constructed for the repression of multiple target genes.• fsRNA repressed multiple genes by only expressing a single sRNA while minimising the cellular burden.• The application of fsRNA showed the increased production titers of violacein (13%) and protocatechuic acid (81%).
Collapse
Affiliation(s)
- Jinho Yeom
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jong Seong Park
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Yong Min Jeon
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Beom Seop Song
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul, 06974, Republic of Korea.
| |
Collapse
|
8
|
Kavita K, Zhang A, Tai CH, Majdalani N, Storz G, Gottesman S. Multiple in vivo roles for the C-terminal domain of the RNA chaperone Hfq. Nucleic Acids Res 2022; 50:1718-1733. [PMID: 35104863 DOI: 10.1093/nar/gkac017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/19/2021] [Accepted: 01/29/2022] [Indexed: 12/22/2022] Open
Abstract
Hfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), the Escherichia coli mutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression of mutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.
Collapse
Affiliation(s)
- Kumari Kavita
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| | - Aixia Zhang
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| | - Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
9
|
Matera G, Altuvia Y, Gerovac M, El Mouali Y, Margalit H, Vogel J. Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity. Mol Cell 2022; 82:629-644.e4. [PMID: 35063132 DOI: 10.1016/j.molcel.2021.12.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 10/04/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022]
Abstract
The envelope of Gram-negative bacteria is a vital barrier that must balance protection and nutrient uptake. Small RNAs are crucial regulators of the envelope composition and function. Here, using RIL-seq to capture the Hfq-mediated RNA-RNA interactome in Salmonella enterica, we discover envelope-related riboregulators, including OppX. We show that OppX acts as an RNA sponge of MicF sRNA, a prototypical porin repressor. OppX originates from the 5' UTR of oppABCDF, encoding the major inner-membrane oligopeptide transporter, and sequesters MicF's seed region to derepress the synthesis of the porin OmpF. Intriguingly, OppX operates as a true sponge, storing MicF in an inactive complex without affecting its levels or stability. Conservation of the opp-OppX-MicF-ompF axis in related bacteria suggests that it serves an important mechanism, adjusting envelope porosity to specific transport capacity. These data also highlight the resource value of this Salmonella RNA interactome, which will aid in unraveling RNA-centric regulation in enteric pathogens.
Collapse
Affiliation(s)
- Gianluca Matera
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Milan Gerovac
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Youssef El Mouali
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany.
| |
Collapse
|
10
|
Lai YJ, Yakhnin H, Pannuri A, Pourciau C, Babitzke P, Romeo T. CsrA regulation via binding to the base-pairing small RNA Spot 42. Mol Microbiol 2022; 117:32-53. [PMID: 34107125 PMCID: PMC10000020 DOI: 10.1111/mmi.14769] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 02/03/2023]
Abstract
The carbon storage regulator system and base-pairing small RNAs (sRNAs) represent two predominant modes of bacterial post-transcriptional regulation, which globally influence gene expression. Binding of CsrA protein to the 5' UTR or initial mRNA coding sequences can affect translation, RNA stability, and/or transcript elongation. Base-pairing sRNAs also regulate these processes, often requiring assistance from the RNA chaperone Hfq. Transcriptomics studies in Escherichia coli have identified many new CsrA targets, including Spot 42 and other base-pairing sRNAs. Spot 42 synthesis is repressed by cAMP-CRP, induced by the presence of glucose, and Spot 42 post-transcriptionally represses operons that facilitate metabolism of nonpreferred carbon sources. CsrA activity is also increased by glucose via effects on CsrA sRNA antagonists, CsrB/C. Here, we elucidate a mechanism wherein CsrA binds to and protects Spot 42 sRNA from RNase E-mediated cleavage. This protection leads to enhanced repression of srlA by Spot 42, a gene required for sorbitol uptake. A second, independent mechanism by which CsrA represses srlA is by binding to and inhibiting translation of srlM mRNA, encoding a transcriptional activator of srlA. Our findings demonstrate a novel means of regulation, by CsrA binding to a sRNA, and indicate that such interactions can help to shape complex bacterial regulatory circuitry.
Collapse
Affiliation(s)
- Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Archana Pannuri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| |
Collapse
|
11
|
Evguenieva-Hackenberg E. Riboregulation in bacteria: From general principles to novel mechanisms of the trp attenuator and its sRNA and peptide products. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1696. [PMID: 34651439 DOI: 10.1002/wrna.1696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/26/2022]
Abstract
Gene expression strategies ensuring bacterial survival and competitiveness rely on cis- and trans-acting RNA-regulators (riboregulators). Among the cis-acting riboregulators are transcriptional and translational attenuators, and antisense RNAs (asRNAs). The trans-acting riboregulators are small RNAs (sRNAs) that bind proteins or base pairs with other RNAs. This classification is artificial since some regulatory RNAs act both in cis and in trans, or function in addition as small mRNAs. A prominent example is the archetypical, ribosome-dependent attenuator of tryptophan (Trp) biosynthesis genes. It responds by transcription attenuation to two signals, Trp availability and inhibition of translation, and gives rise to two trans-acting products, the attenuator sRNA rnTrpL and the leader peptide peTrpL. In Escherichia coli, rnTrpL links Trp availability to initiation of chromosome replication and in Sinorhizobium meliloti, it coordinates regulation of split tryptophan biosynthesis operons. Furthermore, in S. meliloti, peTrpL is involved in mRNA destabilization in response to antibiotic exposure. It forms two types of asRNA-containing, antibiotic-dependent ribonucleoprotein complexes (ARNPs), one of them changing the target specificity of rnTrpL. The posttranscriptional role of peTrpL indicates two emerging paradigms: (1) sRNA reprograming by small molecules and (2) direct involvement of antibiotics in regulatory RNPs. They broaden our view on RNA-based mechanisms and may inspire new approaches for studying, detecting, and using antibacterial compounds. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Collapse
|
12
|
Le Huyen KB, Gonzalez CD, Pascreau G, Bordeau V, Cattoir V, Liu W, Bouloc P, Felden B, Chabelskaya S. A small regulatory RNA alters Staphylococcus aureus virulence by titrating RNAIII activity. Nucleic Acids Res 2021; 49:10644-10656. [PMID: 34554192 PMCID: PMC8501977 DOI: 10.1093/nar/gkab782] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 01/17/2023] Open
Abstract
Staphylococcus aureus is an opportunistic human and animal pathogen with an arsenal of virulence factors that are tightly regulated during bacterial infection. The latter is achieved through a sophisticated network of regulatory proteins and regulatory RNAs. Here, we describe the involvement of a novel prophage-carried small regulatory S. aureus RNA, SprY, in the control of virulence genes. An MS2-affinity purification assay reveals that SprY forms a complex in vivo with RNAIII, a major regulator of S. aureus virulence genes. SprY binds to the 13th stem-loop of RNAIII, a key functional region involved in the repression of multiple mRNA targets. mRNAs encoding the repressor of toxins Rot and the extracellular complement binding protein Ecb are among the targets whose expression is increased by SprY binding to RNAIII. Moreover, SprY decreases S. aureus hemolytic activity and virulence. Our results indicate that SprY titrates RNAIII activity by targeting a specific stem loop. Thus, we demonstrate that a prophage-encoded sRNA reduces the pathogenicity of S. aureus through RNA sponge activity.
Collapse
Affiliation(s)
- Kim Boi Le Huyen
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | | | - Gaëtan Pascreau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Valérie Bordeau
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Vincent Cattoir
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Wenfeng Liu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Philippe Bouloc
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Brice Felden
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| | - Svetlana Chabelskaya
- Inserm, BRM [Bacterial Regulatory RNAs and Medicine] - UMR_S 1230, 35033 Rennes, France
| |
Collapse
|
13
|
Grützner J, Remes B, Eisenhardt KMH, Scheller D, Kretz J, Madhugiri R, McIntosh M, Klug G. sRNA-mediated RNA processing regulates bacterial cell division. Nucleic Acids Res 2021; 49:7035-7052. [PMID: 34125915 PMCID: PMC8266604 DOI: 10.1093/nar/gkab491] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/17/2021] [Accepted: 05/28/2021] [Indexed: 01/16/2023] Open
Abstract
Tight control of cell division is essential for survival of most organisms. For prokaryotes, the regulatory mechanisms involved in the control of cell division are mostly unknown. We show that the small non-coding sRNA StsR has an important role in controlling cell division and growth in the alpha-proteobacterium Rhodobacter sphaeroides. StsR is strongly induced by stress conditions and in stationary phase by the alternative sigma factors RpoHI/HII, thereby providing a regulatory link between cell division and environmental cues. Compared to the wild type, a mutant lacking StsR enters stationary phase later and more rapidly resumes growth after stationary phase. A target of StsR is UpsM, the most abundant sRNA in the exponential phase. It is derived from partial transcriptional termination within the 5' untranslated region of the mRNA of the division and cell wall (dcw) gene cluster. StsR binds to UpsM as well as to the 5' UTR of the dcw mRNA and the sRNA-sRNA and sRNA-mRNA interactions lead to a conformational change that triggers cleavage by the ribonuclease RNase E, affecting the level of dcw mRNAs and limiting growth. These findings provide interesting new insights into the role of sRNA-mediated regulation of cell division during the adaptation to environmental changes.
Collapse
Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Bernhard Remes
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Katrin M H Eisenhardt
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Daniel Scheller
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Jonas Kretz
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, University of Giessen, Schubertstr. 81, D-35392 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| |
Collapse
|
14
|
A fluorescence-based genetic screen reveals diverse mechanisms silencing small RNA signaling in E. coli. Proc Natl Acad Sci U S A 2021; 118:2106964118. [PMID: 34210798 DOI: 10.1073/pnas.2106964118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As key players of gene regulation in many bacteria, small regulatory RNAs (sRNAs) associated with the RNA chaperone Hfq shape numerous phenotypic traits, including metabolism, stress response and adaptation, as well as virulence. sRNAs can alter target messenger RNA (mRNA) translation and stability via base pairing. sRNA synthesis is generally under tight transcriptional regulation, but other levels of regulation of sRNA signaling are less well understood. Here we used a fluorescence-based functional screen to identify regulators that can quench sRNA signaling of the iron-responsive sRNA RyhB in Escherichia coli The identified regulators fell into two classes, general regulators (affecting signaling by many sRNAs) and RyhB-specific regulators; we focused on the specific ones here. General regulators include three Hfq-interacting sRNAs, CyaR, ChiX, and McaS, previously found to act through Hfq competition, RNase T, a 3' to 5' exonuclease not previously implicated in sRNA degradation, and YhbS, a putative GCN5-related N-acetyltransferase (GNAT). Two specific regulators were identified. AspX, a 3'end-derived small RNA, specifically represses RyhB signaling via an RNA sponging mechanism. YicC, a previously uncharacterized but widely conserved protein, triggers rapid RyhB degradation via collaboration with the exoribonuclease PNPase. These findings greatly expand our knowledge of regulation of bacterial sRNA signaling and suggest complex regulatory networks for controlling iron homeostasis in bacteria. The fluorescence-based genetic screen system described here is a powerful tool expected to accelerate the discovery of novel regulators of sRNA signaling in many bacteria.
Collapse
|
15
|
Faigenbaum-Romm R, Reich A, Gatt YE, Barsheshet M, Argaman L, Margalit H. Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation. Cell Rep 2021; 30:3127-3138.e6. [PMID: 32130912 PMCID: PMC7059120 DOI: 10.1016/j.celrep.2020.02.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 01/15/2020] [Accepted: 02/04/2020] [Indexed: 11/28/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are posttranscriptional regulators of gene expression that base pair with complementary sequences on target mRNAs, often in association with the chaperone Hfq. Here, using experimentally identified sRNA-target pairs, along with gene expression measurements, we assess basic principles of regulation by sRNAs. We show that the sRNA sequence dictates the target repertoire, as point mutations in the sRNA shift the target set correspondingly. We distinguish two subsets of targets: targets showing changes in expression levels under overexpression of their sRNA regulator and unaffected targets that interact more sporadically with the sRNA. These differences among targets are associated with their Hfq occupancy, rather than with the sRNA-target base-pairing potential. Our results suggest that competition among targets over Hfq binding plays a major role in the regulatory outcome, possibly awarding targets with higher Hfq binding efficiency an advantage in the competition over binding to the sRNA. Basic concepts of regulation by small RNAs are revealed from large-scale data Small changes in the small RNA sequence shift the target repertoire accordingly A regulatory sRNA affects the expression levels of only a subset of its targets Competition among targets over Hfq binding plays a major role in their regulation
Collapse
Affiliation(s)
- Raya Faigenbaum-Romm
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Avichai Reich
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Meshi Barsheshet
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| |
Collapse
|
16
|
Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021; 10:62438. [PMID: 33460557 PMCID: PMC7815308 DOI: 10.7554/elife.62438] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. In most organisms, specific segments of a cell’s genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are ‘non-coding’ and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.
Collapse
Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, United States
| | - Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kavya Chegireddy
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Molly Monge
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, United States.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| |
Collapse
|
17
|
Denham EL. The Sponge RNAs of bacteria - How to find them and their role in regulating the post-transcriptional network. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194565. [PMID: 32475775 DOI: 10.1016/j.bbagrm.2020.194565] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
In bacteria small regulatory RNAs (sRNAs) interact with their mRNA targets through non-consecutive base-pairing. The loose base-pairing specificity allows sRNAs to regulate large numbers of genes, either affecting the stability and/or the translation of mRNAs. Mechanisms enabling post-transcriptional regulation of the sRNAs themselves have also been described involving so-called sponge RNAs. Sponge RNAs modulate free sRNA levels in the cell through RNA-RNA interactions that sequester ("soak up") the sRNA and/or promote degradation of the target sRNA or the sponge RNA-sRNA complex. The development of complex RNA sequencing strategies for the detection of RNA-RNA interactions has enabled identification of several sponge RNAs, as well as previously known regulatory RNAs able to act as both regulators and sponges. This review highlights techniques that have enabled the identification of these sponge RNAs, the origins of sponge RNAs and the mechanisms by which they function in the post-transcriptional network.
Collapse
Affiliation(s)
- Emma L Denham
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom.
| |
Collapse
|
18
|
Jørgensen MG, Pettersen JS, Kallipolitis BH. sRNA-mediated control in bacteria: An increasing diversity of regulatory mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194504. [PMID: 32061884 DOI: 10.1016/j.bbagrm.2020.194504] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 12/26/2022]
Abstract
Small regulatory RNAs (sRNAs) act as post-transcriptional regulators controlling bacterial adaptation to environmental changes. Our current understanding of the mechanisms underlying sRNA-mediated control is mainly based on studies in Escherichia coli and Salmonella. Ever since the discovery of sRNAs decades ago, these Gram-negative species have served as excellent model organisms in the field of sRNA biology. More recently, the role of sRNAs in gene regulation has become the center of attention in a broader range of species, including Gram-positive model organisms. Here, we highlight some of the most apparent similarities and differences between Gram-negative and Gram-positive bacteria with respect to the mechanisms underlying sRNA-mediated control. Although key aspects of sRNA regulation appear to be highly conserved, novel themes are arising from studies in Gram-positive species, such as a clear abundance of sRNAs acting through multiple C-rich motifs, and an apparent lack of RNA-binding proteins with chaperone activity.
Collapse
Affiliation(s)
- Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jens Sivkær Pettersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Birgitte H Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| |
Collapse
|
19
|
Adams PP, Storz G. Prevalence of small base-pairing RNAs derived from diverse genomic loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194524. [PMID: 32147527 DOI: 10.1016/j.bbagrm.2020.194524] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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.
Collapse
Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
| |
Collapse
|
20
|
Hör J, Matera G, Vogel J, Gottesman S, Storz G. Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0030-2019. [PMID: 32213244 PMCID: PMC7112153 DOI: 10.1128/ecosalplus.esp-0030-2019] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Indexed: 12/20/2022]
Abstract
The last few decades have led to an explosion in our understanding of the major roles that small regulatory RNAs (sRNAs) play in regulatory circuits and the responses to stress in many bacterial species. Much of the foundational work was carried out with Escherichia coli and Salmonella enterica serovar Typhimurium. The studies of these organisms provided an overview of how the sRNAs function and their impact on bacterial physiology, serving as a blueprint for sRNA biology in many other prokaryotes. They also led to the development of new technologies. In this chapter, we first summarize how these sRNAs were identified, defining them in the process. We discuss how they are regulated and how they act and provide selected examples of their roles in regulatory circuits and the consequences of this regulation. Throughout, we summarize the methodologies that were developed to identify and study the regulatory RNAs, most of which are applicable to other bacteria. Newly updated databases of the known sRNAs in E. coli K-12 and S. enterica Typhimurium SL1344 serve as a reference point for much of the discussion and, hopefully, as a resource for readers and for future experiments to address open questions raised in this review.
Collapse
Affiliation(s)
- Jens Hör
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Gianluca Matera
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892
| |
Collapse
|
21
|
Carrier MC, Lalaouna D, Massé E. Broadening the Definition of Bacterial Small RNAs: Characteristics and Mechanisms of Action. Annu Rev Microbiol 2019; 72:141-161. [PMID: 30200848 DOI: 10.1146/annurev-micro-090817-062607] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The first report of trans-acting RNA-based regulation in bacterial cells dates back to 1984. Subsequent studies in diverse bacteria unraveled shared properties of trans-acting small regulatory RNAs, forming a clear definition of these molecules. These shared characteristics have been used extensively to identify new small RNAs (sRNAs) and their interactomes. Recently however, emerging technologies able to resolve RNA-RNA interactions have identified new types of regulatory RNAs. In this review, we present a broader definition of trans-acting sRNA regulators and discuss their newly discovered intrinsic characteristics.
Collapse
Affiliation(s)
- Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
| | - David Lalaouna
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
| |
Collapse
|
22
|
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. [PMID: 31249814 PMCID: PMC6582626 DOI: 10.3389/fcimb.2019.00201] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/23/2019] [Indexed: 01/19/2023] Open
Abstract
Accurate and efficient transcription termination is an important step for cells to generate functional RNA transcripts. In bacteria, two mechanisms are responsible for terminating transcription: intrinsic (Rho-independent) termination and Rho-dependent termination. Growing examples suggest that neither type of transcription termination is static, but instead are highly dynamic and regulated. Regulatory small RNAs (sRNAs) are key players in bacterial stress responses, are frequently expressed under specific growth conditions, and are predominantly terminated through the intrinsic termination mechanism. Once made, sRNAs can base-pair with mRNA targets and regulate mRNA translation and stability. Recent findings suggest that alterations in the efficiency of intrinsic termination for sRNAs under various growth conditions may affect the availability of a given sRNA and the ability of the sRNA to function properly. Moreover, alterations of mRNA structure, translation, and accessibility by sRNAs have the potential to impact the access of Rho factor to mRNAs and thus termination of the mRNA. Indeed, recent studies have revealed that some sRNAs can modulate target gene expression by stimulating or inhibiting Rho-dependent termination, thus expanding the regulatory power of bacterial sRNAs. Here we review the current knowledge on intrinsic termination of sRNAs and sRNA-mediated Rho-dependent termination of protein coding genes in bacteria.
Collapse
Affiliation(s)
- Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Teppei Morita
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.,Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Japan
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| |
Collapse
|
23
|
Grüll MP, Massé E. Mimicry, deception and competition: The life of competing endogenous RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1525. [PMID: 30761752 DOI: 10.1002/wrna.1525] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets. While some ceRNAs seem to be expressed constitutively, others are intricately regulated according to environmental conditions. The outcome of ceRNA binding to a sRNA reaches beyond simple sequestration. Various effects observed on sRNA functions extend from reducing transcriptional noise to promote RNA turnover. Here, we present a historical perspective of the discovery of ceRNAs in eukaryotic organisms and mainly focus on the synthesis and function of select, well-described, ceRNAs in bacterial cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions Translation > Translation Regulation RNA Turnover and Surveillance > Regulation of RNA Stability.
Collapse
Affiliation(s)
- Marc P Grüll
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Eric Massé
- Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
24
|
Small Noncoding Regulatory RNAs from Pseudomonas aeruginosa and Burkholderia cepacia Complex. Int J Mol Sci 2018; 19:ijms19123759. [PMID: 30486355 PMCID: PMC6321483 DOI: 10.3390/ijms19123759] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is the most life-limiting autosomal recessive disorder in Caucasians. CF is characterized by abnormal viscous secretions that impair the function of several tissues, with chronic bacterial airway infections representing the major cause of early decease of these patients. Pseudomonas aeruginosa and bacteria from the Burkholderia cepacia complex (Bcc) are the leading pathogens of CF patients’ airways. A wide array of virulence factors is responsible for the success of infections caused by these bacteria, which have tightly regulated responses to the host environment. Small noncoding RNAs (sRNAs) are major regulatory molecules in these bacteria. Several approaches have been developed to study P. aeruginosa sRNAs, many of which were characterized as being involved in the virulence. On the other hand, the knowledge on Bcc sRNAs remains far behind. The purpose of this review is to update the knowledge on characterized sRNAs involved in P. aeruginosa virulence, as well as to compile data so far achieved on sRNAs from the Bcc and their possible roles on bacteria virulence.
Collapse
|
25
|
Abstract
ABSTRACT
Most noncoding small RNAs (sRNAs) that regulate gene expression do so by base-pairing with mRNAs, affecting their translation and/or stability. Regulators as evolutionarily distant as the
trans
-encoded sRNAs of bacteria and the microRNAs (miRNAs) of higher eukaryotes share the property of targeting short sequence segments that occur in multiple copies in bacterial and eukaryotic transcriptomes. This target promiscuity has major implications for sRNA function. On the one hand, it allows the sRNA to coordinately control several different targets and thus be at the center of regulatory networks. On the other hand, it allows the existence of target mimics or decoys that divert the sRNA/miRNA away from bona fide targets and thus serve as mechanisms to regulate the regulator. In addition, by competing for pairing with the same sRNA, bona fide targets establish a cross talk that can impact on each other’s expression levels. Here we review evidence that target mimicry and competition are important components of the regulatory architecture of bacterial sRNA networks.
Collapse
|
26
|
Stevens JT, Carothers JM. Programming Gene Expression by Engineering Transcript Stability Control and Processing in Bacteria. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jason T. Stevens
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
| | - James M. Carothers
- University of Washington; Center for Synthetic Biology, Molecular Engineering and Sciences Institute, Departments of Chemical Engineering and Bioengineering; 4000 15th Ave NE, Seattle WA 98195-1654 USA
| |
Collapse
|
27
|
Small RNA-mediated regulation in bacteria: A growing palette of diverse mechanisms. Gene 2018; 656:60-72. [PMID: 29501814 DOI: 10.1016/j.gene.2018.02.068] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/19/2018] [Accepted: 02/27/2018] [Indexed: 11/23/2022]
Abstract
Small RNAs (sRNAs) in bacteria have evolved with diverse mechanisms to balance their target gene expression in response to changes in the environment. Accumulating studies on bacterial regulatory processes firmly established that sRNAs modulate their target gene expression generally at the posttranscriptional level. Identification of large number of sRNAs by advanced technologies, like deep sequencing, tilling microarray, indicates the existence of a plethora of distinctive sRNA-mediated regulatory mechanisms in bacteria. Types of the novel mechanisms are increasing with the discovery of new sRNAs. Complementary base pairing between sRNAs and target RNAs assisted by RNA chaperones like Hfq and ProQ, in many occasions, to regulate the cognate gene expression is prevalent in sRNA mechanisms. sRNAs, in most studied cases, can directly base pair with target mRNA to remodel its expression. Base pairing can happen either in the untranslated regions or in the coding regions of mRNA to activate/repress its translation. sRNAs also act as target mimic to titrate away different regulatory RNAs from its target. Other mechanism includes the sequestration of regulatory proteins, especially transcription factors, by sRNAs. Numerous sRNAs, following analogous mechanism, are widespread in bacteria, and thus, has drawn immense attention for the development of RNA-based technologies. Nevertheless, typical sRNA mechanisms are also discovered to be confined in some bacteria. Analysis of the sRNA mechanisms unravels their existence in both the single step processes and the complex regulatory networks with a global effect on cell physiology. This review deals with the diverse array of mechanisms, which sRNAs follow to maintain bacterial lifestyle.
Collapse
|
28
|
Durica-Mitic S, Göpel Y, Görke B. Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs. Microbiol Spectr 2018; 6. [PMID: 29573258 DOI: 10.1128/microbiolspec.rwr-0013-2017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/11/2022] Open
Abstract
Survival of bacteria in ever-changing habitats with fluctuating nutrient supplies requires rapid adaptation of their metabolic capabilities. To this end, carbohydrate metabolism is governed by complex regulatory networks including posttranscriptional mechanisms that involve small regulatory RNAs (sRNAs) and RNA-binding proteins. sRNAs limit the response to substrate availability and set the threshold or time required for induction and repression of carbohydrate utilization systems. Carbon catabolite repression (CCR) also involves sRNAs. In Enterobacteriaceae, sRNA Spot 42 cooperates with the transcriptional regulator cyclic AMP (cAMP)-receptor protein (CRP) to repress secondary carbohydrate utilization genes when a preferred sugar is consumed. In pseudomonads, CCR operates entirely at the posttranscriptional level, involving RNA-binding protein Hfq and decoy sRNA CrcZ. Moreover, sRNAs coordinate fluxes through central carbohydrate metabolic pathways with carbohydrate availability. In Gram-negative bacteria, the interplay between RNA-binding protein CsrA and its cognate sRNAs regulates glycolysis and gluconeogenesis in response to signals derived from metabolism. Spot 42 and cAMP-CRP jointly downregulate tricarboxylic acid cycle activity when glycolytic carbon sources are ample. In addition, bacteria use sRNAs to reprogram carbohydrate metabolism in response to anaerobiosis and iron limitation. Finally, sRNAs also provide homeostasis of essential anabolic pathways, as exemplified by the hexosamine pathway providing cell envelope precursors. In this review, we discuss the manifold roles of bacterial sRNAs in regulation of carbon source uptake and utilization, substrate prioritization, and metabolism.
Collapse
Affiliation(s)
- Svetlana Durica-Mitic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Yvonne Göpel
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Boris Görke
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| |
Collapse
|
29
|
Felden B, Paillard L. When eukaryotes and prokaryotes look alike: the case of regulatory RNAs. FEMS Microbiol Rev 2017; 41:624-639. [PMID: 28981746 DOI: 10.1093/femsre/fux038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 12/26/2022] Open
Abstract
The discovery that all living entities express many RNAs beyond mRNAs, tRNAs and rRNAs has been a surprise in the past two decades. In fact, regulatory RNAs (regRNAs) are plentiful, and we report stunning parallels between their mechanisms and functions in prokaryotes and eukaryotes. For instance, prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats) defense systems are functional analogs to eukaryotic RNA interference processes that preserve the cell against foreign nucleic acid elements. Regulatory RNAs shape the genome in many ways: by controlling mobile element transposition in both domains, via regulation of plasmid counts in prokaryotes, or by directing epigenetic modifications of DNA and associated proteins in eukaryotes. RegRNAs control gene expression extensively at transcriptional and post-transcriptional levels, with crucial roles in fine-tuning cell environmental responses, including intercellular interactions. Although the lengths, structures and outcomes of the regRNAs in all life kingdoms are disparate, they act through similar patterns: by guiding effectors to target molecules or by sequestering macromolecules to hamper their functions. In addition, their biogenesis processes have a lot in common. This unifying vision of regRNAs in all living cells from bacteria to humans points to the possibility of fruitful exchanges between fundamental and applied research in both domains.
Collapse
Affiliation(s)
- Brice Felden
- Inserm U1230 Biochimie Pharmaceutique, Université de Rennes 1, 35043 Rennes, France.,Biosit, Université de Rennes 1, 35043 Rennes, France
| | - Luc Paillard
- Biosit, Université de Rennes 1, 35043 Rennes, France.,Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, 35043 Rennes, France
| |
Collapse
|
30
|
Chitinase Expression in Listeria monocytogenes Is Influenced by lmo0327, Which Encodes an Internalin-Like Protein. Appl Environ Microbiol 2017; 83:AEM.01283-17. [PMID: 28887418 PMCID: PMC5666140 DOI: 10.1128/aem.01283-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/23/2017] [Indexed: 02/02/2023] Open
Abstract
The chitinolytic system of Listeria monocytogenes thus far comprises two chitinases, ChiA and ChiB, and a lytic polysaccharide monooxygenase, Lmo2467. The role of the system in the bacterium appears to be pleiotropic, as besides mediating the hydrolysis of chitin, the second most ubiquitous carbohydrate in nature, the chitinases have been deemed important for the colonization of unicellular molds, as well as mammalian hosts. To identify additional components of the chitinolytic system, we screened a transposon mutant library for mutants exhibiting impaired chitin hydrolysis. The screening yielded a mutant with a transposon insertion in a locus corresponding to lmo0327 of the EGD-e strain. lmo0327 encodes a large (1,349 amino acids [aa]) cell wall-associated protein that has been proposed to possess murein hydrolase activity. The single inactivation of lmo0327, as well as of lmo0325 that codes for a putative transcriptional regulator functionally related to lmo0327, led to an almost complete abolishment of chitinolytic activity. The effect could be traced at the transcriptional level, as both chiA and chiB transcripts were dramatically decreased in the lmo0327 mutant. In accordance with that, we could barely detect ChiA and ChiB in the culture supernatants of the mutant strain. Our results provide new information regarding the function of the lmo0325-lmo0327 locus in L. monocytogenes and link it to the expression of chitinolytic activity. IMPORTANCE Many bacteria from terrestrial and marine environments express chitinase activities enabling them to utilize chitin as the sole source of carbon and nitrogen. Interestingly, several bacterial chitinases may also be involved in host pathogenesis. For example, in the important foodborne pathogen Listeria monocytogenes, the chitinases ChiA and ChiB and the lytic polysaccharide monooxygenase Lmo2467 are implicated in chitin assimilation but also act as virulence factors during the infection of mammalian hosts. Therefore, it is important to identify their regulators and induction cues to understand how the different roles of the chitinolytic system are controlled and mediated. Here, we provide evidence for the importance of lmo0327 and lmo0325, encoding a putative internalin/autolysin and a putative transcriptional activator, respectively, in the efficient expression of chitinase activity in L. monocytogenes and thereby provide new information regarding the function of the lmo0325-lmo0327 locus.
Collapse
|
31
|
Melamed S, Peer A, Faigenbaum-Romm R, Gatt YE, Reiss N, Bar A, Altuvia Y, Argaman L, Margalit H. Global Mapping of Small RNA-Target Interactions in Bacteria. Mol Cell 2017; 63:884-97. [PMID: 27588604 PMCID: PMC5145812 DOI: 10.1016/j.molcel.2016.07.026] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/25/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions. A widely applicable method for in vivo global mapping of small RNA interactome Substantial re-wiring of the network upon changes in cellular conditions Regulatory circuits involving two regulators derived from the same transcript sRNAs acting in trans are encoded within almost every possible genomic element
Collapse
Affiliation(s)
- Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Asaf Peer
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Raya Faigenbaum-Romm
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Niv Reiss
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| |
Collapse
|
32
|
Chen ICK, Velicer GJ, Yu YTN. Divergence of functional effects among bacterial sRNA paralogs. BMC Evol Biol 2017; 17:199. [PMID: 28830343 PMCID: PMC5568312 DOI: 10.1186/s12862-017-1037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus. Specifically, Pxr prevents the initiation of fruiting body development when nutrients are abundant. Previous work has shown that Pxr appears to have a recent origin within a sub-clade of the myxobacteria, which allowed us to infer the most recent common ancestor of pxr and examine the divergence of Pxr since its origin. RESULTS To test for inter-specific divergence in functional effects, extant pxr homologs from several species and their inferred ancestor were introduced into an M. xanthus deletion mutant lacking pxr. Both the inferred ancestral pxr and all extant alleles from species containing only one copy of pxr were found to control development in M. xanthus in a qualitatively similar manner to the native M. xanthus allele. However, multiple paralogs present in Cystobacter species exhibited divergent effects, with two paralogs controlling M. xanthus development but two others failing to do so. These differences may have occurred through changes in gene expression caused by apparent structural differences in the sRNA variants encoded by these paralogs. CONCLUSIONS Taken together, our results suggest that Pxr plays a common fundamental role in developmental gene regulation across diverse species of myxobacteria but also that the functional effects of some Pxr variants may be evolving in some lineages.
Collapse
Affiliation(s)
- I-Chen Kimberly Chen
- Department of Biology, Indiana University, Bloomington, IN47405, USA. .,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland. .,Present address: School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332, USA.
| | - Gregory J Velicer
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Yuen-Tsu Nicco Yu
- Department of Biology, Indiana University, Bloomington, IN47405, USA.,Institute of Integrative Biology, ETH Zurich, CH-8092, Zurich, Switzerland
| |
Collapse
|
33
|
Abstract
Small RNAs (sRNAs) are central regulators of gene expression in bacteria, controlling target genes posttranscriptionally by base pairing with their mRNAs. sRNAs are involved in many cellular processes and have unique regulatory characteristics. In this review, we discuss the properties of regulation by sRNAs and how it differs from and combines with transcriptional regulation. We describe the global characteristics of the sRNA-target networks in bacteria using graph-theoretic approaches and review the local integration of sRNAs in mixed regulatory circuits, including feed-forward loops and their combinations, feedback loops, and circuits made of an sRNA and another regulator, both derived from the same transcript. Finally, we discuss the competition effects in posttranscriptional regulatory networks that may arise over shared targets, shared regulators, and shared resources and how they may lead to signal propagation across the network.
Collapse
Affiliation(s)
- Mor Nitzan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel; .,Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Rotem Rehani
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel;
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel;
| |
Collapse
|
34
|
Pannekoek Y, Huis In 't Veld R, Schipper K, Bovenkerk S, Kramer G, Speijer D, van der Ende A. Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA. FEBS Open Bio 2017; 7:1302-1315. [PMID: 28904860 PMCID: PMC5586341 DOI: 10.1002/2211-5463.12266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/23/2022] Open
Abstract
NrrF is a small regulatory RNA of the human pathogen Neisseria meningitidis. NrrF was previously shown to repress succinate dehydrogenase (sdhCDAB) under control of the ferric uptake regulator (Fur). Here, we provide evidence that cytochrome bc1 , encoded by the polycistronic mRNA petABC, is a NrrF target as well. We demonstrated differential expression of cytochrome bc1 comparing wild-type meningococci and meningococci expressing NrrF when sufficient iron is available. Using a gfp-reporter system monitoring translational control and target recognition of sRNA in Escherichia coli, we show that interaction between NrrF and the 5' untranslated region of the petABC mRNA results in its repression. The NrrF region essential for repression of petABC was identified by site-directed mutagenesis and is fully conserved among meningococci. Our results provide further insights into the mechanism by which Fur controls essential components of the N. meningitidis respiratory chain. Adaptation of cytochrome bc1 complex component levels upon iron limitation is post-transcriptionally regulated via the small regulatory RNA NrrF.
Collapse
Affiliation(s)
- Yvonne Pannekoek
- Department of Medical Microbiology Center for Infection and Immunity Amsterdam (CINIMA) Academic Medical Center The Netherlands
| | - Robert Huis In 't Veld
- Department of Medical Microbiology Center for Infection and Immunity Amsterdam (CINIMA) Academic Medical Center The Netherlands
| | - Kim Schipper
- Department of Medical Microbiology Center for Infection and Immunity Amsterdam (CINIMA) Academic Medical Center The Netherlands
| | - Sandra Bovenkerk
- Department of Medical Microbiology Center for Infection and Immunity Amsterdam (CINIMA) Academic Medical Center The Netherlands
| | - Gertjan Kramer
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands.,Present address: Genome Biology Unit EMBL Heidelberg Heidelberg Germany
| | - Dave Speijer
- Department of Medical Biochemistry Academic Medical Center Amsterdam The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology Center for Infection and Immunity Amsterdam (CINIMA) Academic Medical Center The Netherlands
| |
Collapse
|
35
|
Abstract
Bacterial pathogens must endure or adapt to different environments and stresses during transmission and infection. Posttranscriptional gene expression control by regulatory RNAs, such as small RNAs and riboswitches, is now considered central to adaptation in many bacteria, including pathogens. The study of RNA-based regulation (riboregulation) in pathogenic species has provided novel insight into how these bacteria regulate virulence gene expression. It has also uncovered diverse mechanisms by which bacterial small RNAs, in general, globally control gene expression. Riboregulators as well as their targets may also prove to be alternative targets or provide new strategies for antimicrobials. In this article, we present an overview of the general mechanisms that bacteria use to regulate with RNA, focusing on examples from pathogens. In addition, we also briefly review how deep sequencing approaches have aided in opening new perspectives in small RNA identification and the study of their functions. Finally, we discuss examples of riboregulators in two model pathogens that control virulence factor expression or survival-associated phenotypes, such as stress tolerance, biofilm formation, or cell-cell communication, to illustrate how riboregulation factors into regulatory networks in bacterial pathogens.
Collapse
|
36
|
Migault M, Donnou-Fournet E, Galibert MD, Gilot D. Definition and identification of small RNA sponges: Focus on miRNA sequestration. Methods 2016; 117:35-47. [PMID: 27876678 DOI: 10.1016/j.ymeth.2016.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/18/2016] [Indexed: 02/09/2023] Open
Abstract
Targeting RNAs appears as an important opportunity to modulate biological processes. Here, we overviewed critical parameters implied in RNAs competition to bind small RNAs. These competitions influence small RNA availability and thereby gene expression and cell fate. We focused on the ability of RNAs to sequester small RNA, mainly the microRNAs (miRNAs) and proposed experimental workflows to demonstrate the existence and activity of RNA-sponge. From this basic science, we detailed tailored oligonucleotides, developed to challenge the binding of small RNA. In vitro and in vivo, these tailored oligonucleotides efficiently restore small RNA activity by preventing their sequestration on RNA-sponges.
Collapse
Affiliation(s)
- Mélodie Migault
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Emmanuelle Donnou-Fournet
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France
| | - Marie-Dominique Galibert
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France; Department of Medical Genomic, Rennes University Hospital, Rennes, France.
| | - David Gilot
- Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France; Université de Rennes 1, Rennes, France; Cancer Research Association (ARC) Labelled Team, France.
| |
Collapse
|
37
|
Bossi L, Figueroa-Bossi N. Competing endogenous RNAs: a target-centric view of small RNA regulation in bacteria. Nat Rev Microbiol 2016; 14:775-784. [PMID: 27640758 DOI: 10.1038/nrmicro.2016.129] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many bacterial regulatory small RNAs (sRNAs) have several mRNA targets, which places them at the centre of regulatory networks that help bacteria to adapt to environmental changes. However, different mRNA targets of any given sRNA compete with each other for binding to the sRNA; thus, depending on relative abundances and sRNA affinity, competition for regulatory sRNAs can mediate cross-regulation between bacterial mRNAs. This 'target-centric' perspective of sRNA regulation is reminiscent of the competing endogenous RNA (ceRNA) hypothesis, which posits that competition for a limited pool of microRNAs (miRNAs) in higher eukaryotes mediates cross-regulation of mRNAs. In this Opinion article, we discuss evidence that a similar network of RNA crosstalk operates in bacteria, and that this network also includes crosstalk between sRNAs and competition for RNA-binding proteins.
Collapse
Affiliation(s)
- Lionello Bossi
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), The French Alternative Energies and Atomic Energy Commission (CEA), University Paris-Saclay, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| | - Nara Figueroa-Bossi
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), The French Alternative Energies and Atomic Energy Commission (CEA), University Paris-Saclay, 1 Avenue de la Terrasse, F-91198 Gif-sur-Yvette, France
| |
Collapse
|
38
|
Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK. MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development. PLANT PHYSIOLOGY 2016; 171:944-59. [PMID: 27208307 PMCID: PMC4902582 DOI: 10.1104/pp.15.01831] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/26/2016] [Indexed: 05/08/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, noncoding small RNAs that function as critical regulators of gene expression. In plants, miRNAs have shown their potential as regulators of growth, development, signal transduction, and stress tolerance. Although the miRNA-mediated regulation of several processes is known, the involvement of miRNAs in regulating secondary plant product biosynthesis is poorly understood. In this study, we functionally characterized Arabidopsis (Arabidopsis thaliana) miR858a, which putatively targets R2R3-MYB transcription factors involved in flavonoid biosynthesis. Overexpression of miR858a in Arabidopsis led to the down-regulation of several MYB transcription factors regulating flavonoid biosynthesis. In contrast to the robust growth and early flowering of miR858OX plants, reduction of plant growth and delayed flowering were observed in Arabidopsis transgenic lines expressing an artificial miRNA target mimic (MIM858). Genome-wide expression analysis using transgenic lines suggested that miR858a targets a number of regulatory factors that modulate the expression of downstream genes involved in plant development and hormonal and stress responses. Furthermore, higher expression of MYBs in MIM858 lines leads to redirection of the metabolic flux towards the synthesis of flavonoids at the cost of lignin synthesis. Altogether, our study has established the potential role of light-regulated miR858a in flavonoid biosynthesis and plant growth and development.
Collapse
Affiliation(s)
- Deepika Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Manish Tiwari
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashutosh Pandey
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Chitra Bhatia
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Ashish Sharma
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| | - Prabodh Kumar Trivedi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, India (D.S., M.T., A.P., C.B., A.S., P.K.T.); andAcademy of Scientific and Innovative Research, Anusandhan Bhawan, New Delhi 110 001, India (D.S., C.B., P.K.T.)
| |
Collapse
|
39
|
Arbel-Goren R, Tal A, Parasar B, Dym A, Costantino N, Muñoz-García J, Court DL, Stavans J. Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. Nucleic Acids Res 2016; 44:6707-20. [PMID: 27085802 PMCID: PMC5001584 DOI: 10.1093/nar/gkw273] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli. In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. We observed a monotonic increase of noise with iron stress but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo RyhB-mediated transcript degradation rates. The transcripts’ threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Strikingly, the bacterial cell response exhibits Fur-dependent, switch-like activation instead of a graded response to iron deprivation.
Collapse
Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaf Tal
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Bibudha Parasar
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alvah Dym
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Javier Muñoz-García
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel Departamento de Matemáticas and GISC, Universidad Carlos III de Madrid, Av. de la Universidad 30, 28911 Leganés, Madrid, Spain
| | - Donald L Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
40
|
McCaskill J, Praihirunkit P, Sharp PM, Buck AH. RNA-mediated degradation of microRNAs: A widespread viral strategy? RNA Biol 2015; 12:579-85. [PMID: 25849078 DOI: 10.1080/15476286.2015.1034912] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Regulation of small RNAs by other non-coding RNAs is a ubiquitous feature of gene regulatory systems that can be exploited by viruses. Examples of this have been described in 3 different herpesviruses, where viral non-coding RNAs bind to highly abundant cellular (miRNAs), mediating their degradation: miR-27 is targeted by both murine cytomegalovirus and herpesvirus saimiri, while the miR-17 family is targeted by human cytomegalovirus. We review what is known about RNA-mediated regulation of miRNA stability and propose 3 potential roles that viral non-coding RNAs might assume to initiate the destruction of a miRNA, acting as "recruiters," "localizers" or "exposers." Whereas the miRNAs (miR-17 and miR-27) appear to be ancient and pre-date the common ancestor of all mammalian herpesviruses, comparative analyses of herpesvirus genomes indicate that the 3 known viral regulators of miRNA each evolved independently, and much more recently. Noting that the anti-viral activity of miRNAs might be countered by a variety of mechanisms, we propose that (i) there has been continual turnover of these mechanisms during herpesvirus evolution, and (ii) there may be many other, as yet undescribed, anti-miRNA activities encoded by other herpesviruses and indeed by viruses from other families.
Collapse
Affiliation(s)
- Jana McCaskill
- a Institute of Immunology and Infection Research; School of Biological Sciences; University of Edinburgh ; Edinburgh , UK
| | | | | | | |
Collapse
|
41
|
Barquist L, Vogel J. Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies. Annu Rev Genet 2015; 49:367-94. [PMID: 26473381 DOI: 10.1146/annurev-genet-112414-054804] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decade, bacterial small RNAs (sRNAs) have gone from a biological curiosity to being recognized as a major class of regulatory molecules. High-throughput methods for sampling the transcriptional output of bacterial cells demonstrate that sRNAs are universal features of bacterial transcriptomes, are plentiful, and appear to vary extensively over evolutionary time. With ever more bacteria coming under study, the question becomes how can we accelerate the discovery and functional characterization of sRNAs in diverse organisms. New technologies built on high-throughput sequencing are emerging that can rapidly provide global insight into the numbers and functions of sRNAs in bacteria of interest, providing information that can shape hypotheses and guide research. In this review, we describe recent developments in transcriptomics (RNA-seq) and functional genomics that we expect to help us develop an integrated, systems-level view of sRNA biology in bacteria.
Collapse
Affiliation(s)
- Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany; ,
| |
Collapse
|
42
|
Schu DJ, Zhang A, Gottesman S, Storz G. Alternative Hfq-sRNA interaction modes dictate alternative mRNA recognition. EMBO J 2015; 34:2557-73. [PMID: 26373314 DOI: 10.15252/embj.201591569] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/11/2015] [Indexed: 11/09/2022] Open
Abstract
Many bacteria use small RNAs (sRNAs) and the RNA chaperone Hfq to regulate mRNA stability and translation. Hfq, a ring-shaped homohexamer, has multiple faces that can bind both sRNAs and their mRNA targets. We find that Hfq has at least two distinct ways in which it interacts with sRNAs; these different binding properties have strong effects on the stability of the sRNA in vivo and the sequence requirements of regulated mRNAs. Class I sRNAs depend on proximal and rim Hfq sites for stability and turn over rapidly. Class II sRNAs are more stable and depend on the proximal and distal Hfq sites for stabilization. Using deletions and chimeras, we find that while Class I sRNAs regulate mRNA targets with previously defined ARN repeats, Class II sRNAs regulate mRNAs carrying UA-rich rim-binding sites. We discuss how these different binding modes may correlate with different roles in the cell, with Class I sRNAs acting as emergency responders and Class II sRNAs acting as silencers.
Collapse
Affiliation(s)
- Daniel J Schu
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| | - Aixia Zhang
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
| | - Gisela Storz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| |
Collapse
|
43
|
Knopp M, Andersson DI. Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins. Mol Biol Evol 2015; 32:3252-63. [DOI: 10.1093/molbev/msv195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
44
|
sRNA-Mediated Regulation of P-Fimbriae Phase Variation in Uropathogenic Escherichia coli. PLoS Pathog 2015; 11:e1005109. [PMID: 26291711 PMCID: PMC4546395 DOI: 10.1371/journal.ppat.1005109] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 07/24/2015] [Indexed: 12/21/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) are capable of occupying physiologically distinct intracellular and extracellular niches within the urinary tract. This feat requires the timely regulation of gene expression and small RNAs (sRNAs) are known to mediate such rapid adjustments in response to changing environmental cues. This study aimed to uncover sRNA-mediated gene regulation in the UPEC strain UTI89, during infection of bladder epithelial cells. Hfq is an RNA chaperone known to facilitate and stabilize sRNA and target mRNA interactions with bacterial cells. The co-immunoprecipitation and high throughput RNA sequencing of Hfq bound sRNAs performed in this study, revealed distinct sRNA profiles in UPEC in the extracellular and intracellular environments. Our findings emphasize the importance of studying regulatory sRNAs in a biologically relevant niche. This strategy also led to the discovery of a novel virulence-associated trans-acting sRNA—PapR. Deletion of papR was found to enhance adhesion of UTI89 to both bladder and kidney cell lines in a manner independent of type-1 fimbriae. We demonstrate PapR mediated posttranscriptional repression of the P-fimbriae phase regulator gene papI and postulate a role for such regulation in fimbrial cross-talk at the population level in UPEC. Our results further implicate the Leucine responsive protein (LRP) as a transcriptional activator regulating PapR expression. Our study reports, for the first time, a role for sRNAs in regulation of P-fimbriae phase variation and emphasizes the importance of studying pathogenesis-specific sRNAs within a relevant biological niche. Recent years have seen an increasing emphasis placed on the role of small RNAs (sRNAs) in the regulation of bacterial gene expression and stress adaptation. The advent of high-throughput sequencing methods has now made it possible to directly monitor the appearance of potentially virulence-associated sRNAs that may contribute to rapid adaptation of the pathogen to a changing environment during infection. Uropathogenic Escherichia coli (UPEC) are presumably exposed to a deluge of stimuli from epithelial cell contact, urine and host immune factors and we asked if any regulatory sRNAs would play a role in the transition of UPEC from the extracellular niche to the intracellular one. This study employs co-immunoprecipitation using the RNA chaperone Hfq to identify novel virulence-associated sRNAs in intracellular UPEC, followed by high-throughput RNA-seq. We report the identification of a novel sRNA that we designate PapR (P-fimbriae regulator) and elaborate on this discovery by demonstrating a role for PapR in regulation of P-fimbriae—a UPEC surface virulence factor. The results presented in this study offer new insights into the molecular mechanisms of UPEC pathogenesis and a role for sRNA mediated regulation of virulence factors.
Collapse
|
45
|
Ziebuhr W, Vogel J. The end is not the end: remnants of tRNA precursors live on to sponge up small regulatory RNAs. Mol Cell 2015; 58:389-90. [PMID: 25957803 DOI: 10.1016/j.molcel.2015.04.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Natural RNA sponges sequestering cellular noncoding RNA molecules have been found in diverse organisms. In this issue, Lalaouna et al. (2015) report another type of RNA sponge, showing that stable intermediates of bacterial tRNA processing control endogenous small RNAs.
Collapse
Affiliation(s)
- Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
| |
Collapse
|
46
|
Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades. Sci Rep 2015; 5:12186. [PMID: 26184971 PMCID: PMC4505322 DOI: 10.1038/srep12186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/27/2015] [Indexed: 11/24/2022] Open
Abstract
Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.
Collapse
|
47
|
Park H, Yoon Y, Suk S, Lee JY, Lee Y. Effects of different target sites on antisense RNA-mediated regulation of gene expression. BMB Rep 2015; 47:619-24. [PMID: 24411463 PMCID: PMC4281340 DOI: 10.5483/bmbrep.2014.47.11.257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Indexed: 11/20/2022] Open
Abstract
Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.
Collapse
Affiliation(s)
- Hongmarn Park
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | | | - Shinae Suk
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Ji Young Lee
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon 305-701, Korea
| |
Collapse
|
48
|
Miyakoshi M, Chao Y, Vogel J. Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J 2015; 34:1478-92. [PMID: 25630703 PMCID: PMC4474525 DOI: 10.15252/embj.201490546] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/16/2022] Open
Abstract
There is an expanding list of examples by which one mRNA can posttranscriptionally influence the expression of others. This can involve RNA sponges that sequester regulatory RNAs of mRNAs in the same regulon, but the underlying molecular mechanism of such mRNA cross talk remains little understood. Here, we report sponge-mediated mRNA cross talk in the posttranscriptional network of GcvB, a conserved Hfq-dependent small RNA with one of the largest regulons known in bacteria. We show that mRNA decay from the gltIJKL locus encoding an amino acid ABC transporter generates a stable fragment (SroC) that base-pairs with GcvB. This interaction triggers the degradation of GcvB by RNase E, alleviating the GcvB-mediated mRNA repression of other amino acid-related transport and metabolic genes. Intriguingly, since the gltIJKL mRNA itself is a target of GcvB, the SroC sponge seems to enable both an internal feed-forward loop to activate its parental mRNA in cis and activation of many trans-encoded mRNAs in the same pathway. Disabling this mRNA cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources.
Collapse
Affiliation(s)
- Masatoshi Miyakoshi
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Yanjie Chao
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology University of Würzburg, Würzburg, Germany
| |
Collapse
|
49
|
Fagnocchi L, Bottini S, Golfieri G, Fantappiè L, Ferlicca F, Antunes A, Guadagnuolo S, Del Tordello E, Siena E, Serruto D, Scarlato V, Muzzi A, Delany I. Global transcriptome analysis reveals small RNAs affecting Neisseria meningitidis bacteremia. PLoS One 2015; 10:e0126325. [PMID: 25951061 PMCID: PMC4423775 DOI: 10.1371/journal.pone.0126325] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 03/31/2015] [Indexed: 12/11/2022] Open
Abstract
Most bacterial small RNAs (sRNAs) are post-transcriptional regulators involved in adaptive responses, controlling gene expression by modulating translation or stability of their target mRNAs often in concert with the RNA chaperone Hfq. Neisseria meningitides, the leading cause of bacterial meningitis, is able to adapt to different host niches during human infection. However, only a few sRNAs and their functions have been fully described to date. Recently, transcriptional expression profiling of N. meningitides in human blood ex vivo revealed 91 differentially expressed putative sRNAs. Here we expanded this analysis by performing a global transcriptome study after exposure of N. meningitides to physiologically relevant stress signals (e.g. heat shock, oxidative stress, iron and carbon source limitation). and we identified putative sRNAs that were differentially expressed in vitro. A set of 98 putative sRNAs was obtained by analyzing transcriptome data and 8 new sRNAs were validated, both by Northern blot and by primer extension techniques. Deletion of selected sRNAs caused attenuation of N. meningitides infection in the in vivo infant rat model, leading to the identification of the first sRNAs influencing meningococcal bacteremia. Further analysis indicated that one of the sRNAs affecting bacteremia responded to carbon source availability through repression by a GntR-like transcriptional regulator. Both the sRNA and the GntR-like regulator are implicated in the control of gene expression from a common network involved in energy metabolism.
Collapse
Affiliation(s)
| | | | | | | | | | - Ana Antunes
- Novartis Vaccines and Diagnotics, Siena, Italy
| | | | | | | | | | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Isabel Delany
- Novartis Vaccines and Diagnotics, Siena, Italy
- * E-mail:
| |
Collapse
|
50
|
A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise. Mol Cell 2015; 58:393-405. [DOI: 10.1016/j.molcel.2015.03.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
|