1
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Vogt LN, Panis G, Schäpers A, Peschek N, Huber M, Papenfort K, Viollier PH, Fröhlich KS. Genome-wide profiling of Hfq-bound RNAs reveals the iron-responsive small RNA RusT in Caulobacter crescentus. mBio 2024; 15:e0315323. [PMID: 38511926 PMCID: PMC11005374 DOI: 10.1128/mbio.03153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The alphaproteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. crescentus. Small RNAs (sRNAs) are a prominent class of regulators of bacterial gene expression, and most sRNAs characterized today engage in direct base-pairing interactions to modulate the translation and/or stability of target mRNAs. In many cases, the ubiquitous RNA chaperone, Hfq, contributes to the establishment of RNA-RNA interactions. Although the deletion of the hfq gene is associated with a severe loss of fitness in C. crescentus, the RNA ligands of the chaperone have remained largely unexplored. Here we report on the identification of coding and non-coding transcripts associated with Hfq in C. crescentus and demonstrate Hfq-dependent post-transcriptional regulation in this organism. We show that the Hfq-bound sRNA RusT is transcriptionally controlled by the NtrYX two-component system and induced in response to iron starvation. By combining RusT pulse expression with whole-genome transcriptome analysis, we determine 16 candidate target transcripts that are deregulated, many of which encode outer membrane transporters. We hence suggest RusT to support remodeling of the C. crescentus cell surface when iron supplies are limited.IMPORTANCEThe conserved RNA-binding protein Hfq contributes significantly to the adaptation of bacteria to different environmental conditions. Hfq not only stabilizes associated sRNAs but also promotes inter-molecular base-pairing interactions with target transcripts. Hfq plays a pivotal role for growth and survival, controlling central metabolism and cell wall synthesis in the oligotroph Caulobacter crescentus. However, direct evidence for Hfq-dependent post-transcriptional regulation and potential oligotrophy in C. crescentus has been lacking. Here, we identified sRNAs and mRNAs associated with Hfq in vivo, and demonstrated the requirement of Hfq for sRNA-mediated regulation, particularly of outer membrane transporters in C. crescentus.
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Affiliation(s)
- Laura N. Vogt
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Anna Schäpers
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nikolai Peschek
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michaela Huber
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kai Papenfort
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
| | - Patrick H. Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine/Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
| | - Kathrin S. Fröhlich
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, Munich, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Jena, Germany
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2
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Luo X, Zhang A, Tai CH, Chen J, Majdalani N, Storz G, Gottesman S. An acetyltranferase moonlights as a regulator of the RNA binding repertoire of the RNA chaperone Hfq in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2311509120. [PMID: 38011569 PMCID: PMC10710024 DOI: 10.1073/pnas.2311509120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with their target mRNAs. In Escherichia coli and many other bacteria, this process is dependent on the RNA chaperone Hfq, a mediator for sRNA-mRNA annealing. YhbS (renamed here as HqbA), a putative Gcn5-related N-acetyltransferase (GNAT), was previously identified as a silencer of sRNA signaling in a genomic library screen. Here, we studied how HqbA regulates sRNA signaling and investigated its physiological roles in modulating Hfq activity. Using fluorescent reporter assays, we found that HqbA overproduction suppressed all tested Hfq-dependent sRNA signaling. Direct interaction between HqbA and Hfq was demonstrated both in vivo and in vitro, and mutants that blocked the interaction interfered with HqbA suppression of Hfq. However, an acetylation-deficient HqbA mutant still disrupted sRNA signaling, and HqbA interacted with Hfq at a site far from the active site. This suggests that HqbA may be bifunctional, with separate roles for regulating via Hfq interaction and for acetylation of undefined substrates. Gel shift assays revealed that HqbA strongly reduced the interaction between the Hfq distal face and low-affinity RNAs but not high-affinity RNAs. Comparative RNA immunoprecipitation of Hfq and sequencing showed enrichment of two tRNA precursors, metZWV and proM, by Hfq in mutants that lost the HqbA-Hfq interaction. Our results suggest that HqbA provides a level of quality control for Hfq by competing with low-affinity RNA binders.
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Affiliation(s)
- Xing Luo
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD20892-4417
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Nadim Majdalani
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD20892-4417
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20892
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3
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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.
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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
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4
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Carrier MC, Lalaouna D, Massé E. Hfq protein and GcvB small RNA tailoring of oppA target mRNA to levels allowing translation activation by MicF small RNA in Escherichia coli. RNA Biol 2023; 20:59-76. [PMID: 36860088 PMCID: PMC9988348 DOI: 10.1080/15476286.2023.2179582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Traffic of molecules across the bacterial membrane mainly relies on porins and transporters, whose expression must adapt to environmental conditions. To ensure bacterial fitness, synthesis and assembly of functional porins and transporters are regulated through a plethora of mechanisms. Among them, small regulatory RNAs (sRNAs) are known to be powerful post-transcriptional regulators. In Escherichia coli, the MicF sRNA is known to regulate only four targets, a very narrow targetome for a sRNA responding to various stresses, such as membrane stress, osmotic shock, or thermal shock. Using an in vivo pull-down assay combined with high-throughput RNA sequencing, we sought to identify new targets of MicF to better understand its role in the maintenance of cellular homoeostasis. Here, we report the first positively regulated target of MicF, the oppA mRNA. The OppA protein is the periplasmic component of the Opp ATP-binding cassette (ABC) oligopeptide transporter and regulates the import of short peptides, some of them bactericides. Mechanistic studies suggest that oppA translation is activated by MicF through a mechanism of action involving facilitated access to a translation-enhancing region in oppA 5'UTR. Intriguingly, MicF activation of oppA translation depends on cross-regulation by negative trans-acting effectors, the GcvB sRNA and the RNA chaperone protein Hfq.
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Affiliation(s)
- Marie-Claude Carrier
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - David Lalaouna
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Massé
- Department of Biochemistry and Functional Genomics, RNA Group, Université de Sherbrooke, Sherbrooke, Québec, Canada
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5
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Cossa A, Trépout S, Wien F, Groen J, Le Brun E, Turbant F, Besse L, Pereiro E, Arluison V. Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodeling by Hfq master regulator. J Struct Biol 2022; 214:107912. [PMID: 36283630 DOI: 10.1016/j.jsb.2022.107912] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 09/28/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
The bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, due to the association of DNA with proteins called Nucleoid Associated Proteins (NAPs). Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq forms amyloid-like structures through its C-terminal region, hence belonging to the bridging family of NAPs. Here, using cryo soft X-ray tomography imaging of native unlabeled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid. More specifically, Hfq influences nucleoid density especially during the stationary growth phase when it is more abundant. Our results indicate that Hfq could regulate nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNAs. Taken together, our findings reveal a new role for this protein in nucleoid remodeling in vivo, that may serve in response to stress conditions and in adapting to changing environments.
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Affiliation(s)
- Antoine Cossa
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Sylvain Trépout
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France; Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia.
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
| | - Johannes Groen
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Laetitia Besse
- Institut Curie, Université PSL, CNRS UAR2016, Inserm US43, Université Paris-Saclay, Multimodal Imaging Center, 91400 Orsay, France
| | - Eva Pereiro
- Mistral Beamline, Alba Light Source, Cerdanyola del Valles, 08290 Barcelona, Spain
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; Université Paris Cité, UFR Sciences du vivant, 75006 Paris cedex, France.
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6
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Sarni SH, Roca J, Du C, Jia M, Li H, Damjanovic A, Małecka EM, Wysocki VH, Woodson SA. Intrinsically disordered interaction network in an RNA chaperone revealed by native mass spectrometry. Proc Natl Acad Sci U S A 2022; 119:e2208780119. [PMID: 36375072 PMCID: PMC9704730 DOI: 10.1073/pnas.2208780119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022] Open
Abstract
RNA-binding proteins contain intrinsically disordered regions whose functions in RNA recognition are poorly understood. The RNA chaperone Hfq is a homohexamer that contains six flexible C-terminal domains (CTDs). The effect of the CTDs on Hfq's integrity and RNA binding has been challenging to study because of their sequence identity and inherent disorder. We used native mass spectrometry coupled with surface-induced dissociation and molecular dynamics simulations to disentangle the arrangement of the CTDs and their impact on the stability of Escherichia coli Hfq with and without RNA. The results show that the CTDs stabilize the Hfq hexamer through multiple interactions with the core and between CTDs. RNA binding perturbs this network of CTD interactions, destabilizing the Hfq ring. This destabilization is partially compensated by binding of RNAs that contact multiple surfaces of Hfq. By contrast, binding of short RNAs that only contact one or two subunits results in net destabilization of the complex. Together, the results show that a network of intrinsically disordered interactions integrate RNA contacts with the six subunits of Hfq. We propose that this CTD network raises the selectivity of RNA binding.
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Affiliation(s)
- Samantha H. Sarni
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Jorjethe Roca
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Hantian Li
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Ana Damjanovic
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Ewelina M. Małecka
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sarah A. Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
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7
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Cai H, Roca J, Zhao YF, Woodson SA. Dynamic Refolding of OxyS sRNA by the Hfq RNA Chaperone. J Mol Biol 2022; 434:167776. [PMID: 35934049 PMCID: PMC10044511 DOI: 10.1016/j.jmb.2022.167776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 10/16/2022]
Abstract
The Sm protein Hfq chaperones small non-coding RNAs (sRNAs) in bacteria, facilitating sRNA regulation of target mRNAs. Hfq acts in part by remodeling the sRNA and mRNA structures, yet the basis for this remodeling activity is not understood. To understand how Hfq remodels RNA, we used single-molecule Förster resonance energy transfer (smFRET) to monitor conformational changes in OxyS sRNA upon Hfq binding. The results show that E. coli Hfq first compacts OxyS, bringing its 5' and 3 ends together. Next, Hfq destabilizes an internal stem-loop in OxyS, allowing the RNA to adopt a more open conformation that is stabilized by a conserved arginine on the rim of Hfq. The frequency of transitions between compact and open conformations depend on interactions with Hfqs flexible C-terminal domain (CTD), being more rapid when the CTD is deleted, and slower when OxyS is bound to Caulobacter crescentus Hfq, which has a shorter and more stable CTD than E. coli Hfq. We propose that the CTDs gate transitions between OxyS conformations that are stabilized by interaction with one or more arginines. These results suggest a general model for how basic residues and intrinsically disordered regions of RNA chaperones act together to refold RNA.
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Affiliation(s)
- Huahuan Cai
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA; Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China
| | - Jorjethe Roca
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA
| | - Yu-Fen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, and Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian 361005, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Sarah A Woodson
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., MD 21218, USA.
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8
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Gopan G, Ghaemi Z, Davis CM, Gruebele M. Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM. Nucleic Acids Res 2022; 50:8193-8206. [PMID: 35876068 PMCID: PMC9371917 DOI: 10.1093/nar/gkac599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/19/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
The RNA recognition motif (RRM) occurs widely in RNA-binding proteins, but does not always by itself support full binding. For example, it is known that binding of SL1 RNA to the protein U1-70K in the U1 spliceosomal particle is reduced when a region flanking the RRM is truncated. How the RRM flanking regions that together with the RRM make up an ‘extended RRM’ (eRRM) contribute to complex stability and structural organization is unknown. We study the U1-70K eRRM bound to SL1 RNA by thermal dissociation and laser temperature jump kinetics; long-time molecular dynamics simulations interpret the experiments with atomistic resolution. Truncation of the helix flanking the RRM on its N-terminal side, ‘N-helix,’ strongly reduces overall binding, which is further weakened under higher salt and temperature conditions. Truncating the disordered region flanking the RRM on the C-terminal side, ‘C-IDR’, affects the local binding site. Surprisingly, all-atom simulations show that protein truncation enhances base stacking interactions in the binding site and leaves the overall number of hydrogen bonds intact. Instead, the flanking regions of the eRRM act in a distributed fashion via collective interactions with the RNA when external stresses such as temperature or high salt mimicking osmotic imbalance are applied.
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Affiliation(s)
- Gopika Gopan
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Zhaleh Ghaemi
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Caitlin M Davis
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.,Department of Physics, University of Illinois, Urbana, IL 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.,Department of Physics, University of Illinois, Urbana, IL 61801, USA.,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
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9
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DsrA Modulates Central Carbon Metabolism and Redox Balance by Directly Repressing pflB Expression in Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0152221. [PMID: 35107349 PMCID: PMC8809350 DOI: 10.1128/spectrum.01522-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacterial small RNAs (sRNAs) function as vital regulators in response to various environmental stresses by base pairing with target mRNAs. The sRNA DsrA, an important posttranscriptional regulator, has been reported to play a crucial role in defense against oxidative stress in Salmonella enterica serovar Typhimurium, but its regulatory mechanism remains unclear. The transcriptome sequencing (RNA-seq) results in this study showed that the genes involved in glycolysis, pyruvate metabolism, the tricarboxylic acid (TCA) cycle, and NADH-dependent respiration exhibited significantly different expression patterns between S. Typhimurium wild type (WT) and the dsrA deletion mutant (ΔdsrA strain) before and after H2O2 treatment. This indicated the importance of DsrA in regulating central carbon metabolism (CCM) and NAD(H) homeostasis of S. Typhimurium. To reveal the direct target of DsrA action, fusion proteins of six candidate genes (acnA, srlE, tdcB, nuoH, katG, and pflB) with green fluorescent protein (GFP) were constructed, and the fluorescence analysis showed that the expression of pflB encoding pyruvate-formate lyase was repressed by DsrA. Furthermore, site-directed mutagenesis and RNase E-dependent experiments showed that the direct base pairing of DsrA with pflB mRNA could recruit RNase E to degrade pflB mRNA and reduce the stability of pflB mRNA. In addition, the NAD+/NADH ratio in WT-ppflB-pdsrA was significantly lower than that in WT-ppflB, suggesting that the repression of pflB by DsrA could contribute greatly to the redox balance in S. Typhimurium. Taken together, a novel target of DsrA was identified, and its regulatory role was clarified, which demonstrated that DsrA could modulate CCM and redox balance by directly repressing pflB expression in S. Typhimurium. IMPORTANCE Small RNA DsrA plays an important role in defending against oxidative stress in bacteria. In this study, we identified a novel target (pflB, encoding pyruvate-formate lyase) of DsrA and demonstrated its potential regulatory mechanism in S. Typhimurium by transcriptome analysis. In silico prediction revealed a direct base pairing between DsrA and pflB mRNA, which was confirmed in site-directed mutagenesis experiments. The interaction of DsrA-pflB mRNA could greatly contribute to the regulation of central carbon metabolism and intracellular redox balance in S. Typhimurium. These findings provided a better understanding of the critical roles of small RNA in central metabolism and stress responses in foodborne pathogens.
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10
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Serrão VHB, Fernandes ADF, Basso LGM, Scortecci JF, Crusca Júnior E, Cornélio ML, de Souza BM, Palma MS, de Oliveira Neto M, Thiemann OH. The Specific Elongation Factor to Selenocysteine Incorporation in Escherichia coli: Unique tRNA Sec Recognition and its Interactions. J Mol Biol 2021; 433:167279. [PMID: 34624294 DOI: 10.1016/j.jmb.2021.167279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
Several molecular mechanisms are involved in the genetic code interpretation during translation, as codon degeneration for the incorporation of rare amino acids. One mechanism that stands out is selenocysteine (Sec), which requires a specific biosynthesis and incorporation pathway. In Bacteria, the Sec biosynthesis pathway has unique features compared with the eukaryote pathway as Ser to Sec conversion mechanism is accomplished by a homodecameric enzyme (selenocysteine synthase, SelA) followed by the action of an elongation factor (SelB) responsible for delivering the mature Sec-tRNASec into the ribosome by the interaction with the Selenocysteine Insertion Sequence (SECIS). Besides this mechanism being already described, the sequential events for Sec-tRNASec and SECIS specific recognition remain unclear. In this study, we determined the order of events of the interactions between the proteins and RNAs involved in Sec incorporation. Dissociation constants between SelB and the native as well as unacylated-tRNASec variants demonstrated that the acceptor stem and variable arm are essential for SelB recognition. Moreover, our data support the sequence of molecular events where GTP-activated SelB strongly interacts with SelA.tRNASec. Subsequently, SelB.GTP.tRNASec recognizes the mRNA SECIS to deliver the tRNASec to the ribosome. SelB in complex with its specific RNAs were examined using Hydrogen/Deuterium exchange mapping that allowed the determination of the molecular envelopes and its secondary structural variations during the complex assembly. Our results demonstrate the ordering of events in Sec incorporation and contribute to the full comprehension of the tRNASec role in the Sec amino acid biosynthesis, as well as extending the knowledge of synthetic biology and the expansion of the genetic code.
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Affiliation(s)
- Vitor Hugo Balasco Serrão
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Chemistry and Biochemistry, University California - Santa Cruz, 1156 High St., Santa Cruz, CA 95060, United States
| | - Adriano de Freitas Fernandes
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil
| | - Luis Guilherme Mansor Basso
- Physical Sciences Laboratory, State University of Northern Rio de Janeiro Darcy Ribeiro - UENF, Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Faculty of Science, Philosophy and Letters, University of Sao Paulo, CEP 14040-901 Ribeirão Preto, SP, Brazil
| | - Jéssica Fernandes Scortecci
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Edson Crusca Júnior
- Department of Physical Chemistry, Chemistry Institute of the São Paulo State University - UNESP, CEP 14800-900 Araraquara, SP, Brazil
| | - Marinônio Lopes Cornélio
- Physics Department, Institute of Biosciences, Letters and Exact Sciences (IBILCE), São Paulo State University - UNESP, São Jose do Rio Preto, SP, Brazil
| | - Bibiana Monson de Souza
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mário Sérgio Palma
- Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University - UNESP, Rio Claro, SP, Brazil
| | - Mario de Oliveira Neto
- Bioscience Institute of Universidade Estadual Paulista, Rubião Jr., Botucatu, SP CEP 18618-000, Brazil
| | - Otavio Henrique Thiemann
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP CEP 13566-590, Brazil; Department of Genetics and Evolution, Federal University of São Carlos - UFSCar, 13565-905 São Carlos, SP, Brazil.
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11
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Alipov AA, Lekontseva NV, Mikhailina AO, Fando MS, Tishchenko SV, Nikulin AD. Structure of a Mutant Form of Translation Regulator Hfq with the Extended Loop L4. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Tishchenko SV, Mikhailina AO, Lekontseva NV, Stolboushkina EA, Nikonova EY, Nikonov OS, Nikulin AD. Structural Investigations of RNA–Protein Complexes in Post-Ribosomal Era. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Structural studies of RNA–protein complexes are important for understanding many molecular mechanisms occurring in cells (e.g., regulation of protein synthesis and RNA-chaperone activity of proteins). Various objects investigated at the Institute of Protein Research of the Russian Academy of Sciences are considered. Based on the analysis of the structures of the complexes of the ribosomal protein L1 with specific regions on both mRNA and rRNA, the principles of regulation of the translation of the mRNA of its own operon are presented. The studies of the heterotrimeric translation initiation factor IF2 of archaea and eukaryotes are described, and the data on the interaction of glycyl-tRNA-synthetase with viral IRES are reported. The results of studying the interaction of RNA molecules with one of functionally important sites of the Hfq protein are presented, and the differences in the RNA-binding properties of the Hfq and archaeal Lsm proteins are revealed.
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13
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Turbant F, Wu P, Wien F, Arluison V. The Amyloid Region of Hfq Riboregulator Promotes DsrA: rpoS RNAs Annealing. BIOLOGY 2021; 10:biology10090900. [PMID: 34571778 PMCID: PMC8468756 DOI: 10.3390/biology10090900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/30/2021] [Accepted: 09/05/2021] [Indexed: 11/16/2022]
Abstract
Hfq is a bacterial RNA chaperone which promotes the pairing of small noncoding RNAs to target mRNAs, allowing post-transcriptional regulation. This RNA annealing activity has been attributed for years to the N-terminal region of the protein that forms a toroidal structure with a typical Sm-fold. Nevertheless, many Hfqs, including that of Escherichia coli, have a C-terminal region with unclear functions. Here we use a biophysical approach, Synchrotron Radiation Circular Dichroism (SRCD), to probe the interaction of the E. coli Hfq C-terminal amyloid region with RNA and its effect on RNA annealing. This C-terminal region of Hfq, which has been described to be dispensable for sRNA:mRNA annealing, has an unexpected and significant effect on this activity. The functional consequences of this novel property of the amyloid region of Hfq in relation to physiological stress are discussed.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Pengzhi Wu
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland;
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- UFR Sciences du Vivant, Université de Paris, 75006 Paris, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
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14
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Sudo N, Lee K, Sekine Y, Ohnishi M, Iyoda S. RNA-binding protein Hfq downregulates locus of enterocyte effacement-encoded regulators independent of small regulatory RNA in enterohemorrhagic Escherichia coli. Mol Microbiol 2021; 117:86-101. [PMID: 34411346 DOI: 10.1111/mmi.14799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) causes severe human diseases worldwide. The type 3 secretion system and effector proteins are essential for EHEC infection, and are encoded by the locus of enterocyte effacement (LEE). RNA-binding protein Hfq is essential for small regulatory RNA (sRNA)-mediated regulation at a posttranscriptional level and full virulence of many pathogenic bacteria. Although two early studies indicated that Hfq represses LEE expression by posttranscriptionally controlling the expression of genes grlRA and/or ler, both of which encode LEE regulators mediating a positive regulatory loop, the detailed molecular mechanism and biological significance remain unclear. Herein, we show that LEE overexpression was caused by defective RNA-binding activity of the Hfq distal face, which posttranscriptionally represses grlA and ler expression. In vitro analyses revealed that the Hfq distal face directly binds near the translational initiation site of grlA and ler mRNAs, and inhibits their translation. Taken together, we conclude that Hfq inhibits grlA and ler translation by binding their mRNAs through the distal face in an sRNA-independent manner. Additionally, we show that Hfq-mediated repression of LEE is critical for normal EHEC growth because all suppressor mutations that restored the growth defect in the hfq mutant abolished hfq deletion-induced overexpression of LEE.
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Affiliation(s)
- Naoki Sudo
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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15
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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16
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Malecka EM, Bassani F, Dendooven T, Sonnleitner E, Rozner M, Albanese TG, Resch A, Luisi B, Woodson S, Bläsi U. Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:7075-7087. [PMID: 34139006 PMCID: PMC8266614 DOI: 10.1093/nar/gkab510] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) govern translation of numerous transcripts during carbon catabolite repression. Here, Crc was shown to enhance Hfq-mediated translational repression of several mRNAs. We have developed a single-molecule fluorescence assay to quantitatively assess the cooperation of Hfq and Crc to form a repressive complex on a RNA, encompassing the translation initiation region and the proximal coding sequence of the P. aeruginosa amiE gene. The presence of Crc did not change the amiE RNA-Hfq interaction lifetimes, whereas it changed the equilibrium towards more stable repressive complexes. This observation is in accord with Cryo-EM analyses, which showed an increased compactness of the repressive Hfq/Crc/RNA assemblies. These biophysical studies revealed how Crc protein kinetically stabilizes Hfq/RNA complexes, and how the two proteins together fold a large segment of the mRNA into a more compact translationally repressive structure. In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. Although Hfq is well-known to act with small regulatory RNAs, this study shows how Hfq can collaborate with another protein to down-regulate translation of mRNAs that become targets for the degradative machinery.
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Affiliation(s)
- Ewelina M Malecka
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Marlena Rozner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Ben Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah Woodson
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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17
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Lekontseva NV, Stolboushkina EA, Nikulin AD. Diversity of LSM Family Proteins: Similarities and Differences. BIOCHEMISTRY (MOSCOW) 2021; 86:S38-S49. [PMID: 33827399 DOI: 10.1134/s0006297921140042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Members of the Lsm protein family are found in all three domains of life: bacteria, archaea, and eukarya. They are involved in numerous processes associated with RNA processing and gene expression regulation. A common structural feature of all Lsm family proteins is the presence of the Sm fold consisting of a five-stranded β-sheet and an α-helix at the N-terminus. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the formation of spliceosomes and mRNA decapping. Homohexameric bacterial Lsm protein, Hfq, is involved in the regulation of transcription of different mRNAs by facilitating their interactions with small regulatory RNAs. Furthermore, recently obtained data indicate a new role of Hfq as a ribosome biogenesis factor, as it mediates formation of the productive structure of the 17S rRNA 3'- and 5'-sequences, facilitating their further processing by RNases. Lsm archaeal proteins (SmAPs) form homoheptamers and likely interact with single-stranded uridine-rich RNA elements, although the role of these proteins in archaea is still poorly understood. In this review, we discuss the structural features of the Lsm family proteins from different life domains and their structure-function relationships.
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Affiliation(s)
- Natalia V Lekontseva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey D Nikulin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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18
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Krepl M, Dendooven T, Luisi BF, Sponer J. MD simulations reveal the basis for dynamic assembly of Hfq-RNA complexes. J Biol Chem 2021; 296:100656. [PMID: 33857481 PMCID: PMC8121710 DOI: 10.1016/j.jbc.2021.100656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023] Open
Abstract
The conserved protein Hfq is a key factor in the RNA-mediated control of gene expression in most known bacteria. The transient intermediates Hfq forms with RNA support intricate and robust regulatory networks. In Pseudomonas, Hfq recognizes repeats of adenine–purine–any nucleotide (ARN) in target mRNAs via its distal binding side, and together with the catabolite repression control (Crc) protein, assembles into a translation–repression complex. Earlier experiments yielded static, ensemble-averaged structures of the complex, but details of its interface dynamics and assembly pathway remained elusive. Using explicit solvent atomistic molecular dynamics simulations, we modeled the extensive dynamics of the Hfq–RNA interface and found implications for the assembly of the complex. We predict that syn/anti flips of the adenine nucleotides in each ARN repeat contribute to a dynamic recognition mechanism between the Hfq distal side and mRNA targets. We identify a previously unknown binding pocket that can accept any nucleotide and propose that it may serve as a ‘status quo’ staging point, providing nonspecific binding affinity, until Crc engages the Hfq–RNA binary complex. The dynamical components of the Hfq–RNA recognition can speed up screening of the pool of the surrounding RNAs, participate in rapid accommodation of the RNA on the protein surface, and facilitate competition among different RNAs. The register of Crc in the ternary assembly could be defined by the recognition of a guanine-specific base–phosphate interaction between the first and last ARN repeats of the bound RNA. This dynamic substrate recognition provides structural rationale for the stepwise assembly of multicomponent ribonucleoprotein complexes nucleated by Hfq–RNA binding.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; MRC-LMB, Cambridge, United Kingdom
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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19
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Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. eLife 2021; 10:64207. [PMID: 33616037 PMCID: PMC7987339 DOI: 10.7554/elife.64207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face. Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes. The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs. Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.
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Affiliation(s)
- Seongjin Park
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Emily M Heideman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Muhammad S Azam
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Matthew A Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
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20
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Ng Kwan Lim E, Sasseville C, Carrier MC, Massé E. Keeping Up with RNA-Based Regulation in Bacteria: New Roles for RNA Binding Proteins. Trends Genet 2020; 37:86-97. [PMID: 33077249 DOI: 10.1016/j.tig.2020.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/06/2023]
Abstract
RNA binding proteins (RBPs) are ubiquitously found in all kingdoms of life. They are involved in a plethora of regulatory events, ranging from direct regulation of gene expression to guiding modification of RNA molecules. As bacterial regulators, RBPs can act alone or in concert with RNA-based regulators, such as small regulatory RNAs (sRNAs), riboswitches, or clustered regularly interspaced short palindromic repeats (CRISPR) RNAs. Various functions of RBPs, whether dependent or not on an RNA regulator, have been described in the past. However, the past decade has been a fertile ground for the development of novel high-throughput methods. These methods acted as stepping-stones for the discovery of new functions of RBPs and helped in the understanding of the molecular mechanisms behind previously described regulatory events. Here, we present an overview of the recently identified roles of major bacterial RBPs from different model organisms. Moreover, the tight relationship between RBPs and RNA-based regulators will be explored.
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Affiliation(s)
- Evelyne Ng Kwan Lim
- Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada
| | - Charles Sasseville
- Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada
| | - Marie-Claude Carrier
- Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada
| | - Eric Massé
- Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Université de Sherbrooke, Sherbrooke, J1H 5N4, QC, Canada.
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21
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Orans J, Kovach AR, Hoff KE, Horstmann NM, Brennan RG. Crystal structure of an Escherichia coli Hfq Core (residues 2-69)-DNA complex reveals multifunctional nucleic acid binding sites. Nucleic Acids Res 2020; 48:3987-3997. [PMID: 32133526 PMCID: PMC7144919 DOI: 10.1093/nar/gkaa149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Hfq regulates bacterial gene expression post-transcriptionally by binding small RNAs and their target mRNAs, facilitating sRNA-mRNA annealing, typically resulting in translation inhibition and RNA turnover. Hfq is also found in the nucleoid and binds double-stranded (ds) DNA with a slight preference for A-tracts. Here, we present the crystal structure of the Escherichia coli Hfq Core bound to a 30 bp DNA, containing three 6 bp A-tracts. Although previously postulated to bind to the ‘distal’ face, three statistically disordered double stranded DNA molecules bind across the proximal face of the Hfq hexamer as parallel, straight rods with B-DNA like conformational properties. One DNA duplex spans the diameter of the hexamer and passes over the uridine-binding proximal-face pore, whereas the remaining DNA duplexes interact with the rims and serve as bridges between adjacent hexamers. Binding is sequence-independent with residues N13, R16, R17 and Q41 interacting exclusively with the DNA backbone. Atomic force microscopy data support the sequence-independent nature of the Hfq-DNA interaction and a role for Hfq in DNA compaction and nucleoid architecture. Our structure and nucleic acid-binding studies also provide insight into the mechanism of sequence-independent binding of Hfq to dsRNA stems, a function that is critical for proper riboregulation.
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Affiliation(s)
- Jillian Orans
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alexander R Kovach
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kirsten E Hoff
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicola M Horstmann
- Department of Infectious Diseases, Infection Control Research, University of Texas MD Anderson Cancer Center, Houston TX 77054, USA
| | - Richard G Brennan
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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22
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Sonnleitner E, Pusic P, Wolfinger MT, Bläsi U. Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq. Front Microbiol 2020; 11:1001. [PMID: 32528439 PMCID: PMC7264166 DOI: 10.3389/fmicb.2020.01001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/24/2020] [Indexed: 12/29/2022] Open
Abstract
Carbapenems are often the antibiotics of choice to combat life threatening infections caused by the opportunistic human pathogen Pseudomonas aeruginosa. The outer membrane porins OprD and OpdP serve as entry ports for carbapenems. Here, we report that the RNA chaperone Hfq governs post-transcriptional regulation of the oprD and opdP genes in a distinctive manner. Hfq together with the recently described small regulatory RNAs (sRNAs) ErsA and Sr0161 is shown to mediate translational repression of oprD, whereas opdP appears not to be regulated by sRNAs. At variance, our data indicate that opdP is translationally repressed by a regulatory complex consisting of Hfq and the catabolite repression protein Crc, an assembly known to be key to carbon catabolite repression in P. aeruginosa. The regulatory RNA CrcZ, which is up-regulated during growth of P. aeruginosa on less preferred carbon sources, is known to sequester Hfq, which relieves Hfq-mediated translational repression of genes. The differential carbapenem susceptibility during growth on different carbon sources can thus be understood in light of Hfq-dependent oprD/opdP regulation and of the antagonizing function of the CrcZ RNA on Hfq regulatory complexes.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Petra Pusic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
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23
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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.
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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.
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24
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Cameron TA, Matz LM, Sinha D, De Lay NR. Polynucleotide phosphorylase promotes the stability and function of Hfq-binding sRNAs by degrading target mRNA-derived fragments. Nucleic Acids Res 2019; 47:8821-8837. [PMID: 31329973 PMCID: PMC7145675 DOI: 10.1093/nar/gkz616] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 01/14/2023] Open
Abstract
In many Gram-negative and some Gram-positive bacteria, small regulatory RNAs (sRNAs) that bind the RNA chaperone Hfq have a pivotal role in modulating virulence, stress responses, metabolism and biofilm formation. These sRNAs recognize transcripts through base-pairing, and sRNA–mRNA annealing consequently alters the translation and/or stability of transcripts leading to changes in gene expression. We have previously found that the highly conserved 3′-to-5′ exoribonuclease polynucleotide phosphorylase (PNPase) has an indispensable role in paradoxically stabilizing Hfq-bound sRNAs and promoting their function in gene regulation in Escherichia coli. Here, we report that PNPase contributes to the degradation of specific short mRNA fragments, the majority of which bind Hfq and are derived from targets of sRNAs. Specifically, we found that these mRNA-derived fragments accumulate in the absence of PNPase or its exoribonuclease activity and interact with PNPase. Additionally, we show that mutations in hfq or in the seed pairing region of some sRNAs eliminated the requirement of PNPase for their stability. Altogether, our results are consistent with a model that PNPase degrades mRNA-derived fragments that could otherwise deplete cells of Hfq-binding sRNAs through pairing-mediated decay.
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Affiliation(s)
- Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Lisa M Matz
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Dhriti Sinha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Nicholas R De Lay
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, The University of Texas Health Science Center, Houston, TX 77030, USA
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25
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Abstract
Hfq is a ubiquitous Sm-like RNA-binding protein in bacteria involved in physiological fitness and pathogenesis, while its in vivo binding nature remains elusive. Here we reported genome-wide Hfq-bound RNAs in Yersinia pestis, a causative agent of plague, by using cross-linking immunoprecipitation coupled with deep sequencing (CLIP-seq) approach. We show that the Hfq binding density is enriched in more than 80% mRNAs of Y. pestis and that Hfq also globally binds noncoding small RNAs (sRNAs) encoded by the intergenic, antisense, and 3' regions of mRNAs. An Hfq U-rich stretch is highly enriched in sRNAs, while motifs partially complementary to AGAAUAA and GGGGAUUA are enriched in both mRNAs and sRNAs. Hfq-binding motifs are enriched at both terminal sites and in the gene body of mRNAs. Surprisingly, a large fraction of the sRNA and mRNA regions bound by Hfq and those downstream are destabilized, likely via a 5'P-activated RNase E degradation pathway, which is consistent with a model in which Hfq facilitates sRNA-mRNA base pairing and the coupled degradation in Y. pestis These results together have presented a high-quality Hfq-RNA interaction map in Y. pestis, which should be important for further deciphering the regulatory role of Hfq-sRNAs in Y. pestis IMPORTANCE Discovered in 1968 as an Escherichia coli host factor that was essential for replication of the bacteriophage Qβ, the Hfq protein is a ubiquitous and highly abundant RNA-binding protein in many bacteria. With the assistance of Hfq, small RNAs in bacteria play important roles in regulating the stability and translation of mRNAs by base pairing. In this study, we want to elucidate the Hfq-assisted sRNA-mRNA regulation in Yersinia pestis A global map of Hfq interaction sites in Y. pestis was obtained by sequencing cDNAs converted from the Hfq-bound RNA fragments using UV cross-linking coupled immunoprecipitation technology. We demonstrate that Hfq could bind to hundreds of sRNAs and the majority of mRNAs in Y. pestis The enriched binding motifs in sRNAs and mRNAs are complementary to each other, suggesting a general base-pairing mechanism for sRNA-mRNA interaction. The Hfq-bound sRNA and mRNA regions were both destabilized. The results suggest that Hfq binding facilitates sRNA-mRNA base pairing and coordinates their degradation, which might enable Hfq to surveil the homeostasis of most mRNAs in bacteria.
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26
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Alvarez Paggi D, Esperante SA, Salgueiro M, Camporeale G, de Oliveira GAP, Prat Gay G. A conformational switch balances viral RNA accessibility and protection in a nucleocapsid ring model. Arch Biochem Biophys 2019; 671:77-86. [PMID: 31229488 DOI: 10.1016/j.abb.2019.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/30/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022]
Abstract
Virus from the Mononegavirales order share common features ranging from virion structure arrangement to mechanisms of replication and transcription. One of them is the way the nucleoprotein (N) wraps and protects the RNA genome from degradation by forming a highly ordered helical nucleocapsid. However, crystal structures from numerous Mononegavirales reveal that binding to the nucleoprotein results in occluded nucleotides that hinder base pairing necessary for transcription and replication. This hints at the existence of alternative conformations of the N protein that would impact on the protein-RNA interface, allowing for transient exposure of the nucleotides without complete RNA release. Moreover, the regulation between the alternative conformations should be finely tuned. Recombinant expression of N from the respiratory syncytial virus form regular N/RNA common among all Mononegavirales, and these constitute an ideal minimal unit for investigating the mechanisms through which these structures protect RNA so efficiently while allowing for partial accessibility during transcription and replication. Neither pH nor high ionic strength could dissociate the RNA but led to irreversible aggregation of the nucleoprotein. Low concentrations of guanidine chloride dissociated the RNA moiety but leading to irreversible aggregation of the protein moiety. On the other hand, high concentrations of urea and long incubation periods were required to remove bound RNA. Both denaturants eventually led to unfolding but converged in the formation of an RNA-free β-enriched intermediate species that remained decameric even at high denaturant concentrations. Although the N-RNA rings interact with the phosphoprotein P, the scaffold of the RNA polymerase complex, this interaction did not lead to RNA dissociation from the rings in vitro. Thus, we have uncovered complex equilibria involving changes in secondary structure of N and RNA loosening, processes that must take place in the context of RNA transcription and replication, whose detailed mechanisms and cellular and viral participants need to be established.
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Affiliation(s)
- D Alvarez Paggi
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
| | - S A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - M Salgueiro
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G Camporeale
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina
| | - G A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnêtica Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908-0733, USA
| | - G Prat Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET, Argentina.
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27
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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.
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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
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28
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The RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens. J Bacteriol 2019; 201:JB.00730-18. [PMID: 30885931 DOI: 10.1128/jb.00730-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Riboregulation involving regulatory RNAs, RNA chaperones, and ribonucleases is fundamental for the rapid adaptation of gene expression to changing environmental conditions. The gene coding for the RNase YbeY belongs to the minimal prokaryotic genome set and has a profound impact on physiology in a wide range of bacteria. Here, we show that the Agrobacterium tumefaciens ybeY gene is not essential. Deletion of the gene in the plant pathogen reduced growth, motility, and stress tolerance. Most interestingly, YbeY is crucial for A. tumefaciens-mediated T-DNA transfer and tumor formation. Comparative proteomics by using isobaric tags for relative and absolute quantitation (iTRAQ) revealed dysregulation of 59 proteins, many of which have previously been found to be dependent on the RNA chaperone Hfq. YbeY and Hfq have opposing effects on production of these proteins. Accumulation of a 16S rRNA precursor in the ybeY mutant suggests that A. tumefaciens YbeY is involved in rRNA processing. RNA coimmunoprecipitation-sequencing (RIP-Seq) showed binding of YbeY to the region immediately upstream of the 16S rRNA. Purified YbeY is an oligomer with RNase activity. It does not physically interact with Hfq and thus plays a partially overlapping but distinct role in the riboregulatory network of the plant pathogen.IMPORTANCE Although ybeY gene belongs to the universal bacterial core genome, its biological function is incompletely understood. Here, we show that YbeY is critical for fitness and host-microbe interaction in the plant pathogen Agrobacterium tumefaciens Consistent with the reported endoribonuclease activity of YbeY, A. tumefaciens YbeY acts as a RNase involved in maturation of 16S rRNA. This report adds a worldwide plant pathogen and natural genetic engineer of plants to the growing list of bacteria that require the conserved YbeY protein for host-microbe interaction.
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29
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Hoekzema M, Romilly C, Holmqvist E, Wagner EGH. Hfq-dependent mRNA unfolding promotes sRNA-based inhibition of translation. EMBO J 2019; 38:embj.2018101199. [PMID: 30833291 PMCID: PMC6443205 DOI: 10.15252/embj.2018101199] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 01/11/2023] Open
Abstract
Small RNAs post‐transcriptionally regulate many processes in bacteria. Base‐pairing of sRNAs near ribosome‐binding sites in mRNAs inhibits translation, often requiring the RNA chaperone Hfq. In the canonical model, Hfq simultaneously binds sRNAs and mRNA targets to accelerate pairing. Here, we show that the Escherichia coli sRNAs OmrA and OmrB inhibit translation of the diguanylate cyclase DgcM (previously: YdaM), a player in biofilm regulation. In OmrA/B repression of dgcM, Hfq is not required as an RNA interaction platform, but rather unfolds an inhibitory RNA structure that impedes OmrA/B binding. This restructuring involves distal face binding of Hfq and is supported by RNA structure mapping. A corresponding mutant protein cannot support inhibition in vitro and in vivo; proximal and rim mutations have negligible effects. Strikingly, OmrA/B‐dependent translational inhibition in vitro is restored, in complete absence of Hfq, by a deoxyoligoribonucleotide that base‐pairs to the biochemically mapped Hfq site in dgcM mRNA. We suggest that Hfq‐dependent RNA structure remodeling can promote sRNA access, which represents a mechanism distinct from an interaction platform model.
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Affiliation(s)
- Mirthe Hoekzema
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
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30
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Morita T, Aiba H. Mechanism and physiological significance of autoregulation of the Escherichia coli hfq gene. RNA (NEW YORK, N.Y.) 2019; 25:264-276. [PMID: 30487269 PMCID: PMC6348989 DOI: 10.1261/rna.068106.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/23/2018] [Indexed: 06/09/2023]
Abstract
The RNA chaperone Hfq plays a critical role in sRNA-mediated gene regulation in enteric bacteria. The major role of Hfq is to stimulate base-pairing between sRNAs and target mRNAs by binding both RNAs through three RNA-binding surfaces. To understand the post-transcriptional network exerted by Hfq and its associated sRNAs, it is important to know how the cellular concentration of Hfq is regulated. While an early study showed that hfq translation is repressed by Hfq, the detailed mechanism and biological significance of the hfq autoregulation remain to be studied. Here, we show that the synthesis of Hfq is strictly autoregulated to maintain the cellular concentration of Hfq within a limited range even when the hfq mRNA is overexpressed from a plasmid-borne hfq gene. Mutational and biochemical studies demonstrate that Hfq represses its own translation primarily by binding to the hfq mRNA through the distal face. The growth of cells harboring the hfq plasmid is markedly inhibited due to an increased Hfq level when the distal face of Hfq is mutated or the 5'-UTR of hfq is mutated. A mutation in the rim suppresses the growth inhibition caused by the distal face mutation, suggesting that the interaction of Hfq with undefined RNAs through the rim is responsible for the growth inhibition by the increased Hfq level. In addition, the data suggest that the hfq autoregulation operates not only in cells harboring a multicopy hfq gene but also in the wild-type cells.
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Affiliation(s)
- Teppei Morita
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie, 513-8670, Japan
| | - Hiroji Aiba
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Sciences, Suzuka, Mie, 513-8670, Japan
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31
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Stanek KA, Mura C. Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly. Methods Mol Biol 2019; 1737:273-299. [PMID: 29484599 DOI: 10.1007/978-1-4939-7634-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hfq is a bacterial RNA-binding protein that plays key roles in the post-transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA∙∙∙RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways-including stress response, quorum sensing, and biofilm formation-has motivated genetic and "RNAomic" studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq∙∙∙RNA interactions (in vitro). Indeed, crystallographic and biophysical studies first established Hfq as a member of the phylogenetically conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements, viz.: reconstituting and characterizing an Hfq·RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.
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Affiliation(s)
- Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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32
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Abstract
Despite the central role of bacterial noncoding small RNAs (sRNAs) in posttranscriptional regulation, little is understood about their evolution. Here we compile what has been studied to date and trace a life cycle of sRNAs-from their mechanisms of emergence, through processes of change and frequent neofunctionalization, to their loss from bacterial lineages. Because they possess relatively unrestrictive structural requirements, we find that sRNA origins are varied, and include de novo emergence as well as formation from preexisting genetic elements via duplication events and horizontal gene transfer. The need for only partial complementarity to their mRNA targets facilitates apparent rapid change, which also contributes to significant challenges in tracing sRNAs across broad evolutionary distances. We document that recently emerged sRNAs in particular evolve quickly, mirroring dynamics observed in microRNAs, their functional analogs in eukaryotes. Mutations in mRNA-binding regions, transcriptional regulator or sigma factor binding sites, and protein-binding regions are all likely sources of shifting regulatory roles of sRNAs. Finally, using examples from the few evolutionary studies available, we examine cases of sRNA loss and describe how these may be the result of adaptive in addition to neutral processes. We highlight the need for more-comprehensive analyses of sRNA evolutionary patterns as a means to improve novel sRNA detection, enhance genome annotation, and deepen our understanding of regulatory networks in bacteria.
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33
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Wang C, Pu T, Lou W, Wang Y, Gao Z, Hu B, Fan J. Hfq, a RNA Chaperone, Contributes to Virulence by Regulating Plant Cell Wall-Degrading Enzyme Production, Type VI Secretion System Expression, Bacterial Competition, and Suppressing Host Defense Response in Pectobacterium carotovorum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1166-1178. [PMID: 30198820 DOI: 10.1094/mpmi-12-17-0303-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hfq is a RNA chaperone and participates in a wide range of cellular processes and pathways. In this study, mutation of hfq gene from Pectobacterium carotovorum subsp. carotovorum PccS1 led to significantly reduced virulence and plant cell wall-degrading enzyme (PCWDE) activities. In addition, the mutant exhibited decreased biofilm formation and motility and greatly attenuated carbapenem production as well as secretion of hemolysin coregulated protein (Hcp) as compared with wild-type strain PccS1. Moreover, a higher level of callose deposition was induced in Nicotiana benthamiana leaves when infiltrated with the mutant. A total of 26 small (s)RNA deletion mutants were obtained among a predicted 27 sRNAs, and three mutants exhibited reduced virulence in the host plant. These results suggest that hfq plays a key role in Pectobacterium virulence by positively impacting PCWDE production, secretion of the type VI secretion system, bacterial competition, and suppression of host plant responses.
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Affiliation(s)
- Chunting Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianxin Pu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangying Lou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yujie Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zishu Gao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Baishi Hu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqin Fan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Leistra AN, Gelderman G, Sowa SW, Moon-Walker A, Salis HM, Contreras LM. A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions. Sci Rep 2018; 8:9892. [PMID: 29967470 PMCID: PMC6028588 DOI: 10.1038/s41598-018-27474-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/04/2018] [Indexed: 02/04/2023] Open
Abstract
Bacterial global post-transcriptional regulators execute hundreds of interactions with targets that display varying molecular features while retaining specificity. Herein, we develop, validate, and apply a biophysical, statistical thermodynamic model of canonical target mRNA interactions with the CsrA global post-transcriptional regulator to understand the molecular features that contribute to target regulation. Altogether, we model interactions of CsrA with a pool of 236 mRNA: 107 are experimentally regulated by CsrA and 129 are suspected interaction partners. Guided by current understanding of CsrA-mRNA interactions, we incorporate (i) mRNA nucleotide sequence, (ii) cooperativity of CsrA-mRNA binding, and (iii) minimization of mRNA structural changes to identify an ensemble of likely binding sites and their free energies. The regulatory impact of bound CsrA on mRNA translation is determined with the RBS calculator. Predicted regulation of 66 experimentally regulated mRNAs adheres to the principles of canonical CsrA-mRNA interactions; the remainder implies that other, diverse mechanisms may underlie CsrA-mRNA interaction and regulation. Importantly, results suggest that this global regulator may bind targets in multiple conformations, via flexible stretches of overlapping predicted binding sites. This novel observation expands the notion that CsrA always binds to its targets at specific consensus sequences.
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Affiliation(s)
- A N Leistra
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - G Gelderman
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - S W Sowa
- Microbiology Graduate Program, University of Texas at Austin, 100 E. 24th St. Stop A6500, Austin, TX, 78712, USA
| | - A Moon-Walker
- Biological Sciences Program College of Natural Sciences, University of Texas at Austin, 120 Inner Campus Drive Stop G2500, Austin, TX, 78712, USA
| | - H M Salis
- Department of Chemical Engineering, Pennsylvania State University, 210 Agricultural Engineering Building, University Park, PA, 16802, USA
| | - L M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, 200 E. Dean Keeton St. Stop C0400, Austin, TX, 78712, USA.
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35
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Santiago-Frangos A, Woodson SA. Hfq chaperone brings speed dating to bacterial sRNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1475. [PMID: 29633565 PMCID: PMC6002925 DOI: 10.1002/wrna.1475] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/22/2018] [Accepted: 02/26/2018] [Indexed: 11/11/2022]
Abstract
Hfq is a ubiquitous, Sm-like RNA binding protein found in most bacteria and some archaea. Hfq binds small regulatory RNAs (sRNAs), facilitates base pairing between sRNAs and their mRNA targets, and directly binds and regulates translation of certain mRNAs. Because sRNAs regulate many stress response pathways in bacteria, Hfq is essential for adaptation to different environments and growth conditions. The chaperone activities of Hfq arise from multipronged RNA binding by three different surfaces of the Hfq hexamer. The manner in which the structured Sm core of Hfq binds RNA has been well studied, but recent work shows that the intrinsically disordered C-terminal domain of Hfq modulates sRNA binding, creating a kinetic hierarchy of RNA competition for Hfq and ensuring the release of double-stranded sRNA-mRNA complexes. A combination of structural, biophysical, and genetic experiments reveals how Hfq recognizes its RNA substrates and plays matchmaker for sRNAs and mRNAs in the cell. The interplay between structured and disordered domains of Hfq optimizes sRNA-mediated post-transcriptional regulation, and is a common theme in RNA chaperones. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry.
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Affiliation(s)
- Andrew Santiago-Frangos
- Program in Cellular, Molecular and Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Sarah A Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
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36
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Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB. Sci Rep 2018; 8:8803. [PMID: 29892030 PMCID: PMC5995851 DOI: 10.1038/s41598-018-27131-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/25/2018] [Indexed: 01/26/2023] Open
Abstract
KaiC, the core oscillator of the cyanobacterial circadian clock, is composed of an N-terminal C1 domain and a C-terminal C2 domain, and assembles into a double-ring hexamer upon ATP binding. Cyclic phosphorylation and dephosphorylation at Ser431 and Thr432 in the C2 domain proceed with a period of approximately 24 h in the presence of other clock proteins, KaiA and KaiB, but recent studies have revealed a crucial role for the C1 ring in determining the cycle period. In this study, we mapped dynamic structural changes of the C1 ring in solution using a combination of site-directed tryptophan mutagenesis and fluorescence spectroscopy. We found that the C1 ring undergoes a structural transition, coupled with ATPase activity and the phosphorylation state, while maintaining its hexameric ring structure. This transition triggered by ATP hydrolysis in the C1 ring in specific phosphorylation states is a necessary event for recruitment of KaiB, limiting the overall rate of slow complex formation. Our results provide structural and kinetic insights into the C1-ring rearrangements governing the slow dynamics of the cyanobacterial circadian clock.
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37
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Wen B, Wang W, Zhang J, Gong Q, Shi Y, Wu J, Zhang Z. Structural and dynamic properties of the C-terminal region of the Escherichia coli RNA chaperone Hfq: integrative experimental and computational studies. Phys Chem Chem Phys 2018; 19:21152-21164. [PMID: 28752165 DOI: 10.1039/c7cp01044c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In Escherichia coli, hexameric Hfq is an important RNA chaperone that facilitates small RNA-mediated post-transcriptional regulation. The Hfq monomer consists of an evolutionarily conserved Sm domain (residues 1-65) and a flexible C-terminal region (residues 66-102). It has been recognized that the existence of the C-terminal region is important for the function of Hfq, but its detailed structural and dynamic properties remain elusive due to its disordered nature. In this work, using integrative experimental techniques, such as nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, as well as multi-scale computational simulations, new insights into the structure and dynamics of the C-terminal region in the context of the Hfq hexamer are provided. Although the C-terminal region is intrinsically disordered, some residues (83-86) are motionally restricted. The hexameric core may affect the secondary structure propensity of the C-terminal region, due to transient interactions between them. The residues at the rim and the proximal side of the core have significantly more transient contacts with the C-terminal region than those residues at the distal side, which may facilitate the function of the C-terminal region in the release of double-stranded RNAs and the cycling of small non-coding RNAs. Structure ensembles constructed by fitting the experimental data also support that the C-terminal region prefers to locate at the proximal side. From multi-scale simulations, we propose that the C-terminal region may play a dual role of steric effect (especially at the proximal side) and recruitment (at the both sides) in the binding process of RNA substrates. Interestingly, we have found that these motionally restricted residues may serve as important binding sites for the incoming RNAs that is probably driven by favorable electrostatic interactions. These integrative studies may aid in our understanding of the functional role of the C-terminal region of Hfq.
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Affiliation(s)
- Bin Wen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, P. R. China.
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38
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Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mücke N, Wilmanns M, Gibson TJ, Barabas O. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Sci Rep 2017; 7:9903. [PMID: 28852099 PMCID: PMC5575007 DOI: 10.1038/s41598-017-10085-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022] Open
Abstract
The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a “speed-dating” fashion, thereby supporting their regulatory function.
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Affiliation(s)
- Eike C Schulz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany.,Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Markus Seiler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438, Frankfurt a.M., Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Franka Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Vladimir Rybin
- Protein Expression and Purification Core Facility, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Vivian Pogenberg
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Matthias Wilmanns
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, 22603, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
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39
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Chen J, Gottesman S. Hfq links translation repression to stress-induced mutagenesis in E. coli. Genes Dev 2017; 31:1382-1395. [PMID: 28794186 PMCID: PMC5580658 DOI: 10.1101/gad.302547.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Here, Chen et al. show an example of Hfq repressing translation in the absence of sRNAs via major remodeling of the mRNA. They demonstrate that, by interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis. Mismatch repair (MMR) is a conserved mechanism exploited by cells to correct DNA replication errors both in growing cells and under nongrowing conditions. Hfq (host factor for RNA bacteriophage Qβ replication), a bacterial Lsm family RNA-binding protein, chaperones RNA–RNA interactions between regulatory small RNAs (sRNAs) and target messenger RNAs (mRNAs), leading to alterations of mRNA translation and/or stability. Hfq has been reported to post-transcriptionally repress the DNA MMR gene mutS in stationary phase, possibly limiting MMR to allow increased mutagenesis. Here we report that Hfq deploys dual mechanisms to control mutS expression. First, Hfq binds directly to an (AAN)3 motif within the mutS 5′ untranslated region (UTR), repressing translation in the absence of sRNA partners both in vivo and in vitro. Second, Hfq acts in a canonical pathway, promoting base-pairing of ArcZ sRNA with the mutS leader to inhibit translation. Most importantly, using pathway-specific mutS chromosomal alleles that specifically abrogate either regulatory pathway or both, we demonstrate that tight control of MutS levels in stationary phase contributes to stress-induced mutagenesis. By interacting with the mutS leader, Hfq serves as a critical switch that modulates bacteria from high-fidelity DNA replication to stress-induced mutagenesis.
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Affiliation(s)
- Jiandong Chen
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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40
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Nemchinova M, Balobanov V, Nikonova E, Lekontseva N, Mikhaylina A, Tishchenko S, Nikulin A. An Experimental Tool to Estimate the Probability of a Nucleotide Presence in the Crystal Structures of the Nucleotide-Protein Complexes. Protein J 2017; 36:157-165. [PMID: 28317076 DOI: 10.1007/s10930-017-9709-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A correlation between the ligand-protein affinity and the identification of the ligand in the experimental electron density maps obtained by X-ray crystallography has been tested for a number of RNA-binding proteins. Bacterial translation regulators ProQ, TRAP, Rop, and Hfq together with their archaeal homologues SmAP have been used. The equilibrium dissociation constants for the N-methyl-anthraniloyl-labelled adenosine and guanosine monophosphates titrated by the proteins have been determined by the fluorescent anisotropy measurements. The estimated stability of the nucleotide-protein complexes has been matched with a presence of the nucleotides in the structures of the proposed nucleotide-protein complexes. It has been shown that the ribonucleotides can be definitely identified in the experimental electron density maps at equilibrium dissociation constant <10 μM. At KD of 20-40 μM, long incubation of the protein crystals in the nucleotide solution is required to obtain the structures of the complexes. The complexes with KD value higher than 50 μM are not stable enough to survive in crystallization conditions.
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Affiliation(s)
- Maria Nemchinova
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | - Vitaly Balobanov
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | | | - Alisa Mikhaylina
- Institute of Protein Research RAS, Pushchino, Russian Federation
| | | | - Alexey Nikulin
- Institute of Protein Research RAS, Pushchino, Russian Federation.
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41
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Sonnleitner E, Prindl K, Bläsi U. The Pseudomonas aeruginosa CrcZ RNA interferes with Hfq-mediated riboregulation. PLoS One 2017; 12:e0180887. [PMID: 28686727 PMCID: PMC5501646 DOI: 10.1371/journal.pone.0180887] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022] Open
Abstract
The RNA chaperone Hfq regulates virulence and metabolism in the opportunistic pathogen Pseudomonas aeruginosa. During carbon catabolite repression (CCR) Hfq together with the catabolite repression control protein Crc can act as a translational repressor of catabolic genes. Upon relief of CCR, the level of the Hfq-titrating RNA CrcZ is increasing, which in turn abrogates Hfq-mediated translational repression. As the interdependence of Hfq-mediated and RNA based control mechanisms is poorly understood, we explored the possibility whether the regulatory RNA CrcZ can interfere with riboregulation. We first substantiate that the P. aeruginosa Hfq is proficient and required for riboregulation of the transcriptional activator gene antR by the small RNA PrrF1-2. Our studies further revealed that CrcZ can interfere with PrrF1-2/Hfq-mediated regulation of antR. The competition for Hfq can be rationalized by the higher affinity of Hfq for CrcZ than for antR mRNA.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
- * E-mail:
| | - Konstantin Prindl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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42
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Ryan D, Mukherjee M, Suar M. The expanding targetome of small RNAs in Salmonella Typhimurium. Biochimie 2017; 137:69-77. [DOI: 10.1016/j.biochi.2017.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/10/2017] [Indexed: 10/20/2022]
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43
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Stanek KA, Patterson-West J, Randolph PS, Mura C. Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode. Acta Crystallogr D Struct Biol 2017; 73:294-315. [PMID: 28375142 PMCID: PMC5379935 DOI: 10.1107/s2059798317000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/02/2017] [Indexed: 11/10/2022] Open
Abstract
The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophile Aquifex aeolicus (Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore, Aae Hfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures of Aae Hfq were determined in space groups P1 and P6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6 RNA reveals that the outer rim of the Aae Hfq hexamer features a well defined binding pocket that is selective for uracil. This Aae Hfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.
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Affiliation(s)
- Kimberly A. Stanek
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Jennifer Patterson-West
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Peter S. Randolph
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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44
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Gao M, Nguyen H, Salas González I, Teplitski M. Regulation of fixLJ by Hfq Controls Symbiotically Important Genes in Sinorhizobium meliloti. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:844-853. [PMID: 27712144 DOI: 10.1094/mpmi-09-16-0182-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The RNA-binding chaperone Hfq plays critical roles in the establishment and functionality of the symbiosis between Sinorhizobium meliloti and its legume hosts. A mutation in hfq reduces symbiotic efficiency resulting in a Fix- phenotype, characterized by the inability of the bacterium to fix nitrogen. At least in part, this is due to the ability of Hfq to regulate the fixLJ operon, which encodes a sensor kinase-response regulator pair that controls expression of the nitrogenase genes. The ability of Hfq to bind fixLJ in vitro and in planta was demonstrated with gel shift and coimmunoprecipitation experiments. Two (ARN)2 motifs in the fixLJ message were the likely sites through which Hfq exerted its posttranscriptional control. Consistent with the regulatory effects of Hfq, downstream genes controlled by FixLJ (such as nifK, noeB) were also subject to Hfq regulation in planta.
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Affiliation(s)
- Mengsheng Gao
- Soil and Water Sciences Department, Genetics Institute, University of Florida-Institute of Food and Agricultural Sciences, Gainesville 32611, U.S.A
| | - Hahn Nguyen
- Soil and Water Sciences Department, Genetics Institute, University of Florida-Institute of Food and Agricultural Sciences, Gainesville 32611, U.S.A
| | - Isai Salas González
- Soil and Water Sciences Department, Genetics Institute, University of Florida-Institute of Food and Agricultural Sciences, Gainesville 32611, U.S.A
| | - Max Teplitski
- Soil and Water Sciences Department, Genetics Institute, University of Florida-Institute of Food and Agricultural Sciences, Gainesville 32611, U.S.A
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45
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C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA. Proc Natl Acad Sci U S A 2016; 113:E6089-E6096. [PMID: 27681631 DOI: 10.1073/pnas.1613053113] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The bacterial Sm protein and RNA chaperone Hfq stabilizes small noncoding RNAs (sRNAs) and facilitates their annealing to mRNA targets involved in stress tolerance and virulence. Although an arginine patch on the Sm core is needed for Hfq's RNA chaperone activity, the function of Hfq's intrinsically disordered C-terminal domain (CTD) has remained unclear. Here, we use stopped flow spectroscopy to show that the CTD of Escherichia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA. The Hfq CTD also mediates competition between sRNAs, offering a kinetic advantage to sRNAs that contact both the proximal and distal faces of the Hfq hexamer. The change in sRNA hierarchy caused by deletion of the Hfq CTD in E. coli alters the sRNA accumulation and the kinetics of sRNA regulation in vivo. We propose that the Hfq CTD displaces sRNAs and annealed sRNA⋅mRNA complexes from the Sm core, enabling Hfq to chaperone sRNA-mRNA interactions and rapidly cycle between competing targets in the cell.
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46
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Nikulin A, Mikhailina A, Lekontseva N, Balobanov V, Nikonova E, Tishchenko S. Characterization of RNA-binding properties of the archaeal Hfq-like protein from Methanococcus jannaschii. J Biomol Struct Dyn 2016; 35:1615-1628. [PMID: 27187760 DOI: 10.1080/07391102.2016.1189849] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The Sm and Sm-like proteins are widely distributed among bacteria, archaea and eukarya. They participate in many processes related to RNA-processing and regulation of gene expression. While the function of the bacterial Lsm protein Hfq and eukaryotic Sm/Lsm proteins is rather well studied, the role of Lsm proteins in Archaea is investigated poorly. In this work, the RNA-binding ability of an archaeal Hfq-like protein from Methanococcus jannaschii has been studied by X-ray crystallography, anisotropy fluorescence and surface plasmon resonance. It has been found that MjaHfq preserves the proximal RNA-binding site that usually recognizes uridine-rich sequences. Distal adenine-binding and lateral RNA-binding sites show considerable structural changes as compared to bacterial Hfq. MjaHfq did not bind mononucleotides at these sites and would not recognize single-stranded RNA as its bacterial homologues. Nevertheless, MjaHfq possesses affinity to poly(A) RNA that seems to bind at the unstructured positive-charged N-terminal tail of the protein.
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Affiliation(s)
- Alexey Nikulin
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Alisa Mikhailina
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Natalia Lekontseva
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Vitalii Balobanov
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Ekaterina Nikonova
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
| | - Svetlana Tishchenko
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino , Moscow region , 142290 , Russia
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47
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Wroblewska Z, Olejniczak M. Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure. RNA (NEW YORK, N.Y.) 2016; 22:979-94. [PMID: 27154968 PMCID: PMC4911921 DOI: 10.1261/rna.055251.115] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 04/01/2016] [Indexed: 05/23/2023]
Abstract
The bacterial protein Hfq participates in the regulation of translation by small noncoding RNAs (sRNAs). Several mechanisms have been proposed to explain the role of Hfq in the regulation by sRNAs binding to the 5'-untranslated mRNA regions. However, it remains unknown how Hfq affects those sRNAs that target the coding sequence. Here, the contribution of Hfq to the annealing of three sRNAs, RybB, SdsR, and MicC, to the coding sequence of Salmonella ompD mRNA was investigated. Hfq bound to ompD mRNA with tight, subnanomolar affinity. Moreover, Hfq strongly accelerated the rates of annealing of RybB and MicC sRNAs to this mRNA, and it also had a small effect on the annealing of SdsR. The experiments using truncated RNAs revealed that the contributions of Hfq to the annealing of each sRNA were individually adjusted depending on the structures of interacting RNAs. In agreement with that, the mRNA structure probing revealed different structural contexts of each sRNA binding site. Additionally, the annealing of RybB and MicC sRNAs induced specific conformational changes in ompD mRNA consistent with local unfolding of mRNA secondary structure. Finally, the mutation analysis showed that the long AU-rich sequence in the 5'-untranslated mRNA region served as an Hfq binding site essential for the annealing of sRNAs to the coding sequence. Overall, the data showed that the functional specificity of Hfq in the annealing of each sRNA to the ompD mRNA coding sequence was determined by the sequence and structure of the interacting RNAs.
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Affiliation(s)
- Zuzanna Wroblewska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Mikolaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
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Abstract
Over the last decade, small (often noncoding) RNA molecules have been discovered as important regulators influencing myriad aspects of bacterial physiology and virulence. In particular, small RNAs (sRNAs) have been implicated in control of both primary and secondary metabolic pathways in many bacterial species. This chapter describes characteristics of the major classes of sRNA regulators, and highlights what is known regarding their mechanisms of action. Specific examples of sRNAs that regulate metabolism in gram-negative bacteria are discussed, with a focus on those that regulate gene expression by base pairing with mRNA targets to control their translation and stability.
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49
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Penas C, Mascareñas JL, Vázquez ME. Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA. Chem Sci 2016; 2016:2674-2678. [PMID: 27293537 PMCID: PMC4898589 DOI: 10.1039/c5sc04501k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.
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50
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Updegrove TB, Zhang A, Storz G. Hfq: the flexible RNA matchmaker. Curr Opin Microbiol 2016; 30:133-138. [PMID: 26907610 PMCID: PMC4821791 DOI: 10.1016/j.mib.2016.02.003] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
The RNA chaperone protein Hfq is critical to the function of small, base pairing RNAs in many bacteria. In the past few years, structures and modeling of wild type Hfq and assays of various mutants have documented that the homohexameric Hfq ring can contact RNA at four sites (proximal face, distal face, rim and C-terminal tail) and that different RNAs bind to these sites in various configurations. These studies together with novel in vitro and in vivo experimental approaches are beginning to give mechanistic insights into how Hfq acts to promote small RNA-mRNA pairing and indicate that flexibility is integral to the Hfq role in RNA matchmaking.
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Affiliation(s)
- Taylor B Updegrove
- Division of Molecular and Cellular Biology, NICHD, National Institutes of Health, 18 Library Dr MSC 5430, Bethesda, MD 20892-5430, USA
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, NICHD, National Institutes of Health, 18 Library Dr MSC 5430, Bethesda, MD 20892-5430, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, NICHD, National Institutes of Health, 18 Library Dr MSC 5430, Bethesda, MD 20892-5430, USA.
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