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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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Stibelman AY, Sariles AY, Takahashi MK. Beyond membrane permeability: A role for the small RNA MicF in regulation of chromosome replication and partitioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590647. [PMID: 38712278 PMCID: PMC11071386 DOI: 10.1101/2024.04.22.590647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Small regulatory RNAs (sRNA) have been shown to play a large role in the management of stress responses in Escherichia coli and other bacteria. sRNAs act post-transcriptionally on target mRNA through an imperfect base pairing mechanism to regulate downstream protein expression. The imperfect base pairing allows a single sRNA to bind and regulate a variety mRNA targets which can form intricate regulatory networks that connect different physiological processes for the cell's response. Upon exposure to antimicrobials and superoxide generating agents, the MicF sRNA in E. coli has been shown to regulate a small set of genes involved in the management of membrane permeability. Currently, it is unknown whether MicF acts on other processes to mediate the response to these agents. Using an sRNA interaction prediction tool, we identified genes in E. coli that are potentially regulated by MicF. Through subsequent analysis using a sfGFP-based reporter-gene fusion, we have validated two novel targets of MicF regulation: SeqA, a negative modulator of DNA replication, and ObgE, a GTPase crucial for chromosome partitioning. Importantly, the interaction between MicF and these target mRNAs is contingent upon the presence of the RNA chaperone protein, Hfq. Furthermore, our findings affirm the role of MicF's conserved 5' seed pairing region in initiating these regulatory interactions. Our study suggests that, beyond its established role in membrane permeability management, MicF exerts control over chromosome dynamics in response to distinct environmental cues, implicating a more multifaceted regulatory function in bacterial stress adaptation.
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Wang WS, Lin-Chao S. Hfq-Antisense RNA I Binding Regulates RNase E-Dependent RNA Stability and ColE1 Plasmid Copy Number. Int J Mol Sci 2024; 25:3955. [PMID: 38612765 PMCID: PMC11012335 DOI: 10.3390/ijms25073955] [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: 02/26/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
The mechanisms and consequences of gene regulation by Hfq on trans-encoded small RNAs (sRNAs) have been well studied and documented. Recent employment of Genomic SELEX to search for Hfq-binding motifs has indicated that Hfq might frequently regulate gene expression controlled by cis-antisense RNAs. Here, we use the classic ColE1 plasmid antisense RNA-based regulation model (i.e., RNA I) to study the role of Hfq in controlling antisense regulatory functions. We show that Hfq exhibits a high binding affinity for RNA I and that binding limits RNase E cleavage, thereby stabilizing RNA I and reducing the plasmid copy number. Full-length RNA I displays a binding affinity for Hfq in the sub-micromolar range. In vivo overexpression of Hfq prolongs RNA I stability and reduces the ColE1 plasmid copy number, whereas deletion of hfq reduces RNA I stability and increases the plasmid copy number. RNA I predominantly binds to the proximal face of Hfq and exhibits competitive ability against a chromosome-borne proximal face-bound sRNA (DsrA) for Hfq binding. Through its strong promoter and high gene dosage features, plasmid-encoded antisense RNA I results in high RNA I expression, so it may antagonize the effects of trans-encoded RNAs in controlling target gene expression.
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Affiliation(s)
- Wei-Syuan Wang
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Sue Lin-Chao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11490, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
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Hu W, Huo X, Bai H, Chen Z, Zhang J, Yang H, Feng S. Insights into the complementation potential of the extreme acidophile's orthologue in replacing Escherichia coli hfq gene-particularly in bacterial resistance to environmental stress. World J Microbiol Biotechnol 2024; 40:105. [PMID: 38386219 DOI: 10.1007/s11274-024-03924-0] [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: 12/17/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
Acidithiobacillus caldus is a typical extreme acidophile widely used in the biohydrometallurgical industry, which often experiences extreme environmental stress in its natural habitat. Hfq, an RNA-binding protein, typically functions as a global regulator involved in various cellular physiological processes. Yet, the biological functions of Hfq derived from such extreme acidophile have not been extensively investigated. In this study, the recombinant strain Δhfq/Achfq, constructed by CRISPR/Cas9-mediated chromosome integration, fully or partially restored the phenotypic defects caused by hfq deletion in Escherichia coli, including impaired growth performance, abnormal cell morphology, impaired swarming motility, decreased stress resistance, decreased intracellular ATP and free amino acid levels, and attenuated biofilm formation. Particularly noteworthy, the intracellular ATP level and biofilm production of the recombinant strain were increased by 12.2% and 7.0%, respectively, compared to the Δhfq mutant. Transcriptomic analysis revealed that even under heterologous expression, AcHfq exerted global regulatory effects on multiple cellular processes, including metabolism, environmental signal processing, and motility. Finally, we established a potential working model to illustrate the regulatory mechanism of AcHfq in bacterial resistance to environmental stress.
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Affiliation(s)
- Wenbo Hu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingyu Huo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Haochen Bai
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Zongling Chen
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Jianxin Zhang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, People's Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
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Turbant F, Machiels Q, Waeytens J, Wien F, Arluison V. The Amyloid Assembly of the Bacterial Hfq Is Lipid-Driven and Lipid-Specific. Int J Mol Sci 2024; 25:1434. [PMID: 38338713 PMCID: PMC10855545 DOI: 10.3390/ijms25031434] [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: 12/27/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Under specific conditions, some proteins can self-assemble into fibrillar structures called amyloids. Initially, these proteins were associated with neurodegenerative diseases in eucaryotes. Nevertheless, they have now been identified in the three domains of life. In bacteria, they are involved in diverse biological processes and are usually useful for the cell. For this reason, they are classified as "functional amyloids". In this work, we focus our analysis on a bacterial functional amyloid called Hfq. Hfq is a pleiotropic regulator that mediates several aspects of genetic expression, mainly via the use of small noncoding RNAs. Our previous work showed that Hfq amyloid-fibrils interact with membranes. This interaction influences Hfq amyloid structure formation and stability, but the specifics of the lipid on the dynamics of this process is unknown. Here, we show, using spectroscopic methods, how lipids specifically drive and modulate Hfq amyloid assembly or, conversely, its disassembly. The reported effects are discussed in light of the consequences for bacterial cell life.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Quentin Machiels
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium; (Q.M.); (J.W.)
- Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, CEA Saclay, 91191 Gif-sur-Yvette, France;
- SDV Department, Université Paris Cité, 75006 Paris, France
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Zamba-Campero M, Soliman D, Yu H, Lasseter AG, Chang YY, Liu J, Aravind L, Jewett MW, Storz G, Adams PP. Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574855. [PMID: 38260563 PMCID: PMC10802407 DOI: 10.1101/2024.01.09.574855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Flagella propel pathogens through their environments yet are expensive to synthesize and are immunogenic. Thus, complex hierarchical regulatory networks control flagellar gene expression. Spirochetes are highly motile bacteria, but peculiarly in the Lyme spirochete Borrelia burgdorferi, the archetypal flagellar regulator σ28 is absent. We rediscovered gene bb0268 in B. burgdorferi as flgV, a broadly-conserved gene in the flagellar superoperon alongside σ28 in many Spirochaetes, Firmicutes and other phyla, with distant homologs in Epsilonproteobacteria. We found that B. burgdorferi FlgV is localized within flagellar motors. B. burgdorferi lacking flgV construct fewer and shorter flagellar filaments and are defective in cell division and motility. During the enzootic cycle, B. burgdorferi lacking flgV survive and replicate in Ixodes ticks but are attenuated for dissemination and infection in mice. Our work defines infection timepoints when spirochete motility is most crucial and implicates FlgV as a broadly distributed structural flagellar component that modulates flagellar assembly.
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Affiliation(s)
- Maxime Zamba-Campero
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Soliman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaxin Yu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Amanda G. Lasseter
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Yuen-Yan Chang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Teteneva N, Sanches-Medeiros A, Sourjik V. Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water. THE ISME JOURNAL 2024; 18:wrae096. [PMID: 38874171 PMCID: PMC11188689 DOI: 10.1093/ismejo/wrae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
Although enteric bacteria normally reside within the animal intestine, the ability to persist extraintestinally is an essential part of their overall lifestyle, and it might contribute to transmission between hosts. Despite this potential importance, few genetic determinants of extraintestinal growth and survival have been identified, even for the best-studied model, Escherichia coli. In this work, we thus used a genome-wide library of barcoded transposon insertions to systematically identify functional clusters of genes that are crucial for E. coli fitness in lake water. Our results revealed that inactivation of pathways involved in maintaining outer membrane integrity, nucleotide biosynthesis, and chemotaxis negatively affected E. coli growth or survival in this extraintestinal environment. In contrast, inactivation of another group of genes apparently benefited E. coli growth or persistence in filtered lake water, resulting in higher abundance of these mutants. This group included rpoS, which encodes the general stress response sigma factor, as well as genes encoding several other global transcriptional regulators and RNA chaperones, along with several poorly annotated genes. Based on this co-enrichment, we identified these gene products as novel positive regulators of RpoS activity. We further observed that, despite their enhanced growth, E. coli mutants with inactive RpoS had reduced viability in lake water, and they were not enriched in the presence of the autochthonous microbiota. This highlights the duality of the general stress response pathway for E. coli growth outside the host.
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Affiliation(s)
- Nataliya Teteneva
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| | - Ananda Sanches-Medeiros
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
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Turbant F, Esnouf E, Rosaz F, Wien F, Węgrzyn G, Chauvet H, Arluison V. Role of the Bacterial Amyloid-like Hfq in Fluoroquinolone Fluxes. Microorganisms 2023; 12:53. [PMID: 38257880 PMCID: PMC10819720 DOI: 10.3390/microorganisms12010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Due to their two-cell membranes, Gram-negative bacteria are particularly resistant to antibiotics. Recent investigations aimed at exploring new target proteins involved in Gram-negative bacteria adaptation helped to identify environmental changes encountered during infection. One of the most promising approaches in finding novel targets for antibacterial drugs consists of blocking noncoding RNA-based regulation using the protein cofactor, Hfq. Although Hfq is important in many bacterial pathogens, its involvement in antibiotics response is still unclear. Indeed, Hfq may mediate drug resistance by regulating the major efflux system in Escherichia coli, but it could also play a role in the influx of antibiotics. Here, using an imaging approach, we addressed this problem quantitatively at the single-cell level. More precisely, we analyzed how Hfq affects the dynamic influx and efflux of ciprofloxacin, an antibiotic from the group of fluoroquinolones that is used to treat bacterial infections. Our results indicated that the absence of either whole Hfq or its C-terminal domain resulted in a more effective accumulation of ciprofloxacin, irrespective of the presence of the functional AcrAB-TolC efflux pump. However, overproduction of the MicF small regulatory RNA, which reduces the efficiency of expression of the ompF gene (coding for a porin involved in antibiotics influx) in a Hfq-dependent manner, resulted in impaired accumulation of ciprofloxacin. These results led us to propose potential mechanisms of action of Hfq in the regulation of fluoroquinolone fluxes across the E. coli envelope.
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Affiliation(s)
- Florian Turbant
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Emeline Esnouf
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Francois Rosaz
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland;
| | - Hugo Chauvet
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.); (H.C.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, UMR12 CEA CNRS, CEA Saclay, 91191 Gif-sur-Yvette, France; (E.E.); (F.R.)
- UFR SDV, Université Paris Cité, 75013 Paris, France
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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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Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [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: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
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Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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Štih V, Amenitsch H, Plavec J, Podbevšek P. Spatial arrangement of functional domains in OxyS stress response sRNA. RNA (NEW YORK, N.Y.) 2023; 29:1520-1534. [PMID: 37380360 PMCID: PMC10578473 DOI: 10.1261/rna.079618.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/18/2023] [Indexed: 06/30/2023]
Abstract
Small noncoding RNAs are an important class of regulatory RNAs in bacteria, often regulating responses to changes in environmental conditions. OxyS is a 110 nt, stable, trans-encoded small RNA found in Escherichia coli and is induced by an increased concentration of hydrogen peroxide. OxyS has an important regulatory role in cell stress response, affecting the expression of multiple genes. In this work, we investigated the structure of OxyS and the interaction with fhlA mRNA using nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and unbiased molecular dynamics simulations. We determined the secondary structures of isolated stem-loops and confirmed their structural integrity in OxyS. Unexpectedly, stem-loop SL4 was identified in the region that was predicted to be unstructured. Three-dimensional models of OxyS demonstrate that OxyS adopts an extended structure with four solvent-exposed stem-loops, which are available for interaction with other RNAs and proteins. Furthermore, we provide evidence of base-pairing between OxyS and fhlA mRNA.
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Affiliation(s)
- Vesna Štih
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
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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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13
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King KA, Caudill MT, Caswell CC. A comprehensive review of small regulatory RNAs in Brucella spp. Front Vet Sci 2022; 9:1026220. [PMID: 36532353 PMCID: PMC9751625 DOI: 10.3389/fvets.2022.1026220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/15/2022] [Indexed: 09/29/2023] Open
Abstract
Brucella spp. are Gram-negative bacteria that naturally infect a variety of domesticated and wild animals, often resulting in abortions and sterility. Humans exposed to these animals or animal products can also develop debilitating, flu-like disease. The brucellae are intracellular pathogens that reside predominantly within immune cells, typically macrophages, where they replicate in a specialized compartment. This capacity of Brucella to survive and replicate within macrophages is essential to their ability to cause disease. In recent years, several groups have identified and characterized small regulatory RNAs (sRNAs) as critical factors in the control of Brucella physiology within macrophages and overall disease virulence. sRNAs are generally < 300 nucleotides in length, and these independent sRNA transcripts are encoded either next to (i.e., cis-encoded) or at a distant location to (i.e., trans-encoded) the genes that they regulate. Trans-encoded sRNAs interact with the mRNA transcripts through short stretches of imperfect base pairing that often require the RNA chaperone Hfq to facilitate sRNA-mRNA interaction. In many instances, these sRNA-mRNA interactions inhibit gene expression, usually by occluding the ribosome-binding site (RBS) and/or by decreasing the stability of the mRNA, leading to degradation of the transcript. A number of sRNAs have been predicted and authenticated in Brucella strains, and a variety of approaches, techniques, and means of validation have been employed in these efforts. Nonetheless, some important issues and considerations regarding the study of sRNA regulation in Brucella need to be addressed. For example, the lack of uniform sRNA nomenclature in Brucella has led to difficulty in comparisons of sRNAs across the different Brucella species, and there exist multiple names in the literature for what are functionally the same sRNA. Moreover, even though bona fide sRNAs have been discovered in Brucella, scant functional information is known about the regulatory activities of these sRNAs, or the extent to which these sRNAs are required for the intracellular life and/or host colonization by the brucellae. Therefore, this review summarizes the historical context of Hfq and sRNAs in Brucella; our current understanding of Brucella sRNAs; and some future perspectives and considerations for the field of sRNA biology in the brucellae.
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Affiliation(s)
| | | | - Clayton C. Caswell
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, VA-MD College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
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14
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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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Turbant F, Waeytens J, Campidelli C, Bombled M, Martinez D, Grélard A, Habenstein B, Raussens V, Velez M, Wien F, Arluison V. Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq. Int J Mol Sci 2022; 23:ijms23158739. [PMID: 35955871 PMCID: PMC9369112 DOI: 10.3390/ijms23158739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.
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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
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Camille Campidelli
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Marianne Bombled
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie, 2, Cantoblanco, E-28049 Madrid, Spain
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR SDV, Université Paris Cité, 75006 Paris, France
- Correspondence: (F.W.); (V.A.)
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16
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Role of Hfq in glucose utilization, biofilm formation and quorum sensing system in Bacillus subtilis. Biotechnol Lett 2022; 44:845-855. [PMID: 35614284 DOI: 10.1007/s10529-022-03262-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/09/2022] [Indexed: 11/02/2022]
Abstract
Hfq is an RNA-binding protein, its main function is to participate in post-transcriptional regulation of bacteria and regulate small regulatory RNA (sRNA) and messenger RNA (mRNA) stability, but the Hfq function of Bacillus subtilis (B. subtilis) has not been fully explained. In this study, we used the strains of B. subtilis168 (BS168), BS168Δhfq and BS168Δhfq-C to explore the effects of Hfq on the glucose utilization, biofilm formation and quorum sensing (QS) system of B. subtilis. The results showed that the knockout of hfq resulted in growth defects when bacteria were cultured in the Luria-Bertani (LB) medium, but we did not observe the same effects in Nitrogen medium (NM) and Inorganic Salt-free medium (ISM). We further found that the growth of strains under different glucose concentrations was also different, which was related to the expression of CcpA. Interestingly, the hfq mutant showed increased resistance to a high-glucose environment. Furthermore, the biofilm and extracellular poly saccharides (EPS) formation of BS168Δhfq decreased significantly. At the same time, changes were observed in the morphology of the biofilm, such as larger intercellular space of the biofilm and thinner edge. The qRT-PCR results confirmed that the hfq knockout caused significant up-regulation or down-regulation of gene expression in QS system, and down-regulated genes were involved in the positive regulation of biofilm formation. Taken together, we demonstrated that Hfq plays a vital role in glucose utilization, biofilm formation and QS of B. subtilis, which provides a new perspective for subsequent related research.
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17
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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18
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Li M, Cong Y, Qi Y, Zhang JZH. Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq. Biomolecules 2021; 11:1653. [PMID: 34827651 PMCID: PMC8615722 DOI: 10.3390/biom11111653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/16/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.
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Affiliation(s)
- Mengxin Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
| | - Yifei Qi
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University at Shanghai, Shanghai 200062, China; (M.L.); (Y.C.); (Y.Q.)
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, NY 10003, USA
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19
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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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20
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Sarpong DD, Murphy ER. RNA Regulated Toxin-Antitoxin Systems in Pathogenic Bacteria. Front Cell Infect Microbiol 2021; 11:661026. [PMID: 34084755 PMCID: PMC8167048 DOI: 10.3389/fcimb.2021.661026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/29/2021] [Indexed: 01/05/2023] Open
Abstract
The dynamic host environment presents a significant hurdle that pathogenic bacteria must overcome to survive and cause diseases. Consequently, these organisms have evolved molecular mechanisms to facilitate adaptation to environmental changes within the infected host. Small RNAs (sRNAs) have been implicated as critical regulators of numerous pathways and systems in pathogenic bacteria, including that of bacterial Toxin-Antitoxin (TA) systems. TA systems are typically composed of two factors, a stable toxin, and a labile antitoxin which functions to protect against the potentially deleterious activity of the associated toxin. Of the six classes of bacterial TA systems characterized to date, the toxin component is always a protein. Type I and Type III TA systems are unique in that the antitoxin in these systems is an RNA molecule, whereas the antitoxin in all other TA systems is a protein. Though hotly debated, the involvement of TA systems in bacterial physiology is recognized by several studies, with the Type II TA system being the most extensively studied to date. This review focuses on RNA-regulated TA systems, highlighting the role of Type I and Type III TA systems in several pathogenic bacteria.
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Affiliation(s)
- David D. Sarpong
- Department of Biological Sciences, Ohio University, Athens, OH, United States
- Infectious and Tropical Diseases Institute, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Erin R. Murphy
- Infectious and Tropical Diseases Institute, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Biomedical Sciences, Ohio University, Heritage College of Osteopathic Medicine, Athens, OH, United States
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21
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Basu P, Elgrably-Weiss M, Hassouna F, Kumar M, Wiener R, Altuvia S. RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment. Nat Commun 2021; 12:2249. [PMID: 33883550 PMCID: PMC8060364 DOI: 10.1038/s41467-021-22553-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 03/20/2021] [Indexed: 02/02/2023] Open
Abstract
The RNA chaperone Hfq, acting as a hexamer, is a known mediator of post-transcriptional regulation, expediting basepairing between small RNAs (sRNAs) and their target mRNAs. However, the intricate details associated with Hfq-RNA biogenesis are still unclear. Previously, we reported that the stringent response regulator, RelA, is a functional partner of Hfq that facilitates Hfq-mediated sRNA-mRNA regulation in vivo and induces Hfq hexamerization in vitro. Here we show that RelA-mediated Hfq hexamerization requires an initial binding of RNA, preferably sRNA to Hfq monomers. By interacting with a Shine-Dalgarno-like sequence (GGAG) in the sRNA, RelA stabilizes the initially unstable complex of RNA bound-Hfq monomer, enabling the attachment of more Hfq subunits to form a functional hexamer. Overall, our study showing that RNA binding to Hfq monomers is at the heart of RelA-mediated Hfq hexamerization, challenges the previous concept that only Hfq hexamers can bind RNA.
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Affiliation(s)
- Pallabi Basu
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Maya Elgrably-Weiss
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Fouad Hassouna
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Manoj Kumar
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Reuven Wiener
- grid.9619.70000 0004 1937 0538Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
| | - Shoshy Altuvia
- grid.9619.70000 0004 1937 0538Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem, Israel
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22
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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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23
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Yegorov Y, Sendersky E, Zilberman S, Nagar E, Waldman Ben-Asher H, Shimoni E, Simkovsky R, Golden SS, LiWang A, Schwarz R. A Cyanobacterial Component Required for Pilus Biogenesis Affects the Exoproteome. mBio 2021; 12:e03674-20. [PMID: 33727363 PMCID: PMC8092324 DOI: 10.1128/mbio.03674-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/02/2021] [Indexed: 12/23/2022] Open
Abstract
Protein secretion as well as the assembly of bacterial motility appendages are central processes that substantially contribute to fitness and survival. This study highlights distinctive features of the mechanism that serves these functions in cyanobacteria, which are globally prevalent photosynthetic prokaryotes that significantly contribute to primary production. Our studies of biofilm development in the cyanobacterium Synechococcus elongatus uncovered a novel component required for the biofilm self-suppression mechanism that operates in this organism. This protein, which is annotated as "hypothetical," is denoted EbsA (essential for biofilm self-suppression A) here. EbsA homologs are highly conserved and widespread in diverse cyanobacteria but are not found outside this clade. We revealed a tripartite complex of EbsA, Hfq, and the ATPase homolog PilB (formerly called T2SE) and demonstrated that each of these components is required for the assembly of the hairlike type IV pili (T4P) appendages, for DNA competence, and affects the exoproteome in addition to its role in biofilm self-suppression. These data are consistent with bioinformatics analyses that reveal only a single set of genes in S. elongatus to serve pilus assembly or protein secretion; we suggest that a single complex is involved in both processes. A phenotype resulting from the impairment of the EbsA homolog in the cyanobacterium Synechocystis sp. strain PCC 6803 implies that this feature is a general cyanobacterial trait. Moreover, comparative exoproteome analyses of wild-type and mutant strains of S. elongatus suggest that EbsA and Hfq affect the exoproteome via a process that is independent of PilB, in addition to their involvement in a T4P/secretion machinery.IMPORTANCE Cyanobacteria, environmentally prevalent photosynthetic prokaryotes, contribute ∼25% of global primary production. Cyanobacterial biofilms elicit biofouling, thus leading to substantial economic losses; however, these microbial assemblages can also be beneficial, e.g., in wastewater purification processes and for biofuel production. Mechanistic aspects of cyanobacterial biofilm development were long overlooked, and genetic and molecular information emerged only in recent years. The importance of this study is 2-fold. First, it identifies novel components of cyanobacterial biofilm regulation, thus contributing to the knowledge of these processes and paving the way for inhibiting detrimental biofilms or promoting beneficial ones. Second, the data suggest that cyanobacteria may employ the same complex for the assembly of the motility appendages, type 4 pili, and protein secretion. A shared pathway was previously shown in only a few cases of heterotrophic bacteria, whereas numerous studies demonstrated distinct systems for these functions. Thus, our study broadens the understanding of pilus assembly/secretion in diverse bacteria and furthers the aim of controlling the formation of cyanobacterial biofilms.
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Affiliation(s)
- Yevgeni Yegorov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Shaul Zilberman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S Golden
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Andy LiWang
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, California, USA
- Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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24
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Turbant F, Partouche D, El Hamoui O, Trépout S, Legoubey T, Wien F, Arluison V. Apomorphine Targets the Pleiotropic Bacterial Regulator Hfq. Antibiotics (Basel) 2021; 10:antibiotics10030257. [PMID: 33806663 PMCID: PMC8000489 DOI: 10.3390/antibiotics10030257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 12/15/2022] Open
Abstract
Hfq is a bacterial regulator with key roles in gene expression. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, thanks to its binding to small regulatory noncoding RNAs. This property is of primary importance for bacterial adaptation and survival in hosts. Small RNAs and Hfq are, for instance, involved in the response to antibiotics. Previous work has shown that the E. coli Hfq C-terminal region (Hfq-CTR) self-assembles into an amyloid structure. It was also demonstrated that the green tea compound EpiGallo Catechin Gallate (EGCG) binds to Hfq-CTR amyloid fibrils and remodels them into nonamyloid structures. Thus, compounds that target the amyloid region of Hfq may be used as antibacterial agents. Here, we show that another compound that inhibits amyloid formation, apomorphine, may also serve as a new antibacterial. Our results provide an alternative in order to repurpose apomorphine, commonly used in the treatment of Parkinson’s disease, as an antibiotic to block bacterial adaptation to treat infections.
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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; (F.T.); (D.P.); (T.L.)
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Omar El Hamoui
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France;
| | - Sylvain Trépout
- Institut Curie, Inserm US43, and CNRS UMS2016, 91405 Orsay CEDEX, France;
| | - Théa Legoubey
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France; (F.T.); (D.P.); (T.L.)
| | - 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; (F.T.); (D.P.); (T.L.)
- UFR Sciences du Vivant, Université de Paris, 75006 Paris CEDEX, France
- Correspondence: (F.W.); or (V.A.); Tel.: +33-(0)169359665 (F.W.); +33-(0)169083282 (V.A.)
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25
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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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26
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Vo PNL, Lee HM, Ren J, Na D. Optimized expression of Hfq protein increases Escherichia coli growth. J Biol Eng 2021; 15:7. [PMID: 33602295 PMCID: PMC7890833 DOI: 10.1186/s13036-021-00260-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli is a widely used platform for metabolic engineering due to its fast growth and well-established engineering techniques. However, there has been a demand for faster-growing E. coli for higher production of desired substances. Here, to increase the growth of E. coli cells, we optimized the expression level of Hfq protein, which plays an essential role in stress responses. Six variants of the hfq gene with a different ribosome binding site sequence and thereby a different expression level were constructed. When the Hfq expression level was optimized in DH5α, its growth rate was increased by 12.1% and its cell density was also increased by 4.5%. RNA-seq and network analyses revealed the upregulation of stress response genes and metabolic genes, which increases the tolerance against pH changes. When the same strategy was applied to five other E. coli strains (BL21 (DE3), JM109, TOP10, W3110, and MG1655), all their growth rates were increased by 18-94% but not all their densities were increased (- 12 - + 32%). In conclusion, the Hfq expression optimization can increase cell growth rate and probably their cell densities as well. Since the hfq gene is highly conserved across bacterial species, the same strategy could be applied to other bacterial species to construct faster-growing strains.
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Affiliation(s)
- Phuong N L Vo
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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27
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Peng J, Schachterle JK, Sundin GW. Orchestration of virulence factor expression and modulation of biofilm dispersal in Erwinia amylovora through activation of the Hfq-dependent small RNA RprA. MOLECULAR PLANT PATHOLOGY 2021; 22:255-270. [PMID: 33314618 PMCID: PMC7814967 DOI: 10.1111/mpp.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Erwinia amylovora is the causative agent of the devastating disease fire blight of pome fruit trees. After infection of host plant leaves at apple shoot tips, E. amylovora cells form biofilms in xylem vessels, restrict water flow, and cause wilting symptoms. Although E. amylovora is well known to be able to cause systemic infection, how biofilm cells of E. amylovora transit from the sessile mode of growth in xylem to the planktonic mode of growth in cortical parenchyma remains unknown. Increasing evidence has suggested the important modulatory roles of Hfq-dependent small RNAs (sRNAs) in the pathogenesis of E. amylovora. Here, we demonstrate that the sRNA RprA acts as a positive regulator of amylovoran exopolysaccharide production, the type III secretion system (T3SS), and flagellar-dependent motility, and as a negative regulator of levansucrase activity and cellulose production. We also show that RprA affects the promoter activity of multiple virulence factor genes and regulates hrpS, a critical T3SS regulator, at the posttranscriptional level. We determined that rprA expression can be activated by the Rcs phosphorelay, and that expression is active during T3SS-mediated host infection in an immature pear fruit infection model. We further showed that overexpression of rprA activated the in vitro dispersal of E. amylovora cells from biofilms. Thus, our investigation of the varied role of RprA in affecting E. amylovora virulence provides important insights into the functions of this sRNA in biofilm control and systemic infection.
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Affiliation(s)
- Jingyu Peng
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Jeffrey K. Schachterle
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
- Present address:
US National Arboretum – Floral and Nursery Plants Research UnitUSDA‐ARSBeltsvilleMarylandUSA
| | - George W. Sundin
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
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28
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Turbant F, Hamoui OE, Partouche D, Sandt C, Busi F, Wien F, Arluison V. Identification and characterization of the Hfq bacterial amyloid region DNA interactions. BBA ADVANCES 2021; 1:100029. [PMID: 37082015 PMCID: PMC10074921 DOI: 10.1016/j.bbadva.2021.100029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Nucleic acid amyloid proteins interactions have been observed in the past few years. These interactions often promote protein aggregation. Nevertheless, molecular basis and physiological consequences of these interactions are still poorly understood. Additionally, it is unknown whether the nucleic acid promotes the formation of self-assembly due to direct interactions or indirectly via sequences surrounding the amyloid region. Here we focus our attention on a bacterial amyloid, Hfq. This protein is a pleiotropic bacterial regulator that mediates many aspects of nucleic acids metabolism. The protein notably mediates mRNA stability and translation efficiency by using stress-related small non coding regulatory RNA. In addition, Hfq, thanks to its amyloid C-terminal region, binds and compacts DNA. A combination of experimental methodologies, including synchrotron radiation circular dichroism (SRCD), gel shift assay and infrared (FTIR) spectroscopy have been used to probe the interaction of Hfq C-terminal region with DNA. We clearly identify important amino acids in this region involved in DNA binding and polymerization properties. This allows to understand better how this bacterial amyloid interacts with DNA. Possible functional consequence to answer to stresses 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
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Omar El Hamoui
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florent Busi
- Université de Paris, UFR Sciences du vivant, 75006 Paris cedex, France
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
- Corresponding author.
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Université de Paris, UFR Sciences du vivant, 75006 Paris cedex, France
- Corresponding author.
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29
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Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets. Int J Mol Sci 2020; 21:ijms21249634. [PMID: 33348812 PMCID: PMC7766527 DOI: 10.3390/ijms21249634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.
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30
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Samuels DS, Lybecker MC, Yang XF, Ouyang Z, Bourret TJ, Boyle WK, Stevenson B, Drecktrah D, Caimano MJ. Gene Regulation and Transcriptomics. Curr Issues Mol Biol 2020; 42:223-266. [PMID: 33300497 DOI: 10.21775/cimb.042.223] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.
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Affiliation(s)
- D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO 80918, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40536, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
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31
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Choi O, Kang B, Lee Y, Lee Y, Kim J. Pantoea ananatis carotenoid production confers toxoflavin tolerance and is regulated by Hfq-controlled quorum sensing. Microbiologyopen 2020; 10:e1143. [PMID: 33269542 PMCID: PMC7883899 DOI: 10.1002/mbo3.1143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Carotenoids are widely used in functional foods, cosmetics, and health supplements, and their importance and scope of use are continuously expanding. Here, we characterized carotenoid biosynthetic genes of the plant‐pathogenic bacterium Pantoea ananatis, which carries a carotenoid biosynthetic gene cluster (including crtE, X, Y, I, B, and Z) on a plasmid. Reverse transcription–polymerase chain reaction (RT‐PCR) analysis revealed that the crtEXYIB gene cluster is transcribed as a single transcript and crtZ is independently transcribed in the opposite direction. Using splicing by overlap extension with polymerase chain reaction (SOE by PCR) based on asymmetric amplification, we reassembled crtE–B, crtE–B–I, and crtE–B–I–Y. High‐performance liquid chromatography confirmed that Escherichia coli expressing the reassembled crtE–B, crtE–B–I, and crtE–B–I–Y operons produced phytoene, lycopene, and β‐carotene, respectively. We found that the carotenoids conferred tolerance to UV radiation and toxoflavin. Pantoea ananatis shares rice environments with the toxoflavin producer Burkholderia glumae and is considered to be the first reported example of producing and using carotenoids to withstand toxoflavin. We confirmed that carotenoid production by P. ananatis depends on RpoS, which is positively regulated by Hfq/ArcZ and negatively regulated by ClpP, similar to an important regulatory network of E. coli (HfqArcZ →RpoS Ͱ ClpXP). We also demonstrated that Hfq‐controlled quorum signaling de‐represses EanR to activate RpoS, thereby initiating carotenoid production. Survival genes such as those responsible for the production of carotenoids of the plant‐pathogenic P. ananatis must be expressed promptly to overcome stressful environments and compete with other microorganisms. This mechanism is likely maintained by a brake with excellent performance, such as EanR.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yongsang Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
| | - Jinwoo Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea.,Division of Applied Life Science, Gyeongsang National University, Jinju, Korea.,Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
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32
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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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33
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Effect of rpoE on the Non-coding RNA Expression Profiles of Salmonella enterica serovar Typhi under the Stress of Ampicillin. Curr Microbiol 2020; 77:2405-2412. [DOI: 10.1007/s00284-020-02055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/25/2020] [Indexed: 12/13/2022]
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34
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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35
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Cresser-Brown J, Rizkallah P, Jin Y, Roth C, Miller DJ, Allemann RK. An unexpected co-crystal structure of the calpain PEF(S) domain with Hfq reveals a potential chaperone function of Hfq. Acta Crystallogr F Struct Biol Commun 2020; 76:81-85. [PMID: 32039889 PMCID: PMC7010360 DOI: 10.1107/s2053230x20001181] [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: 12/16/2019] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
Calpain is a Ca2+-activated, heterodimeric cysteine protease consisting of a large catalytic subunit and a small regulatory subunit. Dysregulation of this enzyme is involved in a range of pathological conditions such as cancer, Alzheimer's disease and rheumatoid arthritis, and thus calpain I is a drug target with potential therapeutic applications. Difficulty in the production of this enzyme has hindered structural and functional investigations in the past, although heterodimeric calpain I can be generated by Escherichia coli expression in low yield. Here, an unexpected structure discovered during crystallization trials of heterodimeric calpain I (CAPN1C115S + CAPNS1ΔGR) is reported. A novel co-crystal structure of the PEF(S) domain from the dissociated regulatory small subunit of calpain I and the RNA-binding chaperone Hfq, which was likely to be overproduced as a stress response to the recombinant expression conditions, was obtained, providing unexpected insight in the chaperone function of Hfq.
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Affiliation(s)
- Joel Cresser-Brown
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Pierre Rizkallah
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Christian Roth
- Carbohydrates: Structure and Function, Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Arnimallee 22, 14195 Berlin, Germany
| | - David J. Miller
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
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36
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Xi D, Li Y, Yan J, Li Y, Wang X, Cao B. Small RNA coaR contributes to intestinal colonization in Vibrio cholerae via the two-component system EnvZ/OmpR. Environ Microbiol 2020; 22:4231-4243. [PMID: 31868254 DOI: 10.1111/1462-2920.14906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/20/2019] [Indexed: 11/30/2022]
Abstract
Vibrio cholerae is a waterborne bacterium responsible for worldwide outbreaks of acute and fatal cholera. Recently, small regulatory RNAs (sRNAs) have become increasingly recognized as important regulators of virulence gene expression in response to environmental signals. In this study, we determined that two-component system EnvZ/OmpR was required for intestinal colonization in V. cholerae O1 EI Tor strain E12382. Analysis of the characteristics of OmpR revealed a potential binding site in the intergenic region between vc1470 and vc1471, and qRT-PCR showed that expression of the intergenic region increased 5.3-fold in the small intestine compared to LB medium. Race and northern blot assays were performed and demonstrated a new sRNA, coaR (cholerae osmolarity and acidity related regulatory RNA). A ΔcoaR mutant showed a deficient colonization ability in small intestine with CI of 0.15. We identified a target of coaR, tcpI, a negative regulator of the major pilin subunit of TcpA. The ΔtcpI mutant has an increased colonization with CI of 3.16. The expression of coaR increased 2.8-fold and 3.3-fold under relative acidic and hypertonic condition. In summary, coaR was induced under the condition of high osmolarity and acid stress via EnvZ/OmpR and explained that tcpI relieves pH-mediated repression of toxin co-regulated pilus synthesis.
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Affiliation(s)
- Daoyi Xi
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yujia Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Junxiang Yan
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Yuehua Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Xiaochen Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
| | - Boyang Cao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, 300457, China.,Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Nankai University, Tianjin, 300457, China.,Tianjin Research Center for Functional Genomics and Biochips, TEDA College, Nankai University, Tianjin, 300457, China.,Tianjin Key Laboratory of Microbial Functional Genomics, TEDA College, Nankai University, Tianjin, 300457, China
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37
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Wien F, Martinez D, Le Brun E, Jones NC, Vrønning Hoffmann S, Waeytens J, Berbon M, Habenstein B, Arluison V. The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment. Microorganisms 2019; 7:microorganisms7120639. [PMID: 31816864 PMCID: PMC6956100 DOI: 10.3390/microorganisms7120639] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, B1050 Bruxelles, Belgique;
- Laboratoire de Chimie Physique d’Orsay, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay 91400 Orsay, France
| | - Melanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
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38
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Mai J, Rao C, Watt J, Sun X, Lin C, Zhang L, Liu J. Mycobacterium tuberculosis 6C sRNA binds multiple mRNA targets via C-rich loops independent of RNA chaperones. Nucleic Acids Res 2019; 47:4292-4307. [PMID: 30820540 PMCID: PMC6486639 DOI: 10.1093/nar/gkz149] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
Bacterial small regulatory RNAs (sRNAs) are the most abundant class of post-transcriptional regulators and have been well studied in Gram-negative bacteria. Little is known about the functions and mechanisms of sRNAs in high GC Gram-positive bacteria including Mycobacterium and Streptomyces. Here, we performed an in-depth study of 6C sRNA of Mycobacterium tuberculosis, which is conserved among high GC Gram-positive bacteria. Forty-seven genes were identified as possible direct targets of 6C sRNA and 15 of them were validated using an in vivo translational lacZ fusion system. We found that 6C sRNA plays a pleotropic role and regulates genes involved in various cellular processes, including DNA replication and protein secretion. Mapping the interactions of 6C sRNA with mRNA targets panD and dnaB revealed that the C-rich loops of 6C sRNA act as direct binding sites to mRNA targets. Unlike in Gram-negative bacteria where RNA binding proteins Hfq and ProQ are required, the interactions of 6C sRNA with mRNAs appear to be independent of RNA chaperones. Our findings suggest that the multiple G–C pairings between single stranded regions are sufficient to establish stable interactions between 6C sRNA and mRNA targets, providing a mechanism for sRNAs in high GC Gram-positive bacteria.
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Affiliation(s)
- Juntao Mai
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chitong Rao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jacqueline Watt
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Xian Sun
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Chen Lin
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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39
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Carrier MC, Lalaouna D, Massé E. Broadening the Definition of Bacterial Small RNAs: Characteristics and Mechanisms of Action. Annu Rev Microbiol 2019; 72:141-161. [PMID: 30200848 DOI: 10.1146/annurev-micro-090817-062607] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The first report of trans-acting RNA-based regulation in bacterial cells dates back to 1984. Subsequent studies in diverse bacteria unraveled shared properties of trans-acting small regulatory RNAs, forming a clear definition of these molecules. These shared characteristics have been used extensively to identify new small RNAs (sRNAs) and their interactomes. Recently however, emerging technologies able to resolve RNA-RNA interactions have identified new types of regulatory RNAs. In this review, we present a broader definition of trans-acting sRNA regulators and discuss their newly discovered intrinsic characteristics.
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Affiliation(s)
- Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
| | - David Lalaouna
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada; , ,
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40
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Andreassen PR, Pettersen JS, Szczerba M, Valentin-Hansen P, Møller-Jensen J, Jørgensen MG. sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA. Nucleic Acids Res 2019; 46:6746-6760. [PMID: 29905843 PMCID: PMC6061853 DOI: 10.1093/nar/gky479] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022] Open
Abstract
Production of curli, extracellular protein structures important for Escherichia coli biofilm formation, is governed by a highly complex regulatory mechanism that integrates multiple environmental signals through the involvement of numerous proteins and small non-coding RNAs (sRNAs). No less than seven sRNAs (McaS, RprA, GcvB, RydC, RybB, OmrA and OmrB) are known to repress the expression of the curli activator CsgD. Many of the sRNAs repress CsgD production by binding to the csgD mRNA at sites far upstream of the ribosomal binding site. The precise mechanism behind sRNA-mediated regulation of CsgD synthesis is largely unknown. In this study, we identify a conserved A/U-rich region in the csgD mRNA 5′ untranslated region, which is cleaved upon binding of the small RNAs, McaS, RprA or GcvB, to sites located more than 30 nucleotides downstream. Mutational analysis shows that the A/U-rich region as well as an adjacent stem–loop structure are required for McaS-stimulated degradation, also serving as a binding platform for the RNA chaperone Hfq. Prevention of McaS-activated cleavage completely relieves repression, suggesting that endoribonucleolytic cleavage of csgD mRNA is the primary regulatory effect exerted by McaS. Moreover, we find that McaS-mediated degradation of the csgD 5′ untranslated region requires RNase E.
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Affiliation(s)
- Patrick Rosendahl Andreassen
- 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
| | - Mateusz Szczerba
- Ira A. Fulton Schools of Engineering and School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Biodesign Center for Immunotherapy, Vaccines, and Virotherapy (B-CIVV), Biodesign Institute, Arizona State University. 727 East Tyler Street, Tempe, AZ 85287-5001, USA
| | - Poul Valentin-Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark. Campusvej 55, 5230 Odense M. Denmark
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41
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Li J, Zhang B, Zhou L, Qi L, Yue L, Zhang W, Cheng H, Whitman WB, Dong X. The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis. PLoS Genet 2019; 15:e1008328. [PMID: 31404065 PMCID: PMC6705878 DOI: 10.1371/journal.pgen.1008328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/22/2019] [Accepted: 07/22/2019] [Indexed: 11/27/2022] Open
Abstract
TRAM is a conserved domain among RNA modification proteins that are widely distributed in various organisms. In Archaea, TRAM occurs frequently as a standalone protein with in vitro RNA chaperone activity; however, its biological significance and functional mechanism remain unknown. This work demonstrated that TRAM0076 is an abundant standalone TRAM protein in the genetically tractable methanoarcheaon Methanococcus maripaludis. Deletion of MMP0076, the gene encoding TRAM0076, markedly reduced the growth and altered transcription of 55% of the genome. Substitution mutations of Phe39, Phe42, Phe63, Phe65 and Arg35 in the recombinant TRAM0076 decreased the in vitro duplex RNA unfolding activity. These mutations also prevented complementation of the growth defect of the MMP0076 deletion mutant, indicating that the duplex RNA unfolding activity was essential for its physiological function. A genome-wide mapping of transcription start sites identified many 5' untranslated regions (5'UTRs) of 20-60 nt which could be potential targets of a RNA chaperone. TRAM0076 unfolded three representative 5'UTR structures in vitro and facilitated the in vivo expression of a mCherry reporter system fused to the 5'UTRs, thus behaving like a transcription anti-terminator. Flag-tagged-TRAM0076 co-immunoprecipitated a large number of cellular RNAs, suggesting that TRAM0076 plays multiple roles in addition to unfolding incorrect RNA structures. This work demonstrates that the conserved archaeal RNA chaperone TRAM globally affects gene expression and may represent a transcriptional element in ancient life of the RNA world.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Bo Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Liguang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Wenting Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Huicai Cheng
- Biology Institute, Hebei Academy of Sciences, Shijiazhuang, China
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
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42
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Dienstbier A, Amman F, Štipl D, Petráčková D, Večerek B. Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis. Int J Mol Sci 2019; 20:ijms20123073. [PMID: 31238496 PMCID: PMC6627887 DOI: 10.3390/ijms20123073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/19/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2 = 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that Δhfq strain displays strongly impaired secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other hand, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.
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Affiliation(s)
- Ana Dienstbier
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.
| | - Fabian Amman
- University of Vienna, Institute for Theoretical Chemistry, Währinger Straße 17, A-1090 Vienna, Austria.
- Medical University of Vienna, Division of Cell and Developmental Biology, Schwarzspanierstraße 17, A-1090 Vienna, Austria.
| | - Daniel Štipl
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.
| | - Denisa Petráčková
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.
| | - Branislav Večerek
- Institute of Microbiology v.v.i., Laboratory of post-transcriptional control of gene expression, 14220 Prague, Czech Republic.
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43
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Kim W, Choi JS, Kim D, Shin D, Suk S, Lee Y. Mechanisms for Hfq-Independent Activation of rpoS by DsrA, a Small RNA, in Escherichia coli. Mol Cells 2019; 42:426-439. [PMID: 31085808 PMCID: PMC6537650 DOI: 10.14348/molcells.2019.0040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Many small RNAs (sRNAs) regulate gene expression by base pairing to their target messenger RNAs (mRNAs) with the help of Hfq in Escherichia coli. The sRNA DsrA activates translation of the rpoS mRNA in an Hfq-dependent manner, but this activation ability was found to partially bypass Hfq when DsrA is overproduced. The precise mechanism by which DsrA bypasses Hfq is unknown. In this study, we constructed strains lacking all three rpoS-activating sRNAs (i.e., ArcZ, DsrA, and RprA) in hfq+ and Hfq- backgrounds, and then artificially regulated the cellular DsrA concentration in these strains by controlling its ectopic expression. We then examined how the expression level of rpoS was altered by a change in the concentration of DsrA. We found that the translation and stability of the rpoS mRNA are both enhanced by physiological concentrations of DsrA regardless of Hfq, but that depletion of Hfq causes a rapid degradation of DsrA and thereby decreases rpoS mRNA stability. These results suggest that the observed Hfq dependency of DsrA-mediated rpoS activation mainly results from the destabilization of DsrA in the absence of Hfq, and that DsrA itself contributes to the translational activation and stability of the rpoS mRNA in an Hfq-independent manner.
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Affiliation(s)
- Wonkyong Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Jee Soo Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Daun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Doohang Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Shinae Suk
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Younghoon Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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44
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Liu X, Yan Y, Wu H, Zhou C, Wang X. Biological and transcriptomic studies reveal hfq is required for swimming, biofilm formation and stress response in Xanthomonas axonpodis pv. citri. BMC Microbiol 2019; 19:103. [PMID: 31113370 PMCID: PMC6530196 DOI: 10.1186/s12866-019-1476-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hfq is a widely conserved bacterial RNA-binding protein which generally mediates the global regulatory activities involv ed in physiological process and virulence. The goal of this study was to characterize the biological function of hfq gene in Xanthomonas axonpodis pv. citri (Xac), the causal agent of citrus canker disease. RESULTS An hfq mutant in Xac was generated by plasmid integration. The loss of hfq resulted in attenuation of bacterial growth, motility and biofilm formation. In addition, the hfq mutation impaired Xac resistance to H2O2 and both high and low pH environments, but did not affect the virulence to citrus. RNA-Seq analyses indicated that Hfq played roles in regulating the expression of 746 genes. In hfq mutant, gene expression related to chemotaxis, secretion system, two-component system, quorum sensing and flagellar assembly were repressed, whereas expression of ribosomal genes were significantly up-regulated. The down-regulated expression of three bacterial chemotaxis related genes and seven flagella genes, which involved in cell growth and biofilm formation, were further validated by RT-qPCR. CONCLUSIONS The study demonstrated that hfq was involved in multiple biological processes in Xac. The results could serve as initiate points for identifying regulatory sRNAs and genes controlled by Hfq-sRNA interactions in Xac.
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Affiliation(s)
- Xuelu Liu
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Yuping Yan
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China.,, Present address: Agriculture commission of Guangan district, Guangan, Sichuan, China
| | - Haodi Wu
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Changyong Zhou
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China
| | - Xuefeng Wang
- National Engineering Research Center for Citrus, Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing, 400712, People's Republic of China.
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In Situ Characterization of Hfq Bacterial Amyloid: A Fourier-Transform Infrared Spectroscopy Study. Pathogens 2019; 8:pathogens8010036. [PMID: 30889801 PMCID: PMC6471401 DOI: 10.3390/pathogens8010036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Hfq is a bacterial protein that regulates gene expression at the post-transcriptional level in Gram-negative bacteria. We have previously shown that Escherichia coli Hfq protein, and more precisely its C-terminal region (CTR), self-assembles into an amyloid-like structure in vitro. In the present work, we present evidence that Hfq unambiguously forms amyloid structures also in vivo. Taking into account the role of this protein in bacterial adaptation and virulence, our work opens possibilities to target Hfq amyloid self-assembly and cell location, with important potential to block bacterial adaptation and treat infections.
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46
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Anupama R, Lulu S, Madhusmita R, Vino S, Mukherjee A, Babu S. Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO 2 nanoparticle: An in silico analysis. J Theor Biol 2019; 462:12-25. [PMID: 30391649 DOI: 10.1016/j.jtbi.2018.10.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO2 nanoparticle binding. The major protein of P. aeruginosa targeted by TiO2 was found to be KatA, a major catalase required for H2O2 resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS. To understand the protein-protein physical interaction characteristic of these key proteins involved in biofilm related processes, homology modeling, docking and molecular dynamic simulation were performed. For all these proteins, physical and chemical properties, amino acid composition, nest and cleft analysis were performed using online tools. The interactions between TiO2NPs-KatA and four protein-protein complexes such as KatA-DnaK, KatA-Hfq, KatA-RpoA and KatA-RpoS were studied. Our results indicate that all four key proteins and TiO2NPs can have stable complexation with KatA. The study has given enough clues to understand the interaction of TiO2NPs with P. aeruginosa biofilm in natural environment. Further investigations could lead to development of TiO2NPs based therapeutic and sanitary interventions to combat this pathogenic bacterium.
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Affiliation(s)
- Rani Anupama
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sajitha Lulu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Rout Madhusmita
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Sundararajan Vino
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Amitava Mukherjee
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
| | - Subramanian Babu
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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47
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Du HH, Zhou HZ, Tang P, Huang HQ, Liu M, Hu YH. Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity. Vet Res 2018; 49:120. [PMID: 30537995 PMCID: PMC6288947 DOI: 10.1186/s13567-018-0613-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/15/2018] [Indexed: 11/10/2022] Open
Abstract
Recently, bacterial small RNA (sRNA) has been shown to be involved as a key regulator in stress responses. sRNAs of Edwardsiella piscicida, an important aquatic pathogen, are not well characterized to date. In this study, using RNA-seq technology, we globally found and identified sRNA candidates expressed from E. piscicida grown in normal LB medium, acid pressure, iron deficiency stress, and oxidation pressure. A total of 148 sRNAs were found, including 19 previously annotated sRNAs and 129 novel sRNA candidates by searching against the Rfam database. Compared in normal condition, the expression of 103 sRNAs (DEsRNA, differentially expressed sRNA) and 1615 mRNAs (DEmRNAs, differentially expressed mRNA) showed significant differences in three stress sample. Based on the prediction by IntaRNA and relational analysis between DEsRNAs and DEmRNAs, 103 DEsRNAs were predicted to regulate 769 target mRNAs. Pleiotropic function of target DEmRNAs indicated that sRNAs extensively participated in a variety of physiological processes, including response to adversity and pathogenicity, the latter was further confirmed by infection experiment. A large number transcription factors appeared in target genes of sRNAs, which suggested that sRNAs likely deeply interlaced within complex gene regulatory networks of E. piscicida. Moreover, 49 Hfq-associated sRNAs were also identified in this study. In summary, we globally discovered sRNAs for the first time in pathogenic bacteria of fish, and our findings indicated that sRNAs in E. piscicida have important roles in adaptation to environmental stress and pathogenicity. These results also provide clues for deciphering regulation mechanism of gene expression related to physiological response and pathogenicity.
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Affiliation(s)
- He-He Du
- Institute of Tropical Bioscience and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China
| | - Hai-Zhen Zhou
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Tang
- Yunnan Agricultural University, Kunming, Yunnan, 650200, China
| | - Hui-Qin Huang
- Institute of Tropical Bioscience and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China
| | - Min Liu
- Institute of Tropical Bioscience and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China.
| | - Yong-Hua Hu
- Institute of Tropical Bioscience and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China.
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48
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Epigallocatechin Gallate Remodelling of Hfq Amyloid-Like Region Affects Escherichia coli Survival. Pathogens 2018; 7:pathogens7040095. [PMID: 30513780 PMCID: PMC6313410 DOI: 10.3390/pathogens7040095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022] Open
Abstract
Hfq is a pleiotropic regulator that has key roles in the control of genetic expression. The protein noticeably regulates translation efficiency and RNA decay in Gram-negative bacteria, due to the Hfq-mediated interaction between small regulatory noncoding RNA and mRNA. This property is of primary importance for bacterial adaptation and virulence. We have previously shown that the Hfq E. coli protein, and more precisely its C-terminal region (CTR), self-assembles into an amyloid-like structure. In the present work, we demonstrate that epigallocatechin gallate (EGCG), a major green tea polyphenol compound, targets the Hfq amyloid region and can be used as a potential antibacterial agent. We analysed the effect of this compound on Hfq amyloid fibril stability and show that EGCG both disrupts Hfq-CTR fibrils and inhibits their formation. We show that, even if EGCG affects other bacterial amyloids, it also specifically targets Hfq-CTR in vivo. Our results provide an alternative approach for the utilisation of EGCG that may be used synergistically with conventional antibiotics to block bacterial adaptation and treat infections.
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49
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Small Noncoding Regulatory RNAs from Pseudomonas aeruginosa and Burkholderia cepacia Complex. Int J Mol Sci 2018; 19:ijms19123759. [PMID: 30486355 PMCID: PMC6321483 DOI: 10.3390/ijms19123759] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is the most life-limiting autosomal recessive disorder in Caucasians. CF is characterized by abnormal viscous secretions that impair the function of several tissues, with chronic bacterial airway infections representing the major cause of early decease of these patients. Pseudomonas aeruginosa and bacteria from the Burkholderia cepacia complex (Bcc) are the leading pathogens of CF patients’ airways. A wide array of virulence factors is responsible for the success of infections caused by these bacteria, which have tightly regulated responses to the host environment. Small noncoding RNAs (sRNAs) are major regulatory molecules in these bacteria. Several approaches have been developed to study P. aeruginosa sRNAs, many of which were characterized as being involved in the virulence. On the other hand, the knowledge on Bcc sRNAs remains far behind. The purpose of this review is to update the knowledge on characterized sRNAs involved in P. aeruginosa virulence, as well as to compile data so far achieved on sRNAs from the Bcc and their possible roles on bacteria virulence.
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50
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Malabirade A, Partouche D, El Hamoui O, Turbant F, Geinguenaud F, Recouvreux P, Bizien T, Busi F, Wien F, Arluison V. Revised role for Hfq bacterial regulator on DNA topology. Sci Rep 2018; 8:16792. [PMID: 30429520 PMCID: PMC6235962 DOI: 10.1038/s41598-018-35060-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNA. Besides these RNA-related functions, Hfq has also been described as one of the nucleoid associated proteins shaping the bacterial chromosome. Therefore, Hfq appears as a versatile nucleic acid-binding protein, which functions are probably even more numerous than those initially suggested. For instance, E. coli Hfq, and more precisely its C-terminal region (CTR), has been shown to induce DNA compaction into a condensed form. In this paper, we establish that DNA induces Hfq-CTR amyloidogenesis, resulting in a change of DNA local conformation. Furthermore, we clarify the effect of Hfq on DNA topology. Our results evidence that, even if the protein has a strong propensity to compact DNA thanks to its amyloid region, it does not affect overall DNA topology. We confirm however that hfq gene disruption influences plasmid supercoiling in vivo, indicating that the effect on DNA topology in former reports was indirect. Most likely, this effect is related to small regulatory sRNA-Hfq-based regulation of another protein that influences DNA supercoiling, possibly a nucleoid associated protein such as H-NS or Dps. Finally, we hypothesise that this indirect effect on DNA topology explains, at least partially, the previously reported effect of Hfq on plasmid replication efficiency.
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Affiliation(s)
- Antoine Malabirade
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | - David Partouche
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Omar El Hamoui
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France
| | | | | | - Thomas Bizien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Florent Busi
- Unité de Biologie Fonctionnelle et Adaptative, CNRS UMR8251, Université Paris Diderot, 75013, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint Aubin BP48, 91192, Gif-sur-Yvette, France
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191, Gif-sur-Yvette, France. .,Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.
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