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Faozia S, Hossain T, Cho KH. The Dlt and LiaFSR systems derepress SpeB production independently in the Δpde2 mutant of Streptococcus pyogenes. Front Cell Infect Microbiol 2023; 13:1293095. [PMID: 38029265 PMCID: PMC10679467 DOI: 10.3389/fcimb.2023.1293095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The second messenger molecule, c-di-AMP, plays a critical role in pathogenesis and virulence in S. pyogenes. We previously reported that deleting the c-di-AMP phosphodiesterase gene pde2 severely suppresses SpeB production at the transcriptional level. We performed transposon mutagenesis to gain insight into the mechanism of how Pde2 is involved in SpeB regulation. We identified one of the genes of the dlt operon, dltX, as a suppressor of the SpeB-null phenotype of the Δpde2 mutant. The dlt operon consists of five genes, dltX, dltA, dltB, dltC, and dltD in many Gram-positive bacteria, and its function is to incorporate D-alanine into lipoteichoic acids. DltX, a small membrane protein, is a newly identified member of the operon. The in-frame deletion of dltX or insertional inactivation of dltA in the Δpde2 mutant restored SpeB production, indicating that D-alanylation is crucial for the suppressor phenotype. These mutations did not affect the growth in lab media but showed increased negative cell surface charge and enhanced sensitivity to polymyxin B. Considering that dlt mutations change cell surface charge and sensitivity to cationic antimicrobial peptides, we examined the LiaFSR system that senses and responds to cell envelope stress. The ΔliaR mutation in the Δpde2 mutant also derepressed SpeB production, like the ΔdltX mutation. LiaFSR controls speB expression by regulating the expression of the transcriptional regulator SpxA2. However, the Dlt system did not regulate spxA2 expression. The SpeB phenotype of the Δpde2ΔdltX mutant in higher salt media differed from that of the Δpde2ΔliaR mutant, suggesting a unique pathway for the Dlt system in SpeB production, possibly related to ion transport or turgor pressure regulation.
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Affiliation(s)
| | | | - Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN, United States
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2
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Dubnau E, DeSantis M, Dubnau D. Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF). mBio 2023; 14:e0126923. [PMID: 37555678 PMCID: PMC10470536 DOI: 10.1128/mbio.01269-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023] Open
Abstract
In Bacillus subtilis, the RicT (YaaT), RicA (YmcA), and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny) to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis, which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation. IMPORTANCE The action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In Bacillus subtilis, it has been shown that key transcripts for energy-producing steps of glycolysis, for nitrogen assimilation, and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis [Rny (RNase Y), RicA (YmcA), RicF (YlbF), and RicT (YaaT)] are broadly conserved among the firmicutes, including several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.
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Affiliation(s)
- Eugenie Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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3
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Dubnau E, DeSantis M, Dubnau D. Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541740. [PMID: 37292586 PMCID: PMC10245838 DOI: 10.1101/2023.05.22.541740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In Bacillus subtilis , the RicT (YaaT), RicA (YmcA) and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny), to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny, and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis , which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation. IMPORTANCE The action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In B. subtilis it has been shown that key transcripts for energy producing steps of glycolysis, for nitrogen assimilation and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis (Rny (RNase Y), RicA (YmcA), RicF (YlbF) and RicT (YaaT)) are broadly conserved among the firmicutes, including in several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.
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Affiliation(s)
- Eugenie Dubnau
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
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Structural Insights into the Dimeric Form of Bacillus subtilis RNase Y Using NMR and AlphaFold. Biomolecules 2022; 12:biom12121798. [PMID: 36551226 PMCID: PMC9775385 DOI: 10.3390/biom12121798] [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: 09/23/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
RNase Y is a crucial component of genetic translation, acting as the key enzyme initiating mRNA decay in many Gram-positive bacteria. The N-terminal domain of Bacillus subtilis RNase Y (Nter-BsRNaseY) is thought to interact with various protein partners within a degradosome complex. Bioinformatics and biophysical analysis have previously shown that Nter-BsRNaseY, which is in equilibrium between a monomeric and a dimeric form, displays an elongated fold with a high content of α-helices. Using multidimensional heteronuclear NMR and AlphaFold models, here, we show that the Nter-BsRNaseY dimer is constituted of a long N-terminal parallel coiled-coil structure, linked by a turn to a C-terminal region composed of helices that display either a straight or bent conformation. The structural organization of the N-terminal domain is maintained within the AlphaFold model of the full-length RNase Y, with the turn allowing flexibility between the N- and C-terminal domains. The catalytic domain is globular, with two helices linking the KH and HD modules, followed by the C-terminal region. This latter region, with no function assigned up to now, is most likely involved in the dimerization of B. subtilis RNase Y together with the N-terminal coiled-coil structure.
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Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
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Sun S, He Z, Jiang P, Baral R, Pandelia ME. Metal Dependence and Functional Diversity of Type I Cas3 Nucleases. Biochemistry 2022; 61:327-338. [PMID: 35184547 DOI: 10.1021/acs.biochem.1c00779] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Type I CRISPR-Cas systems provide prokaryotes with protection from parasitic genetic elements by cleaving foreign DNA. In addition, they impact bacterial physiology by regulating pathogenicity and virulence, making them key players in adaptability and evolution. The signature nuclease Cas3 is a phosphodiesterase belonging to the HD-domain metalloprotein superfamily. By directing specific metal incorporation, we map a promiscuous metal ion cofactor profile for Cas3 from Thermobifida fusca (Tf). Tf Cas3 affords significant ssDNA cleavage with four homo-dimetal centers (Fe2+, Co2+, Mn2+, and Ni2+), while the diferrous form is the most active and likely biologically relevant in vivo. Electron paramagnetic resonance (EPR) spectroscopy and Mössbauer spectroscopy show that the diiron cofactor can access three redox forms, while the diferrous form can be readily obtained with mild reductants. We further employ EPR and Mössbauer on Fe-enriched proteins to establish that Cas3″ enzymes harbor a dinuclear cofactor, which was not previously confirmed. We demonstrate that the ancillary His ligand is critical for efficient ssDNA cleavage but not for diiron assembly or small molecule hydrolysis. We further explore the ability of Cas3 to hydrolyze cyclic mononucleotides and show that Tf Cas3 hydrolyzes 2'3'-cAMP with catalytic efficiency comparable to that of the conserved virulence factor A (CvfA), an HD-domain protein hydrolyzing 2'3'-cylic phosphodiester bonds at RNA 3'-termini. Because this CvfA activity is linked to virulence regulation, Cas3 may also utilize 2'3'-cAMP hydrolysis as a possible molecular route to control virulence.
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Affiliation(s)
- Sining Sun
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Zunyu He
- Yale University, New Haven, Connecticut 06520-8055, United States
| | - Paul Jiang
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Rishika Baral
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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7
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Abstract
RNases perform indispensable functions in regulating gene expression in many bacterial pathogens by processing and/or degrading RNAs. Despite the pivotal role of RNases in regulating bacterial virulence factors, the functions of RNases have not yet been studied in the major human respiratory pathogen Streptococcus pneumoniae (pneumococcus). Here, we sought to determine the impact of two conserved RNases, the endoribonuclease RNase Y and exoribonuclease polynucleotide phosphorylase (PNPase), on the physiology and virulence of S. pneumoniae serotype 2 strain D39. We report that RNase Y and PNPase are essential for pneumococcal pathogenesis, as both deletion mutants showed strong attenuation of virulence in murine models of invasive pneumonia. Genome-wide transcriptomic analysis revealed that the abundances of nearly 200 mRNA transcripts were significantly increased, whereas those of several pneumococcal small regulatory RNAs (sRNAs), including the Ccn (CiaR-controlled noncoding RNA) sRNAs, were altered in the Δrny mutant relative to the wild-type strain. Additionally, lack of RNase Y resulted in pleiotropic phenotypes that included defects in pneumococcal cell morphology and growth in vitro. In contrast, Δpnp mutants showed no growth defect in vitro but differentially expressed a total of 40 transcripts, including the tryptophan biosynthesis operon genes and numerous 5' cis-acting regulatory RNAs, a majority of which were previously shown to impact pneumococcal disease progression in mice using the serotype 4 strain TIGR4. Together, our data suggest that RNase Y exerts a global impact on pneumococcal physiology, while PNPase mediates virulence phenotypes, likely through sRNA regulation. IMPORTANCE Streptococcus pneumoniae is a notorious human pathogen that adapts to conditions in distinct host tissues and responds to host cell interactions by adjusting gene expression. RNases are key players that modulate gene expression by mediating the turnover of regulatory and protein-coding transcripts. Here, we characterized two highly conserved RNases, RNase Y and PNPase, and evaluated their impact on the S. pneumoniae transcriptome for the first time. We show that PNPase influences the levels of a narrow set of mRNAs but a large number of regulatory RNAs primarily implicated in virulence control, whereas RNase Y has a more sweeping effect on gene expression, altering levels of transcripts involved in diverse cellular processes, including cell division, metabolism, stress response, and virulence. This study further reveals that RNase Y regulates expression of genes governing competence by mediating the turnover of CiaR-controlled noncoding (Ccn) sRNAs.
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c-di-AMP-Regulated K + Importer KtrAB Affects Biofilm Formation, Stress Response, and SpeB Expression in Streptococcus pyogenes. Infect Immun 2021; 89:IAI.00317-20. [PMID: 33468578 DOI: 10.1128/iai.00317-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/14/2021] [Indexed: 11/20/2022] Open
Abstract
The second messenger cyclic di-AMP (c-di-AMP) controls biofilm formation, stress response, and virulence in Streptococcus pyogenes The deletion of the c-di-AMP synthase gene, dacA, results in pleiotropic effects including reduced expression of the secreted protease SpeB. Here, we report a role for K+ transport in c-di-AMP-mediated SpeB expression. The deletion of ktrB in the ΔdacA mutant restores SpeB expression. KtrB is a subunit of the K+ transport system KtrAB that forms a putative high-affinity K+ importer. KtrB forms a membrane K+ channel, and KtrA acts as a cytosolic gating protein that controls the transport capacity of the system by binding ligands including c-di-AMP. SpeB induction in the ΔdacA mutant by K+ specific ionophore treatment also supports the importance of cellular K+ balance in SpeB production. The ΔdacA ΔktrB double deletion mutant not only produces wild-type levels of SpeB but also partially or fully reverts the defective ΔdacA phenotypes of biofilm formation and stress responses, suggesting that many ΔdacA phenotypes are due to cellular K+ imbalance. However, the null pathogenicity of the ΔdacA mutant in a murine subcutaneous infection model is not restored by ktrB deletion, suggesting that c-di-AMP controls not only cellular K+ balance but also other metabolic and/or virulence pathways. The deletion of other putative K+ importer genes, kup and kimA, does not phenocopy the deletion of ktrB regarding SpeB induction in the ΔdacA mutant, suggesting that KtrAB is the primary K+ importer that is responsible for controlling cellular K+ levels under laboratory growth conditions.
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Muthunayake NS, Tomares DT, Childers WS, Schrader JM. Phase-separated bacterial ribonucleoprotein bodies organize mRNA decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1599. [PMID: 32445438 PMCID: PMC7554086 DOI: 10.1002/wrna.1599] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 01/12/2023]
Abstract
In bacteria, mRNA decay is controlled by megadalton scale macromolecular assemblies called, "RNA degradosomes," composed of nucleases and other RNA decay associated proteins. Recent advances in bacterial cell biology have shown that RNA degradosomes can assemble into phase-separated structures, termed bacterial ribonucleoprotein bodies (BR-bodies), with many analogous properties to eukaryotic processing bodies and stress granules. This review will highlight the functional role that BR-bodies play in the mRNA decay process through its organization into a membraneless organelle in the bacterial cytoplasm. This review will also highlight the phylogenetic distribution of BR-bodies across bacterial species, which suggests that these phase-separated structures are broadly distributed across bacteria, and in evolutionarily related mitochondria and chloroplasts. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
| | - Dylan T Tomares
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
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Adil M, Baig MH, Rupasinghe HV. Impact of Citral and Phloretin, Alone and in Combination, on Major Virulence Traits of Streptococcus pyogenes. Molecules 2019; 24:molecules24234237. [PMID: 31766432 PMCID: PMC6930587 DOI: 10.3390/molecules24234237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 11/17/2022] Open
Abstract
Streptococcus pyogenes is well documented as a multi-virulent and exclusively human pathogen. The LuxS-based signaling in these bacteria has a crucial role in causing several infections through pathways that are pathogenic. This study evaluated the individual and synergistic effects of citral and phloretin against S. pyogenes in relation to major virulence traits. The in vitro synergy of citral and phloretin was evaluated by the checkerboard method. The fractional inhibitory concentration (FIC) values were calculated to determine the interactions between the inhibitors. The bacteria’s virulence properties were tested in the presence of the molecules, individually as well as in combination. Molecules’ cytotoxicity was tested using human tonsil epithelial cells. The synergistic effects of the molecules on the expression of biofilm and quorum sensing genes were tested using quantitative real-time polymerase chain reaction (qRT-PCR). The molecules were also tested for their impact on LuxS protein by molecular docking, modeling, and free-energy calculations. When the two molecules were assessed in combination (synergistic effect, FIC Index of 0.5), a stronger growth inhibitory activity was exhibited than the individual molecules. The cell surface hydrophobicity, as well as genes involved in quorum sensing and biofilm formation, showed greater suppression when the molecules were tested in combination. The in silico findings also suggest the inhibitory potential of the two molecules against LuxS protein. The binding orientation and the binding affinity of citral and phloretin well support the notion that there is a synergistic effect of citral and phloretin. The data reveal the combination of citral and phloretin as a potent antibacterial agent to combat the virulence of S. pyogenes.
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Affiliation(s)
- Mohd Adil
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada;
| | - Mohd Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-ro, Gangnam-gu, Seoul 06273, Korea;
| | - H.P. Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4H7, Canada
- Correspondence:
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11
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Bacterial RNA Degradosomes: Molecular Machines under Tight Control. Trends Biochem Sci 2019; 45:42-57. [PMID: 31679841 DOI: 10.1016/j.tibs.2019.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 01/05/2023]
Abstract
Bacterial RNA degradosomes are multienzyme molecular machines that act as hubs for post-transcriptional regulation of gene expression. The ribonuclease activities of these complexes require tight regulation, as they are usually essential for cell survival while potentially destructive. Recent studies have unveiled a wide variety of regulatory mechanisms including autoregulation, post-translational modifications, and protein compartmentalization. Recently, the subcellular organization of bacterial RNA degradosomes was found to present similarities with eukaryotic messenger ribonucleoprotein (mRNP) granules, membraneless compartments that are also involved in mRNA and protein storage and/or mRNA degradation. In this review, we present the current knowledge on the composition and targets of RNA degradosomes, the most recent developments regarding the regulation of these machineries, and their similarities with the eukaryotic mRNP granules.
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12
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Do H, Makthal N, VanderWal AR, Saavedra MO, Olsen RJ, Musser JM, Kumaraswami M. Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway. Nat Commun 2019; 10:2586. [PMID: 31197146 PMCID: PMC6565748 DOI: 10.1038/s41467-019-10556-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria control gene expression in concert with their population density by a process called quorum sensing, which is modulated by bacterial chemical signals and environmental factors. In the human pathogen Streptococcus pyogenes, production of secreted virulence factor SpeB is controlled by a quorum-sensing pathway and environmental pH. The quorum-sensing pathway consists of a secreted leaderless peptide signal (SIP), and its cognate receptor RopB. Here, we report that the SIP quorum-sensing pathway has a pH-sensing mechanism operative through a pH-sensitive histidine switch located at the base of the SIP-binding pocket of RopB. Environmental acidification induces protonation of His144 and reorganization of hydrogen bonding networks in RopB, which facilitates SIP recognition. The convergence of two disparate signals in the SIP signaling pathway results in induction of SpeB production and increased bacterial virulence. Our findings provide a model for investigating analogous crosstalk in other microorganisms.
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Affiliation(s)
- Hackwon Do
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Nishanth Makthal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Arica R VanderWal
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA.
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13
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Bechhofer DH, Deutscher MP. Bacterial ribonucleases and their roles in RNA metabolism. Crit Rev Biochem Mol Biol 2019; 54:242-300. [PMID: 31464530 PMCID: PMC6776250 DOI: 10.1080/10409238.2019.1651816] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022]
Abstract
Ribonucleases (RNases) are mediators in most reactions of RNA metabolism. In recent years, there has been a surge of new information about RNases and the roles they play in cell physiology. In this review, a detailed description of bacterial RNases is presented, focusing primarily on those from Escherichia coli and Bacillus subtilis, the model Gram-negative and Gram-positive organisms, from which most of our current knowledge has been derived. Information from other organisms is also included, where relevant. In an extensive catalog of the known bacterial RNases, their structure, mechanism of action, physiological roles, genetics, and possible regulation are described. The RNase complement of E. coli and B. subtilis is compared, emphasizing the similarities, but especially the differences, between the two. Included are figures showing the three major RNA metabolic pathways in E. coli and B. subtilis and highlighting specific steps in each of the pathways catalyzed by the different RNases. This compilation of the currently available knowledge about bacterial RNases will be a useful tool for workers in the RNA field and for others interested in learning about this area.
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Affiliation(s)
- David H. Bechhofer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Murray P. Deutscher
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
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14
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The Second Messenger c-di-AMP Regulates Diverse Cellular Pathways Involved in Stress Response, Biofilm Formation, Cell Wall Homeostasis, SpeB Expression, and Virulence in Streptococcus pyogenes. Infect Immun 2019; 87:IAI.00147-19. [PMID: 30936159 DOI: 10.1128/iai.00147-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Cyclic di-AMP (c-di-AMP) is a recently discovered second messenger in bacteria. The cellular level of c-di-AMP in Streptococcus pyogenes is predicted to be controlled by the synthase DacA and two putative phosphodiesterases, GdpP and Pde2. To investigate the role of c-di-AMP in S. pyogenes, we generated null mutants in each of these proteins by gene deletion. Unlike those in other Gram-positive pathogens such as Staphylococcus aureus and Listeria monocytogenes, DacA in S. pyogenes was not essential for growth in rich media. The DacA null mutant presented a growth defect that manifested through an increased lag time, produced no detectable biofilm, and displayed increased susceptibility toward environmental stressors such as high salt, low pH, reactive oxygen radicals, and cell wall-targeting antibiotics, suggesting that c-di-AMP plays significant roles in crucial cellular processes involved in stress management. The Pde2 null mutant exhibited a lower growth rate and increased biofilm formation, and interestingly, these phenotypes were distinct from those of the null mutant of GdpP, suggesting that Pde2 and GdpP play distinctive roles in c-di-AMP signaling. DacA and Pde2 were critical to the production of the virulence factor SpeB and to the overall virulence of S. pyogenes, as both DacA and Pde2 null mutants were highly attenuated in a mouse model of subcutaneous infection. Collectively, these results show that c-di-AMP is an important global regulator and is required for a proper response to stress and for virulence in S. pyogenes, suggesting that its signaling pathway could be an attractive antivirulence drug target against S. pyogenes infections.
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15
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Menschner L, Falke U, Konrad P, Berner R, Toepfner N. Hydrogen Peroxide Production of Group A Streptococci (GAS) is emm-Type Dependent and Increased at Low Temperatures. Curr Microbiol 2019; 76:698-705. [PMID: 30955044 DOI: 10.1007/s00284-019-01683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/01/2019] [Indexed: 11/30/2022]
Abstract
Group A streptococcus (GAS) is an important human pathogen whose clinical isolates differ in their ability to produce hydrogen peroxide (H2O2). H2O2 is primarily produced by the enzyme lactate oxidase (LctO), an in depth in silico research revealed that all genome-sequenced GAS possess the required gene lctO. The importance of lctO for GAS is underlined by its highly conserved catabolite control element (cre box) as well as its perfect promotor sequence in comparison to the known consensus sequences of the Gram-positive model organism Bacillus subtilis. In this study, we provide further insight in the function and regulation of lactate oxidase by analyzing a large group of clinical GAS isolates. We found that H2O2 production increased over time in the late stationary phase; after 4 days of incubation, 5.4% of the isolates showed a positive result at 37 °C, while the rate increased to 16.4% at 20 °C. This correlation between H2O2 production and low temperatures suggests additional regulatory mechanisms for lctO besides catabolite control protein A (CcpA) and indicates that lctO might play a role for GAS energy metabolism at sub-body temperatures. Furthermore, we could identify that H2O2 production was different among clinical isolates; we could correlate H2O2 production to emm-types, indicating that emm-types 6 and 75 had the highest rate of H2O2 production. The emm-type- and temperature-dependent H2O2 production of clinical GAS isolates might contribute to their different survival strategies.
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Affiliation(s)
- Leonhard Menschner
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
| | - Uta Falke
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Peter Konrad
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Reinhard Berner
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Nicole Toepfner
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
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16
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Chen Z, Raghavan R, Qi F, Merritt J, Kreth J. Genome-wide screening of potential RNase Y-processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131. Microbiologyopen 2019; 8:e00671. [PMID: 29900693 PMCID: PMC6460267 DOI: 10.1002/mbo3.671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/07/2018] [Accepted: 05/15/2018] [Indexed: 01/28/2023] Open
Abstract
RNase Y is a major endoribonuclease in Group A streptococcus (GAS) and other Gram-positive bacteria. Our previous study showed that RNase Y was involved in mRNA degradation and processing in GAS. We hypothesized that mRNA processing regulated the expression of important GAS virulence factors via altering their mRNA stabilities and that RNase Y mediated at least some of the mRNA-processing events. The aims of this study were to (1) identify mRNAs that were processed by RNase Y and (2) confirm the mRNA-processing events. The transcriptomes of Streptococcus pyogenes NZ131 wild type and its RNase Y mutant (Δrny) were examined with RNA-seq. The data were further analyzed to define GAS operons. The mRNA stabilities of the wild type and Δrny at subgene level were determined with tiling array analysis. Operons displaying segmental stability in the wild type but not in the Δrny were predicted to be RNase Y processed. Overall 865 operons were defined and their boundaries predicted. Further analysis narrowed down 15 mRNAs potentially processed by RNase Y. A selection of four candidates including folC1 (folylpolyglutamate synthetase), prtF (fibronectin-binding protein), speG (streptococcal exotoxin G), ropB (transcriptional regulator of speB), and ypaA (riboflavin transporter) mRNAs was examined with Northern blot analysis. However, only folC1 was confirmed to be processed, but it is unlikely that RNase Y is responsible. We conclude that GAS use RNase Y to selectively process mRNA, but the overall impact is confined to selected virulence factors.
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Affiliation(s)
- Zhiyun Chen
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahoma
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme EnvironmentsPortland State UniversityPortlandOregon
| | - Fengxia Qi
- Department of Microbiology and ImmunologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahoma
| | - Justin Merritt
- Department of Restorative DentistryOregon Health and Science UniversityPortlandOregon
- Department of Molecular Microbiology and ImmunologyOregon Health and Science UniversityPortlandOregon
| | - Jens Kreth
- Department of Restorative DentistryOregon Health and Science UniversityPortlandOregon
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17
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Broglia L, Materne S, Lécrivain AL, Hahnke K, Le Rhun A, Charpentier E. RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B. RNA Biol 2018; 15:1336-1347. [PMID: 30290721 PMCID: PMC6284565 DOI: 10.1080/15476286.2018.1532253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.
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Affiliation(s)
- Laura Broglia
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany
| | - Solange Materne
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anne-Laure Lécrivain
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Karin Hahnke
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany
| | - Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Department of Regulation in Infection Biology , Max Planck Institute for Infection Biology , Berlin , Germany.,c Institute for Biology , Humboldt University , Berlin , Germany.,d Department of Regulation in Infection Biology , Helmholtz Centre for Infection Research , Braunschweig , Germany.,e The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology , Umeå University , Umeå , Sweden
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18
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Koch G, Wermser C, Acosta IC, Kricks L, Stengel ST, Yepes A, Lopez D. Attenuating Staphylococcus aureus Virulence by Targeting Flotillin Protein Scaffold Activity. Cell Chem Biol 2017; 24:845-857.e6. [PMID: 28669526 DOI: 10.1016/j.chembiol.2017.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 01/13/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S. aureus toxin expression. Small molecules that altered FloA oligomerization also reduced Rny function and decreased the virulence potential of S. aureus in vitro, as well as in vivo, using invertebrate and murine infection models. Our results suggest that flotillin assists in the assembly of protein complexes involved in S. aureus virulence, and could thus be an attractive target for the development of new antimicrobial therapies.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ivan C Acosta
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Lara Kricks
- National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany; National Centre for Biotechnology (CNB), Spanish Research Council (CSIC), Darwin 3, Madrid 28049, Spain.
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19
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Hausmann S, Guimarães VA, Garcin D, Baumann N, Linder P, Redder P. Both exo- and endo-nucleolytic activities of RNase J1 from Staphylococcus aureus are manganese dependent and active on triphosphorylated 5'-ends. RNA Biol 2017; 14:1431-1443. [PMID: 28277929 DOI: 10.1080/15476286.2017.1300223] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
RNA decay and RNA maturation are important steps in the regulation of bacterial gene expression. RNase J, which is present in about half of bacterial species, has been shown to possess both endo- and 5' to 3' exo-ribonuclease activities. The exonucleolytic activity is clearly involved in the degradation of mRNA and in the maturation of at least the 5' end of 16S rRNA in the 2 Firmicutes Staphylococcus aureus and Bacillus subtilis. The endoribonuclease activity of RNase J from several species has been shown to be weak in vitro and 3-D structural data of different RNase J orthologs have not provided a clear explanation for the molecular basis of this activity. Here, we show that S. aureus RNase J1 is a manganese dependent homodimeric enzyme with strong 5' to 3' exo-ribonuclease as well as endo-ribonuclease activity. In addition, we demonstrated that SauJ1 can efficiently degrade 5' triphosphorylated RNA. Our results highlight RNase J1 as an important player in RNA turnover in S. aureus.
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Affiliation(s)
- Stéphane Hausmann
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland
| | - Vanessa Andrade Guimarães
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland
| | - Dominique Garcin
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland
| | - Natalia Baumann
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland
| | - Patrick Linder
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland
| | - Peter Redder
- a Department of Microbiology and Molecular Medicine , Medical Faculty, University of Geneva , Geneva , Switzerland.,b Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse III Toulouse , France
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20
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Cho KH. The Structure and Function of the Gram-Positive Bacterial RNA Degradosome. Front Microbiol 2017; 8:154. [PMID: 28217125 PMCID: PMC5289998 DOI: 10.3389/fmicb.2017.00154] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/20/2017] [Indexed: 11/24/2022] Open
Abstract
The RNA degradosome is a highly structured protein complex responsible for bulk RNA decay in bacteria. The main components of the complex, ribonucleases, an RNA helicase, and glycolytic enzymes are well-conserved in bacteria. Some components of the degradosome are essential for growth and the disruption of degradosome formation causes slower growth, indicating that this complex is required for proper cellular function. The study of the Escherichia coli degradosome has been performed extensively for the last several decades and has revealed detailed information on its structure and function. On the contrary, the Gram-positive bacterial degradosome, which contains ribonucleases different from the E. coli one, has been studied only recently. Studies on the Gram-positive degradosome revealed that its major component RNase Y was necessary for the full virulence of medically important Gram-positive bacterial pathogens, suggesting that it could be a target of antimicrobial therapy. This review describes the structures and function of Gram-positive bacterial RNA degradosomes, especially those of a Gram-positive model organism Bacillus subtilis, and two important Gram-positive pathogens, Staphylococcus aureus and Streptococcus pyogenes.
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Affiliation(s)
- Kyu Hong Cho
- Department of Biology, Indiana State University Terre Haute, IN, USA
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21
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Presence of a Prophage Determines Temperature-Dependent Capsule Production in Streptococcus pyogenes. Genes (Basel) 2016; 7:genes7100074. [PMID: 27669311 PMCID: PMC5083913 DOI: 10.3390/genes7100074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/17/2022] Open
Abstract
A hyaluronic acid capsule is a major virulence factor in the pathogenesis of Streptococcus pyogenes. It acts as an anti-phagocytic agent and adhesin to keratinocytes. The expression of the capsule is primarily regulated at the transcriptional level by the two-component regulatory system CovRS, in which CovR acts as a transcriptional repressor. The covRS genes are frequently mutated in many invasive strains, and a subset of the invasive CovRS mutants does not produce a detectable level of the capsule at 37 °C, but produces a significant amount of the capsule at sub-body temperatures. Here, we report that a prophage has a crucial role in this capsule thermoregulation. Passaging CovR-null strains showing capsule thermoregulation using a lab medium produced spontaneous mutants producing a significant amount of the capsule regardless of incubation temperature and this phenotypic change was caused by curing of a particular prophage. The lab strain HSC5 contains three prophages on the chromosome, and only ΦHSC5.3 was cured in all spontaneous mutants. This result indicates that the prophage ΦHSC5.3 plays a crucial role in capsule thermoregulation, most likely by repressing capsule production at 37 °C.
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22
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Monteiro R, Hébraud M, Chafsey I, Poeta P, Igrejas G. How different is the proteome of the extended spectrum β-lactamase producing Escherichia coli strains from seagulls of the Berlengas natural reserve of Portugal? J Proteomics 2016; 145:167-176. [PMID: 27118263 DOI: 10.1016/j.jprot.2016.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 01/19/2023]
Abstract
UNLABELLED β-Lactam antibiotics like cefotaxime are the most commonly used antibacterial agents. Escherichia coli strains 5A, 10A, 12A and 23B isolated from Seagulls feces, are cefotaxime-resistant strains that produces extended-spectrum beta-lactamases. Bacterial resistance to these antibiotics occurs predominantly through structural modification on the penicillin-binding proteins and enzymatic inactivation by extended-spectrum β-lactamases. Using classical proteomic techniques (2D-GE) coupled to mass spectrometry and bioinformatics extended analysis, in this study, we report several significant differences in cytoplasmic proteins expression when the strains were submitted to antibiotic stress and when the resistant strains were compared with a non-resistant strain. A total of 79 differentially expressed spots were collected for protein identification. Significant level of expression was found in antibiotic resistant proteins like β-lactamase CTX-M-1 and TEM and also in proteins related with oxidative stress. This approach might help us understand which pathways form barriers for antibiotics, another possible new pathways involved in antibiotic resistance to devise appropriate strategies for their control already recognized by the World Health Organization and the European Commission. BIOLOGICAL SIGNIFICANCE This study highlights the protein differences when a resistant strain is under antibiotic pressure and how different can be a sensible and resistant strain at the protein level. This survey might help us to understand the specifics barriers for antibiotics and which pathways are involved in its resistance crosswise the wildlife.
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Affiliation(s)
- R Monteiro
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - M Hébraud
- UR454 Microbiology, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France; Plate-Forme d'Exploration du Métabolisme composante protéomique, UR370 QuaPA, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France
| | - I Chafsey
- UR454 Microbiology, Institut National de la Recherche Agronomique (INRA), Centre Auvergne-Rhône-Alpes, site de Theix, Saint-Genès Champanelle, France
| | - P Poeta
- Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal
| | - G Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal.
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23
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Salvo E, Alabi S, Liu B, Schlessinger A, Bechhofer DH. Interaction of Bacillus subtilis Polynucleotide Phosphorylase and RNase Y: STRUCTURAL MAPPING AND EFFECT ON mRNA TURNOVER. J Biol Chem 2016; 291:6655-63. [PMID: 26797123 DOI: 10.1074/jbc.m115.711044] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 11/06/2022] Open
Abstract
Polynucleotide phosphorylase (PNPase), a 3'-to-5' phosphorolytic exoribonuclease, is thought to be the primary enzyme responsible for turnover ofBacillus subtilismRNA. The role of PNPase inB. subtilismRNA decay has been analyzed previously by comparison of mRNA profiles in a wild-type strainversusa strain that is deleted forpnpA, the gene encoding PNPase. Recent studies have provided evidence for a degradosome-like complex inB. subtilisthat is built around the major decay-initiating endonuclease, RNase Y, and there is ample evidence for a strong interaction between PNPase and RNase Y. The role of the PNPase-RNase Y interaction in the exonucleolytic function of PNPase needs to be clarified. We sought to construct aB. subtilisstrain containing a catalytically active PNPase that could not interact with RNase Y. Mapping studies of the PNPase-RNase Y interaction were guided by a homology model ofB. subtilisPNPase based on the known structure of theEscherichia coliPNPase in complex with an RNase E peptide. Mutations inB. subtilisresidues predicted to be involved in RNase Y binding showed a loss of PNPase-RNase Y interaction. Two mRNAs whose decay is dependent on RNase Y and PNPase were examined in strains containing full-length PNPase that was either catalytically active but unable to interact with RNase Y, or catalytically inactive but able to interact with RNase Y. At least for these two mRNAs, disruption of the PNPase-RNase Y interaction did not appear to affect mRNA turnover.
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Affiliation(s)
- Elizabeth Salvo
- From the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shanique Alabi
- From the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Bo Liu
- From the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Avner Schlessinger
- From the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - David H Bechhofer
- From the Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029
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24
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Khemici V, Prados J, Linder P, Redder P. Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation. PLoS Genet 2015; 11:e1005577. [PMID: 26473962 PMCID: PMC4608709 DOI: 10.1371/journal.pgen.1005577] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Bacteria depend on efficient RNA turnover, both during homeostasis and when rapidly altering gene expression in response to changes. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram-positive pathogens. We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.
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Affiliation(s)
- Vanessa Khemici
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Patrick Linder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Peter Redder
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
- * E-mail:
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25
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Abstract
Pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. Thermal regulation can be achieved at the level of DNA, RNA or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. Understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often influenced by complex regulatory networks involving multiple transcription factors in bacteria. Here we highlight some recent insights into thermal regulation of virulence in pathogenic bacteria. We focus on bacteria which cause disease in mammalian hosts, which are at a significantly higher temperature than the outside environment. We outline the mechanisms of thermal regulation and how understanding this fundamental aspect of the biology of bacteria has implications for pathogenesis and human health.
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Affiliation(s)
- Oliver Lam
- a The Sir William Dunn School of Pathology ; University of Oxford ; Oxford , UK
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26
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Chemical genetics and its application to moonlighting in glycolytic enzymes. Biochem Soc Trans 2015; 42:1756-61. [PMID: 25399602 DOI: 10.1042/bst20140201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Glycolysis is an ancient biochemical pathway that breaks down glucose into pyruvate to produce ATP. The structural and catalytic properties of glycolytic enzymes are well-characterized. However, there is growing appreciation that these enzymes participate in numerous moonlighting functions that are unrelated to glycolysis. Recently, chemical genetics has been used to discover novel moonlighting functions in glycolytic enzymes. In the present mini-review, we introduce chemical genetics and discuss how it can be applied to the discovery of protein moonlighting. Specifically, we describe the application of chemical genetics to uncover moonlighting in two glycolytic enzymes, enolase and glyceraldehyde dehydrogenase. This led to the discovery of moonlighting roles in glucose homoeostasis, cancer progression and diabetes-related complications. Finally, we also provide a brief overview of the latest progress in unravelling the myriad moonlighting roles for these enzymes.
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Li J, Wang Q, Li M, Yang B, Shi M, Guo W, McDermott TR, Rensing C, Wang G. Proteomics and Genetics for Identification of a Bacterial Antimonite Oxidase in Agrobacterium tumefaciens. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:5980-5989. [PMID: 25909855 DOI: 10.1021/es506318b] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Antimony (Sb) and its compounds are listed by the United States Environmental Protection Agency (USEPA, 1979) and the European Union (CEC, 1976) as a priority pollutant. Microbial redox transformations are presumed to be an important part of antimony cycling in nature; however, regulation of these processes and the enzymology involved are unknown. In this study, comparative proteomics and reverse transcriptase-PCR analysis of Sb(III)-oxidizing bacterium Agrobacterium tumefaciens GW4 revealed an oxidoreductase (anoA) is widely distributed in microorganisms, including at least some documented to be able to oxidize Sb(III). Deletion of the anoA gene reduced Sb(III) resistance and decreased Sb(III) oxidation by ∼27%, whereas the anoA complemented strain was similar to the wild type GW4 and a GW4 anoA overexpressing strain increased Sb(III) oxidation by ∼34%. Addition of Sb(III) up-regulated anoA expression and cloning anoA to Escherichia coli demonstrated direct transferability of this activity. A His-tag purified AnoA was found to require NADP(+) as cofactor, and exhibited a K(m) for Sb(III) of 64 ± 10 μM and a V(max) of 150 ± 7 nmol min(-1) mg(-1). This study contributes important initial steps toward a mechanistic understanding of microbe-antimony interactions and enhances our understanding of how microorganisms participate in antimony biogeochemical cycling in nature.
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Affiliation(s)
- Jingxin Li
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Qian Wang
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Mingshun Li
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Birong Yang
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Manman Shi
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wei Guo
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Timothy R McDermott
- ‡Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717, United States
| | - Christopher Rensing
- §Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, DK-1871, Denmark
| | - Gejiao Wang
- †State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, P. R. China
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Durand S, Tomasini A, Braun F, Condon C, Romby P. sRNA and mRNA turnover in Gram-positive bacteria. FEMS Microbiol Rev 2015; 39:316-30. [PMID: 25934118 DOI: 10.1093/femsre/fuv007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2015] [Indexed: 01/18/2023] Open
Abstract
It is widely recognized that RNA degradation plays a critical role in gene regulation when fast adaptation of cell growth is required to respond to stress and changing environmental conditions. Bacterial ribonucleases acting alone or in concert with various trans-acting regulatory factors are important mediators of RNA degradation. Here, we will give an overview of what is known about ribonucleases in several Gram-positive bacteria, their specificities and mechanisms of action. In addition, we will illustrate how sRNAs act in a coordinated manner with ribonucleases to regulate the turnover of particular mRNA targets, and the complex interplay existing between the ribosome, the ribonucleases and RNAs.
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Affiliation(s)
- Sylvain Durand
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Arnaud Tomasini
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France
| | - Frédérique Braun
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ciarán Condon
- CNRS FRE 3630 (affiliated with Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pascale Romby
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France
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Cho KH, Kim JH. Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens. Front Genet 2015; 6:110. [PMID: 25859258 PMCID: PMC4374534 DOI: 10.3389/fgene.2015.00110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/03/2015] [Indexed: 01/19/2023] Open
Abstract
Due to recent advances of bioinformatics and high throughput sequencing technology, discovery of regulatory non-coding RNAs in bacteria has been increased to a great extent. Based on this bandwagon, many studies searching for trans-acting small non-coding RNAs in streptococci have been performed intensively, especially in the important human pathogen, group A and B streptococci. However, studies for cis-encoded non-coding antisense RNAs in streptococci have been scarce. A recent study shows antisense RNAs are involved in virulence gene regulation in group B streptococcus, S. agalactiae. This suggests antisense RNAs could have important roles in the pathogenesis of streptococcal pathogens. In this review, we describe recent discoveries of chromosomal cis-encoded antisense RNAs in streptococcal pathogens and other low GC Gram (+) bacteria to provide a guide for future studies.
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Affiliation(s)
- Kyu Hong Cho
- Department of Biology, Indiana State University Terre Haute, IN, USA
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Science Washington, DC, USA
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Nuclease activity of Legionella pneumophila Cas2 promotes intracellular infection of amoebal host cells. Infect Immun 2014; 83:1008-18. [PMID: 25547789 DOI: 10.1128/iai.03102-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Legionella pneumophila, the primary agent of Legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. Recently, we determined that the Cas2 protein of L. pneumophila promotes intracellular infection of Acanthamoeba castellanii and Hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. The Cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein (Cas) system that constitutes a form of adaptive immunity against phage and plasmid. However, the infection event mediated by L. pneumophila Cas2 appeared to be distinct from this function, because cas2 mutants exhibited infectivity defects in the absence of added phage or plasmid and since mutants lacking the CRISPR array or any one of the other cas genes were not impaired in infection ability. We now report that the Cas2 protein of L. pneumophila has both RNase and DNase activities, with the RNase activity being more pronounced. By characterizing a catalytically deficient version of Cas2, we determined that nuclease activity is critical for promoting infection of amoebae. Also, introduction of Cas2, but not its catalytic mutant form, into a strain of L. pneumophila that naturally lacks a CRISPR-Cas locus caused that strain to be 40- to 80-fold more infective for amoebae, unequivocally demonstrating that Cas2 facilitates the infection process independently of any other component encoded within the CRISPR-Cas locus. Finally, a cas2 mutant was impaired for infection of Willaertia magna but not Naegleria lovaniensis, suggesting that Cas2 promotes infection of most but not all amoebal hosts.
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Beema Shafreen RM, Selvaraj C, Singh SK, Karutha Pandian S. In silico and in vitro studies of cinnamaldehyde and their derivatives against LuxS in Streptococcus pyogenes: effects on biofilm and virulence genes. J Mol Recognit 2014; 27:106-16. [PMID: 24436128 DOI: 10.1002/jmr.2339] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/22/2013] [Accepted: 10/31/2013] [Indexed: 01/23/2023]
Abstract
The LuxS-based signalling pathway has an important role in physiological and pathogenic functions that are capable of causing different infections. In the present study, cinnamaldehyde (CN) and their derivatives were evaluated for their inhibitory efficiency against LuxS by molecular modelling, docking, dynamics and free-energy calculations. Sequence and structure-similarity analysis of LuxS protein, five different amino acids were found to be highly conserved, of which GLY128 was identified as the key residue involved in the effective binding of the ligands. Quantum-polarized ligand docking protocol showed that 2nitro and 4nitro CN has a higher binding efficiency than CN, which very well corroborates with the in vitro studies. COMSTAT analysis for the microscopic images of the S. pyogenes biofilm showed that the ligands have antibiofilm potential. In addition, the results of quantitative polymerase chain reaction (qPCR) analysis revealed that the transcripts treated with the compounds showed decrease in luxS expression, which directly reflects with the reduction in expression of speB. No substantial effect was observed on the virulence regulator (srv) transcript. These results confirm that speB is controlled by the regulation of luxS. The decreased rate of S. pyogenes survival in the presence of these ligands envisaged the fact that the compounds could readily enhance opsonophagocytosis with the reduction of virulence factor secretion. Thus, the overall data supports the use of CN derivatives against quorum sensing-mediated infections caused by S. pyogenes.
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Numata S, Nagata M, Mao H, Sekimizu K, Kaito C. CvfA protein and polynucleotide phosphorylase act in an opposing manner to regulate Staphylococcus aureus virulence. J Biol Chem 2014; 289:8420-31. [PMID: 24492613 DOI: 10.1074/jbc.m114.554329] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously identified CvfA (SA1129) as a Staphylococcus aureus virulence factor using a silkworm infection model. S. aureus cvfA-deleted mutants exhibit decreased expression of the agr locus encoding a positive regulator of hemolysin genes and decreased hemolysin production. CvfA protein hydrolyzes a 2',3'-cyclic phosphodiester bond at the RNA 3' terminus, producing RNA with a 3'-phosphate (3'-phosphorylated RNA, RNA with a 3'-phosphate). Here, we report that the cvfA-deleted mutant phenotype (decreased agr expression and hemolysin production) was suppressed by disrupting pnpA-encoding polynucleotide phosphorylase (PNPase) with 3'- to 5'-exonuclease activity. The suppression was blocked by introducing a pnpA-encoding PNPase with exonuclease activity but not by a pnpA-encoding mutant PNPase without exonuclease activity. Therefore, loss of PNPase exonuclease activity suppressed the cvfA-deleted mutant phenotype. Purified PNPase efficiently degraded RNA with 2',3'-cyclic phosphate at the 3' terminus (2',3'-cyclic RNA), but it inefficiently degraded 3'-phosphorylated RNA. These findings indicate that 3'-phosphorylated RNA production from 2',3'-cyclic RNA by CvfA prevents RNA degradation by PNPase and contributes to the expression of agr and hemolysin genes. We speculate that in the cvfA-deleted mutant, 2',3'-cyclic RNA is not converted to the 3'-phosphorylated form and is efficiently degraded by PNPase, resulting in the loss of RNA essential for expressing agr and hemolysin genes, whereas in the cvfA/pnpA double-disrupted mutant, 2',3'-cyclic RNA is not degraded by PNPase, leading to hemolysin production. These findings suggest that CvfA and PNPase competitively regulate RNA degradation essential for S. aureus virulence.
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Affiliation(s)
- Shunsuke Numata
- From the Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 3-1, 7-chome, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Merritt J, Chen Z, Liu N, Kreth J. Posttranscriptional regulation of oral bacterial adaptive responses. ACTA ACUST UNITED AC 2014; 1:50-58. [PMID: 24695639 DOI: 10.1007/s40496-013-0005-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Within the past 10 years, it has become increasingly evident that posttranscriptional regulation is among the most important mechanisms used by bacteria to modulate gene expression in response to environmental perturbations. Posttranscriptional mechanisms provide a much faster response and lower energy burden compared to most transcription regulatory pathways and they have the unique advantage that they can override existing transcriptional responses once the environment changes. Because of this, virulence factor gene expression is particularly suited for posttranscriptional control, and not surprisingly, an abundance of recent evidence indicates that posttranscriptional regulators are the predominant virulence regulators of human pathogens. Typically, this involves global riboregulators that primarily serve as modulators of virulence gene translation initiation and/or mRNA stability. Surprisingly little has been reported about posttranscriptional regulatory pathways in oral bacteria, but recent results suggest that oral species are equally dependent upon posttranscriptional control of their adaptive genetic responses. In this report, we discuss the major themes in RNA-based regulation of gene expression and review the available literature related to the most commonly studied oral bacterial species.
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Affiliation(s)
- Justin Merritt
- Department of Microbiology & immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Zhiyun Chen
- Department of Microbiology & immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Nan Liu
- Department of Microbiology & immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Jens Kreth
- Department of Microbiology & immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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Streptococcus pyogenes arginine and citrulline catabolism promotes infection and modulates innate immunity. Infect Immun 2013; 82:233-42. [PMID: 24144727 DOI: 10.1128/iai.00916-13] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A bacterium's ability to acquire nutrients from its host during infection is an essential component of pathogenesis. For the Gram-positive pathogen Streptococcus pyogenes, catabolism of the amino acid arginine via the arginine deiminase (ADI) pathway supplements energy production and provides protection against acid stress in vitro. Its expression is enhanced in murine models of infection, suggesting an important role in vivo. To gain insight into the function of the ADI pathway in pathogenesis, the virulence of mutants defective in each of its enzymes was examined. Mutants unable to use arginine (ΔArcA) or citrulline (ΔArcB) were attenuated for carriage in a murine model of asymptomatic mucosal colonization. However, in a murine model of inflammatory infection of cutaneous tissue, the ΔArcA mutant was attenuated but the ΔArcB mutant was hyperattenuated, revealing an unexpected tissue-specific role for citrulline metabolism in pathogenesis. When mice defective for the arginine-dependent production of nitric oxide (iNOS(-/-)) were infected with the ΔArcA mutant, cutaneous virulence was rescued, demonstrating that the ability of S. pyogenes to utilize arginine was dispensable in the absence of nitric oxide-mediated innate immunity. This work demonstrates the importance of arginine and citrulline catabolism and suggests a novel mechanism of virulence by which S. pyogenes uses its metabolism to modulate innate immunity through depletion of an essential host nutrient.
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Cho KH, Wright J, Svencionis J, Kim JH. The prince and the pauper: which one is real? The problem of secondary mutation during mutagenesis in Streptococcus pyogenes. Virulence 2013; 4:664-5. [PMID: 24128432 PMCID: PMC3925696 DOI: 10.4161/viru.26767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Kyu Hong Cho
- Department of Microbiology; Southern Illinois University; Carbondale, IL USA
| | - Jordan Wright
- Department of Microbiology; Southern Illinois University; Carbondale, IL USA
| | - Juan Svencionis
- Department of Microbiology; Southern Illinois University; Carbondale, IL USA
| | - Jeong-Ho Kim
- Department of Biochemistry and Molecular Medicine; The George Washington University Medical Center; Washington, DC USA
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Gera K, McIver KS. Laboratory growth and maintenance of Streptococcus pyogenes (the Group A Streptococcus, GAS). ACTA ACUST UNITED AC 2013; 30:9D.2.1-9D.2.13. [PMID: 24510893 DOI: 10.1002/9780471729259.mc09d02s30] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Streptococcus pyogenes is a Gram-positive bacterium that strictly infects humans. It is the causative agent of a broad spectrum of diseases accounting for millions of infections and at least 517,000 deaths each year worldwide. It is a nutritionally fastidious organism that ferments sugars to produce lactic acid and has strict requirements for growth. To aid in the study of this organism, this unit describes the growth and maintenance of S. pyogenes.
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Affiliation(s)
- Kanika Gera
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
| | - Kevin S McIver
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland
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Initiation of mRNA decay in bacteria. Cell Mol Life Sci 2013; 71:1799-828. [PMID: 24064983 PMCID: PMC3997798 DOI: 10.1007/s00018-013-1472-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 12/24/2022]
Abstract
The instability of messenger RNA is fundamental to the control of gene expression. In bacteria, mRNA degradation generally follows an "all-or-none" pattern. This implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. Studies of E. coli and B. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. The early view that mRNA decay in these two model organisms is radically different has given way to new models that can be resumed by "different enzymes-similar strategies". The recent characterization of key ribonucleases sheds light on an impressive case of convergent evolution that illustrates that the surprisingly similar functions of these totally unrelated enzymes are of general importance to RNA metabolism in bacteria. We now know that the major mRNA decay pathways initiate with an endonucleolytic cleavage in E. coli and B. subtilis and probably in many of the currently known bacteria for which these organisms are considered representative. We will discuss here the different pathways of eubacterial mRNA decay, describe the major players and summarize the events that can precede and/or favor nucleolytic inactivation of a mRNA, notably the role of the 5' end and translation initiation. Finally, we will discuss the role of subcellular compartmentalization of transcription, translation, and the RNA degradation machinery.
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Complete Genome Sequence of emm Type 14 Streptococcus pyogenes Strain HSC5. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00612-13. [PMID: 23950122 PMCID: PMC3744678 DOI: 10.1128/genomea.00612-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptococcus pyogenes causes a greater diversity of human disease than any other bacterial pathogen. Here, we present the complete genome sequence of the emm type 14 S. pyogenes strain HSC5. This strain is a robust producer of the cysteine protease SpeB and is capable of producing infection in several different animal models.
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Multiple roles of RNase Y in Streptococcus pyogenes mRNA processing and degradation. J Bacteriol 2013; 195:2585-94. [PMID: 23543715 DOI: 10.1128/jb.00097-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Control over mRNA stability is an essential part of gene regulation that involves both endo- and exoribonucleases. RNase Y is a recently identified endoribonuclease in Gram-positive bacteria, and an RNase Y ortholog has been identified in Streptococcus pyogenes (group A streptococcus [GAS]). In this study, we used microarray and Northern blot analyses to determine the S. pyogenes mRNA half-life of the transcriptome and to understand the role of RNase Y in global mRNA degradation and processing. We demonstrated that S. pyogenes has an unusually high mRNA turnover rate, with median and mean half-lives of 0.88 min and 1.26 min, respectively. A mutation of the RNase Y-encoding gene (rny) led to a 2-fold increase in overall mRNA stability. RNase Y was also found to play a significant role in the mRNA processing of virulence-associated genes as well as in the rapid degradation of rnpB read-through transcripts. From these results, we conclude that RNase Y is a pleiotropic regulator required for mRNA stability, mRNA processing, and removal of read-through transcripts in S. pyogenes.
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Intracellular ribonucleases involved in transcript processing and decay: precision tools for RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:491-513. [PMID: 23545199 DOI: 10.1016/j.bbagrm.2013.03.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/19/2013] [Accepted: 03/22/2013] [Indexed: 12/15/2022]
Abstract
In order to adapt to changing environmental conditions and regulate intracellular events such as division, cells are constantly producing new RNAs while discarding old or defective transcripts. These functions require the coordination of numerous ribonucleases that precisely cleave and trim newly made transcripts to produce functional molecules, and rapidly destroy unnecessary cellular RNAs. In recent years our knowledge of the nature, functions and structures of these enzymes in bacteria, archaea and eukaryotes has dramatically expanded. We present here a synthetic overview of the recent development in this dynamic area which has seen the identification of many new endoribonucleases and exoribonucleases. Moreover, the increasing pace at which the structures of these enzymes, or of their catalytic domains, have been solved has provided atomic level detail into their mechanisms of action. Based on sequence conservation and structural data, these proteins have been grouped into families, some of which contain only ribonuclease members, others including a variety of nucleolytic enzymes that act upon DNA and/or RNA. At the other extreme some ribonucleases belong to families of proteins involved in a wide variety of enzymatic reactions. Functional characterization of these fascinating enzymes has provided evidence for the extreme diversity of their biological functions that include, for example, removal of poly(A) tails (deadenylation) or poly(U) tails from eukaryotic RNAs, processing of tRNA and mRNA 3' ends, maturation of rRNAs and destruction of unnecessary mRNAs. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Gunderson FF, Cianciotto NP. The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. mBio 2013; 4:e00074-13. [PMID: 23481601 PMCID: PMC3604779 DOI: 10.1128/mbio.00074-13] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Recent studies have shown that the clustered regularly interspaced palindromic repeats (CRISPR) array and its associated (cas) genes can play a key role in bacterial immunity against phage and plasmids. Upon analysis of the Legionella pneumophila strain 130b chromosome, we detected a subtype II-B CRISPR-Cas locus that contains cas9, cas1, cas2, cas4, and an array with 60 repeats and 58 unique spacers. Reverse transcription (RT)-PCR analysis demonstrated that the entire CRISPR-Cas locus is expressed during 130b extracellular growth in both rich and minimal media as well as during intracellular infection of macrophages and aquatic amoebae. Quantitative reverse transcription-PCR (RT-PCR) further showed that the levels of cas transcripts, especially those of cas1 and cas2, are elevated during intracellular growth relative to exponential-phase growth in broth. Mutants lacking components of the CRISPR-Cas locus were made and found to grow normally in broth and on agar media. cas9, cas1, cas4, and CRISPR array mutants also grew normally in macrophages and amoebae. However, cas2 mutants, although they grew typically in macrophages, were significantly impaired for infection of both Hartmannella and Acanthamoeba species. A complemented cas2 mutant infected the amoebae at wild-type levels, confirming that cas2 is required for intracellular infection of these host cells. IMPORTANCE Given that infection of amoebae is critical for L. pneumophila persistence in water systems, our data indicate that cas2 has a role in the transmission of Legionnaires' disease. Because our experiments were done in the absence of added phage, plasmid, or nucleic acid, the event that is facilitated by Cas2 is uniquely distinct from current dogma concerning CRISPR-Cas function.
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Affiliation(s)
- Felizza F Gunderson
- Department of Microbiology and Immunology, Northwestern University, Medical School, Chicago, Illinois, USA
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Le Breton Y, Mistry P, Valdes KM, Quigley J, Kumar N, Tettelin H, McIver KS. Genome-wide identification of genes required for fitness of group A Streptococcus in human blood. Infect Immun 2013; 81:862-75. [PMID: 23297387 PMCID: PMC3584890 DOI: 10.1128/iai.00837-12] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/15/2012] [Indexed: 12/27/2022] Open
Abstract
The group A streptococcus (GAS) is a strict human pathogen responsible for a wide spectrum of diseases. Although GAS genome sequences are available, functional genomic analyses have been limited. We developed a mariner-based transposon, osKaR, designed to perform Transposon-Site Hybridization (TraSH) in GAS and successfully tested its use in several invasive serotypes. A complex osKaR mutant library in M1T1 GAS strain 5448 was subjected to negative selection in human blood to identify genes important for GAS fitness in this clinically relevant environment. Mutants underrepresented after growth in blood (output pool) compared to growth in rich media (input pool) were identified using DNA microarray hybridization of transposon-specific tags en masse. Using blood from three different donors, we identified 81 genes that met our criteria for reduced fitness in blood from at least two individuals. Genes known to play a role in survival of GAS in blood were found, including those encoding the virulence regulator Mga (mga), the peroxide response regulator PerR (perR), and the RofA-like regulator Ralp-3 (ralp3). We also identified genes previously reported for their contribution to sepsis in other pathogens, such as de novo nucleotide synthesis (purD, purA, pyrB, carA, carB, guaB), sugar metabolism (scrB, fruA), zinc uptake (adcC), and transcriptional regulation (cpsY). To validate our findings, independent mutants with mutations in 10 different genes identified in our screen were confirmed to be defective for survival in blood bactericidal assays. Overall, this work represents the first use of TraSH in GAS to identify potential virulence genes.
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Affiliation(s)
- Yoann Le Breton
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Pragnesh Mistry
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Kayla M. Valdes
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Jeffrey Quigley
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
| | - Nikhil Kumar
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hervé Tettelin
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kevin S. McIver
- Department of Cell Biology & Molecular Genetics and Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, USA
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43
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Vega LA, Caparon MG. Cationic antimicrobial peptides disrupt the Streptococcus pyogenes ExPortal. Mol Microbiol 2012; 85:1119-32. [PMID: 22780862 DOI: 10.1111/j.1365-2958.2012.08163.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although they possess a well-characterized ability to porate the bacterial membrane, emerging research suggests that cationic antimicrobial peptides (CAPs) can influence pathogen behaviour at levels that are sublethal. In this study, we investigated the interaction of polymyxin B and human neutrophil peptide (HNP-1) with the human pathogen Streptococcus pyogenes. At sublethal concentrations, these CAPs preferentially targeted the ExPortal, a unique microdomain of the S. pyogenes membrane, specialized for protein secretion and processing. A consequence of this interaction was the disruption of ExPortal organization and a redistribution of ExPortal components into the peripheral membrane. Redistribution was associated with inhibition of secretion of certain toxins, including the SpeB cysteine protease and the streptolysin O (SLO) cytolysin, but not SIC, a protein that protects S. pyogenes from CAPs. These data suggest a novel function for CAPs in targeting the ExPortal and interfering with secretion of factors required for infection and survival. This mechanism may prove valuable for the design of new types of antimicrobial agents to combat the emergence of antibiotic-resistant pathogens.
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Affiliation(s)
- Luis Alberto Vega
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110-1093, USA
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Marincola G, Schäfer T, Behler J, Bernhardt J, Ohlsen K, Goerke C, Wolz C. RNase Y of Staphylococcus aureus and its role in the activation of virulence genes. Mol Microbiol 2012; 85:817-32. [PMID: 22780584 DOI: 10.1111/j.1365-2958.2012.08144.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNase Y of Bacillus subtilis is a key member of the degradosome and important for bulk mRNA turnover. In contrast to B. subtilis, the RNase Y homologue (rny/cvfA) of Staphylococcus aureus is not essential for growth. Here we found that RNase Y plays a major role in virulence gene regulation. Accordingly, rny deletion mutants demonstrated impaired virulence in a murine bacteraemia model. RNase Y is important for the processing and stabilization of the immature transcript of the global virulence regulator system SaePQRS. Moreover, RNase Y is involved in the activation of virulence gene expression at the promoter level. This control is independent of both the virulence regulator agr and the saePQRS processing and may be mediated by small RNAs some of which were shown to be degraded by RNase Y. Besides this regulatory effect, mRNA levels of several operons were significantly increased in the rny mutant and the half-life of one of these operons was shown to be extremely extended. However, the half-life of many mRNA species was not significantly altered. Thus, RNase Y in S. aureus influences mRNA expression in a tightly controlled regulatory manner and is essential for coordinated activation of virulence genes.
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Affiliation(s)
- Gabriella Marincola
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Germany
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45
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Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J. RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 2012; 84:1005-17. [PMID: 22568516 DOI: 10.1111/j.1365-2958.2012.08072.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
RNA processing and degradation are key processes in the control of transcript accumulation and thus in the control of gene expression. In Escherichia coli, the underlying mechanisms and components of RNA decay are well characterized. By contrast, Gram-positive bacteria do not possess several important players of E. coli RNA degradation, most notably the essential enzyme RNase E. Recent research on the model Gram-positive organism, Bacillus subtilis, has identified the essential RNases J1 and Y as crucial enzymes in RNA degradation. While RNase J1 is the first bacterial exoribonuclease with 5'-to-3' processivity, RNase Y is the founding member of a novel class of endoribonucleases. Both RNase J1 and RNase Y have a broad impact on the stability of B. subtilis mRNAs; a depletion of either enzyme affects more than 25% of all mRNAs. RNases J1 and Y as well as RNase J2, the polynucleotide phosphorylase PNPase, the RNA helicase CshA and the glycolytic enzymes enolase and phosphofructokinase have been proposed to form a complex, the RNA degradosome of B. subtilis. This review presents a model, based on recent published data, of RNA degradation in B. subtilis. Degradation is initiated by RNase Y-dependent endonucleolytic cleavage, followed by processive exoribonucleolysis of the generated fragments both in 3'-to-5' and in 5'-to-3' directions. The implications of these findings for pathogenic Gram-positive bacteria are also discussed.
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Affiliation(s)
- Martin Lehnik-Habrink
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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Kang SO, Wright JO, Tesorero RA, Lee H, Beall B, Cho KH. Thermoregulation of capsule production by Streptococcus pyogenes. PLoS One 2012; 7:e37367. [PMID: 22615992 PMCID: PMC3355187 DOI: 10.1371/journal.pone.0037367] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/20/2012] [Indexed: 11/18/2022] Open
Abstract
The capsule of Streptococcus pyogenes serves as an adhesin as well as an anti-phagocytic factor by binding to CD44 on keratinocytes of the pharyngeal mucosa and the skin, the main entry sites of the pathogen. We discovered that S. pyogenes HSC5 and MGAS315 strains are further thermoregulated for capsule production at a post-transcriptional level in addition to the transcriptional regulation by the CovRS two-component regulatory system. When the transcription of the hasABC capsular biosynthetic locus was de-repressed through mutation of the covRS system, the two strains, which have been used for pathogenesis studies in the laboratory, exhibited markedly increased capsule production at sub-body temperature. Employing transposon mutagenesis, we found that CvfA, a previously identified membrane-associated endoribonuclease, is required for the thermoregulation of capsule synthesis. The mutation of the cvfA gene conferred increased capsule production regardless of temperature. However, the amount of the capsule transcript was not changed by the mutation, indicating that a post-transcriptional regulator mediates between CvfA and thermoregulated capsule production. When we tested naturally occurring invasive mucoid strains, a high percentage (11/53, 21%) of the strains exhibited thermoregulated capsule production. As expected, the mucoid phenotype of these strains at sub-body temperature was due to mutations within the chromosomal covRS genes. Capsule thermoregulation that exhibits high capsule production at lower temperatures that occur on the skin or mucosal surface potentially confers better capability of adhesion and invasion when S. pyogenes penetrates the epithelial surface.
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Affiliation(s)
- Song Ok Kang
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
| | - Jordan O. Wright
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
| | - Rafael A. Tesorero
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
| | - Hyunwoo Lee
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois, United States of America
| | - Bernard Beall
- Streptococcus Laboratory, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kyu Hong Cho
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, Illinois, United States of America
- * E-mail:
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When ribonucleases come into play in pathogens: a survey of gram-positive bacteria. Int J Microbiol 2012; 2012:592196. [PMID: 22550495 PMCID: PMC3328962 DOI: 10.1155/2012/592196] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/27/2011] [Indexed: 11/20/2022] Open
Abstract
It is widely acknowledged that RNA stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. Bacterial ribonucleases acting alone or in concert with regulatory RNAs or RNA binding proteins are the mediators of the regulatory outcome on RNA stability. We will give a current update of what is known about ribonucleases in the model Gram-positive organism Bacillus subtilis and will describe their established roles in virulence in several Gram-positive pathogenic bacteria that are imposing major health concerns worldwide. Implications on bacterial evolution through stabilization/transfer of genetic material (phage or plasmid DNA) as a result of ribonucleases' functions will be covered. The role of ribonucleases in emergence of antibiotic resistance and new concepts in drug design will additionally be discussed.
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Fuchs TM, Eisenreich W, Heesemann J, Goebel W. Metabolic adaptation of human pathogenic and related nonpathogenic bacteria to extra- and intracellular habitats. FEMS Microbiol Rev 2012; 36:435-62. [DOI: 10.1111/j.1574-6976.2011.00301.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 07/21/2011] [Indexed: 01/02/2023] Open
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Eidem TM, Roux CM, Dunman PM. RNA decay: a novel therapeutic target in bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:443-54. [PMID: 22374855 DOI: 10.1002/wrna.1110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The need for novel antibiotics is greater now than perhaps any time since the pre-antibiotic era. Indeed, the recent collapse of most pharmaceutical antibacterial groups, combined with the emergence of hypervirulent and pan-antibiotic-resistant bacteria have, in effect, created a 'perfect storm' that has severely compromised infection treatment options and led to dramatic increases in the incidence and severity of bacterial infections. To put simply, it is imperative that we develop new classes of antibiotics for the therapeutic intervention of bacterial infections. In that regard, RNA degradation is an essential biological process that has not been exploited for antibiotic development. Herein we discuss the factors that govern bacterial RNA degradation, highlight members of this machinery that represent attractive antimicrobial drug development targets and describe the use of high-throughput screening as a means of developing antimicrobials that target these enzymes. Such agents would represent first-in-class antibiotics that would be less apt to inactivation by currently encountered enzymatic antibiotic-resistance determinants.
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Affiliation(s)
- Tess M Eidem
- Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE, USA
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50
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LiF Reduces MICs of Antibiotics against Clinical Isolates of Gram-Positive and Gram-Negative Bacteria. Int J Microbiol 2012; 2012:454065. [PMID: 22518143 PMCID: PMC3299231 DOI: 10.1155/2012/454065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/16/2011] [Indexed: 11/22/2022] Open
Abstract
Antibiotic resistance is an ever-growing problem yet the development of new antibiotics has slowed to a trickle, giving rise to the use of combination therapy to eradicate infections. The purpose of this study was to evaluate the combined inhibitory effect of lithium fluoride (LiF) and commonly used antimicrobials on the growth of the following bacteria: Enterococcus faecalis, Staphyloccoccus aureus, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, and Streptococcus pneumoniae. The in vitro activities of ceftazidime, sulfamethoxazole-trimethoprim, streptomycin, erythromycin, amoxicillin, and ciprofloxacin, doxycycline, alone or combined with LiF were performed by microdilution method. MICs were determined visually following 18–20 h of incubation at 37°C. We observed reduced MICs of antibiotics associated with LiF ranging from two-fold to sixteen-fold. The strongest decreases of MICs observed were for streptomycin and erythromycin associated with LiF against Acinetobacter baumannii and Streptococcus pneumoniae. An eight-fold reduction was recorded for streptomycin against S. pneumoniae whereas an eight-fold and a sixteen-fold reduction were obtained for erythromycin against A. baumannii and S. pneumoniae. This suggests that LiF exhibits a synergistic effect with a wide range of antibiotics and is indicative of its potential as an adjuvant in antibiotic therapy.
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