1
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Cory MB, Li A, Hurley CM, Carman PJ, Pumroy RA, Hostetler ZM, Perez RM, Venkatesh Y, Li X, Gupta K, Petersson EJ, Kohli RM. The LexA-RecA* structure reveals a cryptic lock-and-key mechanism for SOS activation. Nat Struct Mol Biol 2024:10.1038/s41594-024-01317-3. [PMID: 38755298 DOI: 10.1038/s41594-024-01317-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024]
Abstract
The bacterial SOS response plays a key role in adaptation to DNA damage, including genomic stress caused by antibiotics. SOS induction begins when activated RecA*, an oligomeric nucleoprotein filament that forms on single-stranded DNA, binds to and stimulates autoproteolysis of the repressor LexA. Here, we present the structure of the complete Escherichia coli SOS signal complex, constituting full-length LexA bound to RecA*. We uncover an extensive interface unexpectedly including the LexA DNA-binding domain, providing a new molecular rationale for ordered SOS gene induction. We further find that the interface involves three RecA subunits, with a single residue in the central engaged subunit acting as a molecular key, inserting into an allosteric binding pocket to induce LexA cleavage. Given the pro-mutagenic nature of SOS activation, our structural and mechanistic insights provide a foundation for developing new therapeutics to slow the evolution of antibiotic resistance.
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Affiliation(s)
- Michael B Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Christina M Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter J Carman
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruth A Pumroy
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ryann M Perez
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Xinning Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Plumet L, Morsli M, Ahmad-Mansour N, Clavijo-Coppens F, Berry L, Sotto A, Lavigne JP, Costechareyre D, Molle V. Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers. Viruses 2023; 15:2287. [PMID: 38140529 PMCID: PMC10747802 DOI: 10.3390/v15122287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
Staphylococcus sp. is the most common bacterial genus in infections related to diabetic foot ulcers (DFUs). The emergence of multidrug-resistant bacteria places a serious burden on public health systems. Phage therapy is an alternative treatment to antibiotics, overcoming the issue of antibiotic resistance. In this study, six phages (SAVM01 to SAVM06) were isolated from effluents and were used against a panel of staphylococcal clinical samples isolated from DFUs. A genomic analysis revealed that the phages belonged to the Herelleviridae family, with sequences similar to those of the Kayvirus genus. No lysogeny-associated genes, known virulence or drug resistance genes were identified in the phage genomes. The phages displayed a strong lytic and antibiofilm activity against DFU clinical isolates, as well as against opportunistic pathogenic coagulase-negative staphylococci. The results presented here suggest that these phages could be effective biocontrol agents against staphylococcal clinical isolates from DFUs.
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Affiliation(s)
- Lucile Plumet
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | - Madjid Morsli
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | - Nour Ahmad-Mansour
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
| | | | - Laurence Berry
- Laboratory of Pathogen and Host Immunity, CNRS UMR5294, University of Montpellier, 34095 Montpellier, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Department of Infectious Diseases, University of de Montpellier, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
| | | | - Virginie Molle
- VBIC, INSERM U1047, University of Montpellier, 34095 Montpellier, France; (L.P.); (N.A.-M.)
- VBIC, INSERM U1047, Department of Microbiology and Hospital Hygiene, University of Montpellier, CHU Nîmes, 30908 Nîmes, France; (M.M.); (J.-P.L.)
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3
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Zhou Y, Liao H, Pei L, Pu Y. Combatting persister cells: The daunting task in post-antibiotics era. CELL INSIGHT 2023; 2:100104. [PMID: 37304393 PMCID: PMC10250163 DOI: 10.1016/j.cellin.2023.100104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/25/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023]
Abstract
Over the years, much attention has been drawn to antibiotic resistance bacteria, but drug inefficacy caused by a subgroup of special phenotypic variants - persisters - has been largely neglected in both scientific and clinical field. Interestingly, this subgroup of phenotypic variants displayed their power of withstanding sufficient antibiotics exposure in a mechanism different from antibiotic resistance. In this review, we summarized the clinical importance of bacterial persisters, the evolutionary link between resistance, tolerance, and persistence, redundant mechanisms of persister formation as well as methods of studying persister cells. In the light of our recent findings of membrane-less organelle aggresome and its important roles in regulating bacterial dormancy depth, we propose an alternative approach for anti-persister therapy. That is, to force a persister into a deeper dormancy state to become a VBNC (viable but non-culturable) cell that is incapable of regrowth. We hope to provide the latest insights on persister studies and call upon more research interest into this field.
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Affiliation(s)
- Yidan Zhou
- Department of Clinical Laboratory, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Hebin Liao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Linsen Pei
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
| | - Yingying Pu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei- MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430079, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430079, China
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4
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Cory MB, Jones CM, Shaffer KD, Venkatesh Y, Giannakoulias S, Perez RM, Lougee MG, Hummingbird E, Pagar VV, Hurley CM, Li A, Mach RH, Kohli RM, Petersson EJ. FRETing about the details: Case studies in the use of a genetically encoded fluorescent amino acid for distance-dependent energy transfer. Protein Sci 2023; 32:e4633. [PMID: 36974585 PMCID: PMC10108435 DOI: 10.1002/pro.4633] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Förster resonance energy transfer (FRET) is a valuable method for monitoring protein conformation and biomolecular interactions. Intrinsically fluorescent amino acids that can be genetically encoded, such as acridonylalanine (Acd), are particularly useful for FRET studies. However, quantitative interpretation of FRET data to derive distance information requires careful use of controls and consideration of photophysical effects. Here we present two case studies illustrating how Acd can be used in FRET experiments to study small molecule induced conformational changes and multicomponent biomolecular complexes.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Chloe M. Jones
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Kyle D. Shaffer
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Yarra Venkatesh
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Sam Giannakoulias
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Ryann M. Perez
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Marshall G. Lougee
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Eshe Hummingbird
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Vinayak V. Pagar
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Christina M. Hurley
- Graduate Group in Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Allen Li
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Robert H. Mach
- Department of RadiologyPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - Rahul M. Kohli
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of MedicinePerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
| | - E. James Petersson
- Department of ChemistrySchool of Arts and Sciences, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
- Department of Biochemistry and BiophysicsPerelman School of Medicine, University of PennsylvaniaPhiladelphiaPennsylvania19104USA
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5
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Moreau PL. Regulation of phosphate starvation-specific responses in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972330 DOI: 10.1099/mic.0.001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Toxic agents added into the medium of rapidly growing Escherichia coli induce specific stress responses through the activation of specialized transcription factors. Each transcription factor and downstream regulon (e.g. SoxR) are linked to a unique stress (e.g. superoxide stress). Cells starved of phosphate induce several specific stress regulons during the transition to stationary phase when the growth rate is steadily declining. Whereas the regulatory cascades leading to the expression of specific stress regulons are well known in rapidly growing cells stressed by toxic products, they are poorly understood in cells starved of phosphate. The intent of this review is to both describe the unique mechanisms of activation of specialized transcription factors and discuss signalling cascades leading to the induction of specific stress regulons in phosphate-starved cells. Finally, I discuss unique defence mechanisms that could be induced in cells starved of ammonium and glucose.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire Chimie Bactérienne, LCB-UMR 7283, Institut Microbiologie Méditerranée, CNRS/Université Aix-Marseille, Marseille, France
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6
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Schuurs ZP, McDonald JP, Croft LV, Richard DJ, Woodgate R, Gandhi NS. Integration of molecular modelling and in vitro studies to inhibit LexA proteolysis. Front Cell Infect Microbiol 2023; 13:1051602. [PMID: 36936756 PMCID: PMC10020695 DOI: 10.3389/fcimb.2023.1051602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction As antibiotic resistance has become more prevalent, the social and economic impacts are increasingly pressing. Indeed, bacteria have developed the SOS response which facilitates the evolution of resistance under genotoxic stress. The transcriptional repressor, LexA, plays a key role in this response. Mutation of LexA to a non-cleavable form that prevents the induction of the SOS response sensitizes bacteria to antibiotics. Achieving the same inhibition of proteolysis with small molecules also increases antibiotic susceptibility and reduces drug resistance acquisition. The availability of multiple LexA crystal structures, and the unique Ser-119 and Lys-156 catalytic dyad in the protein enables the rational design of inhibitors. Methods We pursued a binary approach to inhibit proteolysis; we first investigated β-turn mimetics, and in the second approach we tested covalent warheads targeting the Ser-119 residue. We found that the cleavage site region (CSR) of the LexA protein is a classical Type II β-turn, and that published 1,2,3-triazole compounds mimic the β-turn. Generic covalent molecule libraries and a β-turn mimetic library were docked to the LexA C-terminal domain using molecular modelling methods in FlexX and CovDock respectively. The 133 highest-scoring molecules were screened for their ability to inhibit LexA cleavage under alkaline conditions. The top molecules were then tested using a RecA-mediated cleavage assay. Results The β-turn library screen did not produce any hit compounds that inhibited RecA-mediated cleavage. The covalent screen discovered an electrophilic serine warhead that can inhibit LexA proteolysis, reacting with Ser-119 via a nitrile moiety. Discussion This research presents a starting point for hit-to-lead optimisation, which could lead to inhibition of the SOS response and prevent the acquisition of antibiotic resistance.
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Affiliation(s)
- Zachariah P. Schuurs
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - John P. McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Laura V. Croft
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
| | - Derek J. Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Neha S. Gandhi, ; Roger Woodgate,
| | - Neha S. Gandhi
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology (QUT), Translational Research Institute (TRI), Brisbane, QLD, Australia
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD, Australia
- *Correspondence: Neha S. Gandhi, ; Roger Woodgate,
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7
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Cory MB, Li A, Hurley CM, Hostetler ZM, Venkatesh Y, Jones CM, Petersson EJ, Kohli RM. Engineered RecA Constructs Reveal the Minimal SOS Activation Complex. Biochemistry 2022; 61:2884-2896. [PMID: 36473084 PMCID: PMC9982712 DOI: 10.1021/acs.biochem.2c00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The SOS response is a bacterial DNA damage response pathway that has been heavily implicated in bacteria's ability to evolve resistance to antibiotics. Activation of the SOS response is dependent on the interaction between two bacterial proteins, RecA and LexA. RecA acts as a DNA damage sensor by forming lengthy oligomeric filaments (RecA*) along single-stranded DNA (ssDNA) in an ATP-dependent manner. RecA* can then bind to LexA, the repressor of SOS response genes, triggering LexA degradation and leading to induction of the SOS response. Formation of the RecA*-LexA complex therefore serves as the key "SOS activation signal." Given the challenges associated with studying a complex involving multiple macromolecular interactions, the essential constituents of RecA* that allow LexA cleavage are not well defined. Here, we leverage head-to-tail linked and end-capped RecA constructs as tools to define the minimal RecA* filament that can engage LexA. In contrast to previously postulated models, we found that as few as three linked RecA units are capable of ssDNA binding, LexA binding, and LexA cleavage. We further demonstrate that RecA oligomerization alone is insufficient for LexA cleavage, with an obligate requirement for ATP and ssDNA binding to form a competent SOS activation signal with the linked constructs. Our minimal system for RecA* highlights the limitations of prior models for the SOS activation signal and offers a novel tool that can inform efforts to slow acquired antibiotic resistance by targeting the SOS response.
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Affiliation(s)
- Michael B. Cory
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Allen Li
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Christina M. Hurley
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yarra Venkatesh
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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8
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Chen E, Culyba MJ. Pulling the wool over a pathogen's eyes: Llama nanobody inhibitors of the bacterial SOS response. Structure 2022; 30:1467-1469. [PMID: 36332609 DOI: 10.1016/j.str.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this issue of Structure, Maso et al. (2022) discover nanobodies that inhibit the SOS response of Escherichia coli by targeting the LexA repressor-protease. High-resolution structures of the novel LexA-nanobody complexes reveal they function by stabilizing LexA in its inactive conformation and preventing co-proteolysis by RecA∗.
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Affiliation(s)
- Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew J Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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9
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Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway. Structure 2022; 30:1479-1493.e9. [DOI: 10.1016/j.str.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/29/2022] [Accepted: 09/18/2022] [Indexed: 11/05/2022]
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10
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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11
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The DdrR Coregulator of the Acinetobacter baumannii Mutagenic DNA Damage Response Potentiates UmuDAb Repression of Error-Prone Polymerases. J Bacteriol 2022; 204:e0016522. [PMID: 36194009 PMCID: PMC9664961 DOI: 10.1128/jb.00165-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii
is a nosocomial pathogen that acquires antibiotic resistance genes through conjugative transfer and carries out a robust mutagenic DNA damage response. After exposure to conditions typically encountered in health care settings, such as antibiotics, UV light, and desiccation, this species induces error-prone UmuD′
2
C polymerases.
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12
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Locking down SOS Mutagenesis Repression in a Dynamic Pathogen. J Bacteriol 2022; 204:e0022022. [PMID: 36194008 PMCID: PMC9664947 DOI: 10.1128/jb.00220-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The article "The DdrR coregulator of the Acinetobacter baumannii mutagenic DNA damage response potentiates UmuDAb repression of error-prone polymerases" in this issue of the J Bacteriol, (D. Cook, M. D. Flannigan, B. V. Candra, K. D. Compton, and J. M. Hare., J Bacteriol 204:e00165-22, 2022, https://doi.org/10.1128/jb.00165-22) reveals a more detailed understanding of the regulatory mechanism of the SOS response in Acinetobacter baumannii. This information provides novel targets for development of antimicrobial therapies against this ESKAPE pathogen and new insight into the complex regulation of the SOS stress-response.
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13
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Jaramillo AVC, Cory MB, Li A, Kohli RM, Wuest WM. Exploration of inhibitors of the bacterial LexA repressor-protease. Bioorg Med Chem Lett 2022; 65:128702. [PMID: 35351585 DOI: 10.1016/j.bmcl.2022.128702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022]
Abstract
Resistant and tolerant bacterial infections lead to billions in healthcare costs and cause hundreds of thousands of deaths each year. The bulk of current antibiotic research efforts focus on molecules which, although novel, are not immune from acquired resistance and seldomly affect tolerant populations. The bacterial SOS response has been implicated in several resistance and tolerance mechanisms, making it an attractive antibiotic target. Using small molecule inhibitors targeting a key step in the deployment of the SOS response, our approach focused on preventing the deployment of mechanisms such as biofilm formation, horizontal gene transfer, and error-prone DNA repair. Herein we report the synthesis and testing of analogs of a triazole-containing tricyclic inhibitor of LexA proteolysis, the key event in the SOS response. Our results hint that our inhibitor's may function by adopting a β-hairpin conformation, reminiscent of the native cleavage loop of LexA.
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Affiliation(s)
| | - Michael B Cory
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - William M Wuest
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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14
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Fagerlund A, Aspholm M, Węgrzyn G, Lindbäck T. High diversity in the regulatory region of Shiga toxin encoding bacteriophages. BMC Genomics 2022; 23:230. [PMID: 35331132 PMCID: PMC8951638 DOI: 10.1186/s12864-022-08428-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Background Enterohemorrhagic Escherichia coli (EHEC) is an emerging health challenge worldwide and outbreaks caused by this pathogen poses a serious public health concern. Shiga toxin (Stx) is the major virulence factor of EHEC, and the stx genes are carried by temperate bacteriophages (Stx phages). The switch between lysogenic and lytic life cycle of the phage, which is crucial for Stx production and for severity of the disease, is regulated by the CI repressor which maintain latency by preventing transcription of the replication proteins. Three EHEC phage replication units (Eru1-3) in addition to the classical lambdoid replication region have been described previously, and Stx phages carrying the Eru1 replication region were associated with highly virulent EHEC strains. Results In this study, we have classified the Eru replication region of 419 Stx phages. In addition to the lambdoid replication region and three already described Erus, ten novel Erus (Eru4 to Eru13) were detected. The lambdoid type, Eru1, Eru4 and Eru7 are widely distributed in Western Europe. Notably, EHEC strains involved in severe outbreaks in England and Norway carry Stx phages with Eru1, Eru2, Eru5 and Eru7 replication regions. Phylogenetic analysis of CI repressors from Stx phages revealed eight major clades that largely separate according to Eru type. Conclusion The classification of replication regions and CI proteins of Stx phages provides an important platform for further studies aimed to assess how characteristics of the replication region influence the regulation of phage life cycle and, consequently, the virulence potential of the host EHEC strain. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08428-5.
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Affiliation(s)
- Annette Fagerlund
- Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Marina Aspholm
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdañsk, Gdañsk, Poland
| | - Toril Lindbäck
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway.
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15
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The small DdrR protein directly interacts with the UmuDAb regulator of the mutagenic DNA damage response in Acinetobacter baumannii. J Bacteriol 2022; 204:e0060121. [PMID: 35191762 DOI: 10.1128/jb.00601-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii poses a great threat in healthcare settings worldwide with clinical isolates displaying an ever-evolving multidrug-resistance. In strains of A. baumannii, expression of multiple error-prone polymerase genes is co-repressed by UmuDAb, a member of the LexA superfamily, and a small protein, DdrR. It is currently unknown how DdrR establishes this repression. Here, we use surface plasmon resonance spectrometry to show that DdrR forms a stable complex with the UmuDAb regulator. Our results indicate that the carboxy-terminal dimerization domain of UmuDAb forms the interaction interface with DdrR. Our in vitro data also show that RecA-mediated inactivation of UmuDAb is inhibited when this transcription factor is bound to its target DNA. In addition, we show that DdrR interacts with a putative prophage repressor, homologous to LexA superfamily proteins. These data suggest that DdrR modulates DNA damage response and prophage induction in A. baumannii by binding to LexA-like regulators. Importance We previously identified a 50-residue bacteriophage protein, gp7, which interacts with and modulates the function of the LexA transcription factor from Bacillus thuringiensis. Here we present data that indicates that the small DdrR protein from A. baumannii likely coordinates the SOS response and prophage processes by also interacting with LexA superfamily members. We suggest that similar small proteins that interact with LexA-like proteins to coordinate DNA repair and bacteriophage functions may be common to many bacteria that mount the SOS response.
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16
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Hu J, Ye H, Wang S, Wang J, Han D. Prophage Activation in the Intestine: Insights Into Functions and Possible Applications. Front Microbiol 2021; 12:785634. [PMID: 34966370 PMCID: PMC8710666 DOI: 10.3389/fmicb.2021.785634] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/25/2021] [Indexed: 01/20/2023] Open
Abstract
Prophage activation in intestinal environments has been frequently reported to affect host adaptability, pathogen virulence, gut bacterial community composition, and intestinal health. Prophage activation is mostly caused by various stimulators, such as diet, antibiotics, some bacterial metabolites, gastrointestinal transit, inflammatory environment, oxidative stress, and quorum sensing. Moreover, with advancements in biotechnology and the deepening cognition of prophages, prophage activation regulation therapy is currently applied to the treatment of some bacterial intestinal diseases such as Shiga toxin-producing Escherichia coli infection. This review aims to make headway on prophage induction in the intestine, in order to make a better understanding of dynamic changes of prophages, effects of prophage activation on physiological characteristics of bacteria and intestinal health, and subsequently provide guidance on prophage activation regulation therapy.
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Affiliation(s)
| | | | | | | | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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17
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Diaz-Diaz S, Recacha E, García-Duque A, Docobo-Pérez F, Blázquez J, Pascual A, Rodríguez-Martínez JM. Effect of RecA inactivation and detoxification systems on the evolution of ciprofloxacin resistance in Escherichia coli. J Antimicrob Chemother 2021; 77:641-645. [PMID: 34878138 PMCID: PMC8864997 DOI: 10.1093/jac/dkab445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
Background Suppression of SOS response and overproduction of reactive oxygen species (ROS) through detoxification system suppression enhance the activity of fluoroquinolones. Objectives To evaluate the role of both systems in the evolution of resistance to ciprofloxacin in an isogenic model of Escherichia coli. Methods Single-gene deletion mutants of E. coli BW25113 (wild-type) (ΔrecA, ΔkatG, ΔkatE, ΔsodA, ΔsodB), double-gene (ΔrecA-ΔkatG, ΔrecA-ΔkatE, ΔrecA-ΔsodA, ΔrecA-ΔsodB, ΔkatG-ΔkatE, ΔsodB-ΔsodA) and triple-gene (ΔrecA-ΔkatG-ΔkatE) mutants were included. The response to sudden high ciprofloxacin pressure was evaluated by mutant prevention concentration (MPC). The gradual antimicrobial pressure response was evaluated through experimental evolution and antibiotic resistance assays. Results For E. coli BW25113 strain, ΔkatE, ΔsodB and ΔsodB/ΔsodA mutants, MPC values were 0.25 mg/L. The ΔkatG, ΔsodA, ΔkatG/katE and ΔrecA mutants showed 2-fold reductions (0.125 mg/L). The ΔkatG/ΔrecA, ΔkatE/ΔrecA, ΔsodA/ΔrecA, ΔsodB/ΔrecA and ΔkatG/ΔkatE/ΔrecA strains showed 4–8-fold reductions (0.03–0.06 mg/L) relative to the wild-type. Gradual antimicrobial pressure increased growth capacity for ΔsodA and ΔsodB and ΔsodB/ΔsodA mutants (no growth in 4 mg/L) compared with the wild-type (no growth in the range of 0.5–2 mg/L). Accordingly, increased growth was observed with the mutants ΔrecA/ΔkatG (no growth in 2 mg/L), ΔrecA/ΔkatE (no growth in 2 mg/L), ΔrecA/ΔsodA (no growth in 0.06 mg/L), ΔrecA/ΔsodB (no growth in 0.25 mg/L) and ΔrecA/ΔkatG/ΔkatE (no growth in 0.5 mg/L) compared with ΔrecA (no growth in the range of 0.002–0.015 mg/L). Conclusions After RecA inactivation, gradual exposure to ciprofloxacin reduces the evolution of resistance. After suppression of RecA and detoxification systems, sudden high exposure to ciprofloxacin reduces the evolution of resistance in E. coli.
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Affiliation(s)
- S Diaz-Diaz
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - E Recacha
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - A García-Duque
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - F Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - J Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - A Pascual
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - J M Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Sevilla, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
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18
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Sánchez-Osuna M, Cortés P, Lee M, Smith AT, Barbé J, Erill I. Non-canonical LexA proteins regulate the SOS response in the Bacteroidetes. Nucleic Acids Res 2021; 49:11050-11066. [PMID: 34614190 PMCID: PMC8565304 DOI: 10.1093/nar/gkab773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/18/2021] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Lesions to DNA compromise chromosome integrity, posing a direct threat to cell survival. The bacterial SOS response is a widespread transcriptional regulatory mechanism to address DNA damage. This response is coordinated by the LexA transcriptional repressor, which controls genes involved in DNA repair, mutagenesis and cell-cycle control. To date, the SOS response has been characterized in most major bacterial groups, with the notable exception of the Bacteroidetes. No LexA homologs had been identified in this large, diverse and ecologically important phylum, suggesting that it lacked an inducible mechanism to address DNA damage. Here, we report the identification of a novel family of transcriptional repressors in the Bacteroidetes that orchestrate a canonical response to DNA damage in this phylum. These proteins belong to the S24 peptidase family, but are structurally different from LexA. Their N-terminal domain is most closely related to CI-type bacteriophage repressors, suggesting that they may have originated from phage lytic phase repressors. Given their role as SOS regulators, however, we propose to designate them as non-canonical LexA proteins. The identification of a new class of repressors orchestrating the SOS response illuminates long-standing questions regarding the origin and plasticity of this transcriptional network.
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Affiliation(s)
- Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Mark Lee
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Jordi Barbé
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain
| | - Ivan Erill
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08192 Bellaterra, Spain.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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19
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Giannakoulias S, Shringari SR, Ferrie JJ, Petersson EJ. Biomolecular simulation based machine learning models accurately predict sites of tolerability to the unnatural amino acid acridonylalanine. Sci Rep 2021; 11:18406. [PMID: 34526629 PMCID: PMC8443755 DOI: 10.1038/s41598-021-97965-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/17/2021] [Indexed: 11/08/2022] Open
Abstract
The incorporation of unnatural amino acids (Uaas) has provided an avenue for novel chemistries to be explored in biological systems. However, the successful application of Uaas is often hampered by site-specific impacts on protein yield and solubility. Although previous efforts to identify features which accurately capture these site-specific effects have been unsuccessful, we have developed a set of novel Rosetta Custom Score Functions and alternative Empirical Score Functions that accurately predict the effects of acridon-2-yl-alanine (Acd) incorporation on protein yield and solubility. Acd-containing mutants were simulated in PyRosetta, and machine learning (ML) was performed using either the decomposed values of the Rosetta energy function, or changes in residue contacts and bioinformatics. Using these feature sets, which represent Rosetta score function specific and bioinformatics-derived terms, ML models were trained to predict highly abstract experimental parameters such as mutant protein yield and solubility and displayed robust performance on well-balanced holdouts. Model feature importance analyses demonstrated that terms corresponding to hydrophobic interactions, desolvation, and amino acid angle preferences played a pivotal role in predicting tolerance of mutation to Acd. Overall, this work provides evidence that the application of ML to features extracted from simulated structural models allow for the accurate prediction of diverse and abstract biological phenomena, beyond the predictivity of traditional modeling and simulation approaches.
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Affiliation(s)
- Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA
| | - Sumant R Shringari
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA
| | - John J Ferrie
- Department of Molecular & Cell Biology, University of California, Berkeley, 475B Li Ka Shing Center, Berkeley, CA, 94720, USA.
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St, Philadelphia, PA, 19104, USA.
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20
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Kiran K, Patil KN. Expression and Characterization of the Staphylococcus aureus RecA protein: A mapping of canonical functions. Protein Expr Purif 2021; 189:105967. [PMID: 34481085 DOI: 10.1016/j.pep.2021.105967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/27/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022]
Abstract
Recombinases are responsible for homologous recombination (HR), proper genome maintenance, and accurate deoxyribonucleic acid (DNA) duplication. Moreover, HR plays a determining role in DNA transaction processes such as DNA replication, repair, recombination, and transcription. Staphylococcus aureus, an opportunistic pathogen, usually causes respiratory infections such as sinusitis, skin infections, and food poisoning. To date, the role of the RecA gene product in S. aureus remains obscure. In this study, we attempted to map the functional properties of the RecA protein. S. aureus expresses the recA gene product in vivo upon exposure to the DNA-damaging agents, ultraviolet radiation, and methyl methanesulfonate. The recombinant purified S. aureus RecA protein displayed strong single-stranded DNA affinity compared to feeble binding to double-stranded DNA. Interestingly, the RecA protein is capable of invasion and formed displacement loops and readily performed strand-exchange activities with an oligonucleotide-based substrate. Notably, the S. aureus RecA protein hydrolyzed the DNA-dependent adenosine triphosphate and cleaved LexA, showing the conserved function of coprotease. This study provides the functional characterization of the S. aureus RecA protein and sheds light on the canonical processes of homologous recombination, which are conserved in the gram-positive foodborne pathogen S. aureus.
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Affiliation(s)
- Kajal Kiran
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - K Neelakanteshwar Patil
- Department of Protein Chemistry and Technology, Council of Scientific & Industrial Research-Central Food Technological Research Institute (CSIR-CFTRI), Mysuru, 570 020, Karnataka, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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21
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Brady A, Felipe-Ruiz A, Gallego Del Sol F, Marina A, Quiles-Puchalt N, Penadés JR. Molecular Basis of Lysis-Lysogeny Decisions in Gram-Positive Phages. Annu Rev Microbiol 2021; 75:563-581. [PMID: 34343015 DOI: 10.1146/annurev-micro-033121-020757] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Temperate bacteriophages (phages) are viruses of bacteria. Upon infection of a susceptible host, a temperate phage can establish either a lytic cycle that kills the host or a lysogenic cycle as a stable prophage. The life cycle pursued by an infecting temperate phage can have a significant impact not only on the individual host bacterium at the cellular level but also on bacterial communities and evolution in the ecosystem. Thus, understanding the decision processes of temperate phages is crucial. This review delves into the molecular mechanisms behind lysis-lysogeny decision-making in Gram-positive phages. We discuss a variety of molecular mechanisms and the genetic organization of these well-understood systems. By elucidating the strategies used by phages to make lysis-lysogeny decisions, we can improve our understanding of phage-host interactions, which is crucial for a variety of studies including bacterial evolution, community and ecosystem diversification, and phage therapeutics. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Aisling Brady
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - Alonso Felipe-Ruiz
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Alberto Marina
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain;
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom;
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom; .,MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom;
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22
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Targeting the bacterial SOS response for new antimicrobial agents: drug targets, molecular mechanisms and inhibitors. Future Med Chem 2021; 13:143-155. [PMID: 33410707 DOI: 10.4155/fmc-2020-0310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is a pressing threat to global health, with multidrug-resistant pathogens becoming increasingly prevalent. The bacterial SOS pathway functions in response to DNA damage that occurs during infection, initiating several pro-survival and resistance mechanisms, such as DNA repair and hypermutation. This makes SOS pathway components potential targets that may combat drug-resistant pathogens and decrease resistance emergence. This review discusses the mechanism of the SOS pathway; the structure and function of potential targets AddAB, RecBCD, RecA and LexA; and efforts to develop selective small-molecule inhibitors of these proteins. These inhibitors may serve as valuable tools for target validation and provide the foundations for desperately needed novel antibacterial therapeutics.
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23
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Takashima K, Nagao S, Kizawa A, Suzuki T, Dohmae N, Hihara Y. The role of transcriptional repressor activity of LexA in salt-stress responses of the cyanobacterium Synechocystis sp. PCC 6803. Sci Rep 2020; 10:17393. [PMID: 33060671 PMCID: PMC7567884 DOI: 10.1038/s41598-020-74534-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Different from typical LexA repressors in heterotrophic bacteria exerting SOS response by auto-cleavage, cyanobacterial LexAs, especially that of Synechocystis sp. PCC 6803 (S.6803), have been suggested be involved in regulation of a number of genes related to various cellular processes, rather than the typical SOS regulon. When and how cyanobacterial LexAs are triggered to regulate its target genes have remained unknown. In this study, we found the profound repressing effect of LexA on salt-stress inducible genes in S.6803. The repressing activity of LexA was likely to persist during salt stress and the salt response of these genes was mainly achieved by other regulators than LexA, suggesting that the physiological role of LexA is fine-tuning of gene expression in response to environmental changes. Although the amount and oligomeric state of LexA were unchanged upon salt stress, two-dimensional electrophoresis and liquid chromatography-tandem mass spectrometry analyses detected a change in posttranslational modification in a small fraction of LexA molecules, possibly dephosphorylation of Ser173, after 30 min upon the upshift in salt concentration. Activity of LexA in S.6803 may be under gradual control by posttranslational modification to fine-tune gene expression, which is contrasted with the digital switching-off regulation by auto-cleavage in heterotrophic bacteria.
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Affiliation(s)
- Kosuke Takashima
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570, Japan
| | - Syota Nagao
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570, Japan
| | - Ayumi Kizawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570, Japan.,Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Saitama, 338-8570, Japan.
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24
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Memar MY, Yekani M, Celenza G, Poortahmasebi V, Naghili B, Bellio P, Baghi HB. The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy. Life Sci 2020; 262:118562. [PMID: 33038378 DOI: 10.1016/j.lfs.2020.118562] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023]
Abstract
Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.
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Affiliation(s)
- Mohammad Yousef Memar
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran; Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Vahdat Poortahmasebi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrooz Naghili
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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25
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Klimova AN, Sandler SJ. An Epistasis Analysis of recA and recN in Escherichia coli K-12. Genetics 2020; 216:381-393. [PMID: 32816866 PMCID: PMC7536844 DOI: 10.1534/genetics.120.303476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
RecA is essential for double-strand-break repair (DSBR) and the SOS response in Escherichia coli K-12. RecN is an SOS protein and a member of the Structural Maintenance of Chromosomes family of proteins thought to play a role in sister chromatid cohesion/interactions during DSBR. Previous studies have shown that a plasmid-encoded recA4190 (Q300R) mutant had a phenotype similar to ∆recN (mitomycin C sensitive and UV resistant). It was hypothesized that RecN and RecA physically interact, and that recA4190 specifically eliminated this interaction. To test this model, an epistasis analysis between recA4190 and ∆recN was performed in wild-type and recBC sbcBC cells. To do this, recA4190 was first transferred to the chromosome. As single mutants, recA4190 and ∆recN were Rec+ as measured by transductional recombination, but were 3-fold and 10-fold decreased in their ability to do I-SceI-induced DSBR, respectively. In both cases, the double mutant had an additive phenotype relative to either single mutant. In the recBC sbcBC background, recA4190 and ∆recN cells were very UVS (sensitive), Rec-, had high basal levels of SOS expression and an altered distribution of RecA-GFP structures. In all cases, the double mutant had additive phenotypes. These data suggest that recA4190 (Q300R) and ∆recN remove functions in genetically distinct pathways important for DNA repair, and that RecA Q300 was not important for an interaction between RecN and RecA in vivorecA4190 (Q300R) revealed modest phenotypes in a wild-type background and dramatic phenotypes in a recBC sbcBC strain, reflecting greater stringency of RecA's role in that background.
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Affiliation(s)
- Anastasiia N Klimova
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Massachusetts 01003
| | - Steven J Sandler
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Massachusetts 01003
- Department of Microbiology, University of Massachusetts Amherst, Massachusetts 01003
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26
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Myka KK, Marians KJ. Two components of DNA replication-dependent LexA cleavage. J Biol Chem 2020; 295:10368-10379. [PMID: 32513870 PMCID: PMC7383369 DOI: 10.1074/jbc.ra120.014224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/04/2020] [Indexed: 12/19/2022] Open
Abstract
Induction of the SOS response, a cellular system triggered by DNA damage in bacteria, depends on DNA replication for the generation of the SOS signal, ssDNA. RecA binds to ssDNA, forming filaments that stimulate proteolytic cleavage of the LexA transcriptional repressor, allowing expression of > 40 gene products involved in DNA repair and cell cycle regulation. Here, using a DNA replication system reconstituted in vitro in tandem with a LexA cleavage assay, we studied LexA cleavage during DNA replication of both undamaged and base-damaged templates. Only a ssDNA-RecA filament supported LexA cleavage. Surprisingly, replication of an undamaged template supported levels of LexA cleavage like that induced by a template carrying two site-specific cyclobutane pyrimidine dimers. We found that two processes generate ssDNA that could support LexA cleavage. 1) During unperturbed replication, single-stranded regions formed because of stochastic uncoupling of the leading-strand DNA polymerase from the replication fork DNA helicase, and 2) on the damaged template, nascent leading-strand gaps were generated by replisome lesion skipping. The two pathways differed in that RecF stimulated LexA cleavage during replication of the damaged template, but not normal replication. RecF appears to facilitate RecA filament formation on the leading-strand ssDNA gaps generated by replisome lesion skipping.
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Affiliation(s)
- Kamila K Myka
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
| | - Kenneth J Marians
- Molecular Biology Program, Sloan Kettering Institute Memorial Sloan Kettering Cancer Center, New York, New York USA
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27
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Merrikh H, Kohli RM. Targeting evolution to inhibit antibiotic resistance. FEBS J 2020; 287:4341-4353. [PMID: 32434280 DOI: 10.1111/febs.15370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/21/2022]
Abstract
Drug-resistant bacterial infections have led to a global health crisis. Although much effort is placed on the development of new antibiotics or variants that are less subject to existing resistance mechanisms, history shows that this strategy by itself is unlikely to solve the problem of drug resistance. Here, we discuss inhibiting evolution as a strategy that, in combination with antibiotics, may resolve the problem. Although mutagenesis is the main driver of drug resistance development, attacking the drivers of genetic diversification in pathogens has not been well explored. Bacteria possess active mechanisms that increase the rate of mutagenesis, especially at times of stress, such as during replication within eukaryotic host cells, or exposure to antibiotics. We highlight how the existence of these promutagenic proteins (evolvability factors) presents an opportunity that can be capitalized upon for the effective inhibition of drug resistance development. To help move this idea from concept to execution, we first describe a set of criteria that an 'optimal' evolvability factor would likely have to meet to be a viable therapeutic target. We then discuss the intricacies of some of the known mutagenic mechanisms and evaluate their potential as drug targets to inhibit evolution. In principle, and as suggested by recent studies, we argue that the inhibition of these and other evolvability factors should reduce resistance development. Finally, we discuss the challenges of transitioning anti-evolution drugs from the laboratory to the clinic.
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Affiliation(s)
- Houra Merrikh
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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28
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Hostetler ZM, Cory MB, Jones CM, Petersson EJ, Kohli RM. The Kinetic and Molecular Basis for the Interaction of LexA and Activated RecA Revealed by a Fluorescent Amino Acid Probe. ACS Chem Biol 2020; 15:1127-1133. [PMID: 31999086 DOI: 10.1021/acschembio.9b00886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The bacterial DNA damage response (the SOS response) is a key pathway involved in antibiotic evasion and a promising target for combating acquired antibiotic resistance. Activation of the SOS response is controlled by two proteins: the repressor LexA and the DNA damage sensor RecA. Following DNA damage, direct interaction between RecA and LexA leads to derepression of the SOS response. However, the exact molecular details of this interaction remain unknown. Here, we employ the fluorescent unnatural amino acid acridonylalanine (Acd) as a minimally perturbing probe of the E. coli RecA:LexA complex. Using LexA labeled with Acd, we report the first kinetic model for the reversible binding of LexA to activated RecA. We also characterize the effects that specific amino acid truncations or substitutions in LexA have on RecA:LexA binding strength and demonstrate that a mobile loop encoding LexA residues 75-84 comprises a key recognition interface for RecA. Beyond insights into SOS activation, our approach also further establishes Acd as a sensitive fluorescent probe for investigating the dynamics of protein-protein interactions in other complex systems.
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Affiliation(s)
- Zachary M. Hostetler
- Graduate Group in Cell and Molecular Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael B. Cory
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chloe M. Jones
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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29
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Marx P, Sang Y, Qin H, Wang Q, Guo R, Pfeifer C, Kreth J, Merritt J. Environmental stress perception activates structural remodeling of extant Streptococcus mutans biofilms. NPJ Biofilms Microbiomes 2020; 6:17. [PMID: 32221309 PMCID: PMC7101444 DOI: 10.1038/s41522-020-0128-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/12/2020] [Indexed: 01/28/2023] Open
Abstract
Transcription regulators from the LexA-like Protein Superfamily control a highly diverse assortment of genetic pathways in response to environmental stress. All characterized members of this family modulate their functionality and stability via a strict coordination with the coprotease function of RecA. Using the LexA-like protein IrvR from Streptococcus mutans, we demonstrate an exception to the RecA paradigm and illustrate how this evolutionary innovation has been coopted to diversify the stress responsiveness of S. mutans biofilms. Using a combination of genetics and biophysical measurements, we demonstrate how non-SOS stresses and SOS stresses each trigger separate regulatory mechanisms that stimulate production of a surface lectin responsible for remodeling the viscoelastic properties of extant biofilms during episodes of environmental stress. These studies demonstrate how changes in the external environment or even anti-biofilm therapeutic agents can activate biofilm-specific adaptive mechanisms responsible for bolstering the integrity of established biofilm communities. Such changes in biofilm community structure are likely to play central roles in the notorious recalcitrance of biofilm infections.
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Affiliation(s)
- Patrick Marx
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Yu Sang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Hua Qin
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Qingjing Wang
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Rongkai Guo
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Carmem Pfeifer
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA
| | - Jens Kreth
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Justin Merritt
- 0000 0000 9758 5690grid.5288.7Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR 97239 USA ,0000 0000 9758 5690grid.5288.7Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
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30
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Jin H, Kim R, Bhaya D. Deciphering proteolysis pathways for the error-prone DNA polymerase in cyanobacteria. Environ Microbiol 2020; 23:559-571. [PMID: 31908125 DOI: 10.1111/1462-2920.14911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/18/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
Protein quality control pathways require AAA+ proteases, such as Clp and Lon. Lon protease maintains UmuD, an important component of the error-prone DNA repair polymerase (Pol V), at very low levels in E. coli. Most members of the phylum Cyanobacteria lack Lon (including the model cyanobacterium, Synechocystis sp. PCC6803), so maintenance of UmuD at low levels must employ different proteases. We demonstrate that the first 19 residues from the N-terminus of UmuD (Sug1-19 ) fused to a reporter protein are adequate to trigger complete proteolysis and that mutation of a single leucine residue (L6) to aspartic acid inhibits proteolysis. This process appears to follow the N-end rule and is mediated by ClpA/P protease and the ClpS adaptor. Additionally, mutations of arginine residues in the Sug1-19 tag suggest that the ClpX/P pathway also plays a role in proteolysis. We propose that there is a dual degron at the N-terminus of the UmuD protein in Synechocystis sp. PCC6803, which is distinct from the degron required for degradation of UmuD in E. coli. The use of two proteolysis pathways to tune levels of UmuD might reflect how a photosynthetic organism responds to multiple environmental stressors.
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Affiliation(s)
- Haojie Jin
- State Key Laboratory for Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Biology, Carnegie Institution for Science, Stanford, 94305, CA, USA
| | - Rick Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, 94305, CA, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, 94305, CA, USA
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31
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Torres R, Carrasco B, Gándara C, Baidya AK, Ben-Yehuda S, Alonso JC. Bacillus subtilis DisA regulates RecA-mediated DNA strand exchange. Nucleic Acids Res 2019; 47:5141-5154. [PMID: 30916351 PMCID: PMC6547438 DOI: 10.1093/nar/gkz219] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 01/12/2023] Open
Abstract
Bacillus subtilis diadenylate cyclase DisA converts two ATPs into c-di-AMP, but this activity is suppressed upon interaction with sites of DNA damage. DisA forms a rapid moving focus that pauses upon induction of DNA damage during spore development. We report that DisA pausing, however, was not observed in the absence of the RecO mediator or of the RecA recombinase, suggesting that DisA binds to recombination intermediates formed by RecA in concert with RecO. DisA, which physically interacts with RecA, was found to reduce its ATPase activity without competing for nucleotides or ssDNA. Furthermore, increasing DisA concentrations inhibit RecA-mediated DNA strand exchange, but this inhibition failed to occur when RecA was added prior to DisA, and was independent of RecA-mediated nucleotide hydrolysis or increasing concentrations of c-di-AMP. We propose that DisA may preserve genome integrity by downregulating RecA activities at several steps of the DNA damage tolerance pathway, allowing time for the repair machineries to restore genome stability. DisA might reduce RecA-mediated template switching by binding to a stalled or reversed fork.
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Affiliation(s)
- Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain
| | - Carolina Gándara
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain
| | - Amit K Baidya
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, POB 12272, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain
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32
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Bellio P, Mancini A, Di Pietro L, Cracchiolo S, Franceschini N, Reale S, de Angelis F, Perilli M, Amicosante G, Spyrakis F, Tondi D, Cendron L, Celenza G. Inhibition of the transcriptional repressor LexA: Withstanding drug resistance by inhibiting the bacterial mechanisms of adaptation to antimicrobials. Life Sci 2019; 241:117116. [PMID: 31790690 DOI: 10.1016/j.lfs.2019.117116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Abstract
AIMS LexA protein is a transcriptional repressor which regulates the expression of more than 60 genes belonging to the SOS global regulatory network activated by damages to bacterial DNA. Considering its role in bacteria, LexA represents a key target to counteract bacterial resistance: the possibility to modulate SOS response through the inhibition of LexA autoproteolysis may lead to reduced drug susceptibility and acquisition of resistance in bacteria. In our study we investigated boron-containing compounds as potential inhibitors of LexA self-cleavage. MAIN METHODS The inhibition of LexA self-cleavage was evaluated by following the variation of the first-order rate constant by LC-MS at several concentrations of inhibitors. In silico analysis was applied to predict the binding orientations assumed by the inhibitors in the protein active site, upon covalent binding to the catalytic Ser-119. Bacterial filamentation assay was used to confirm the ability of (3-aminophenyl)boronic acid to interfere with SOS induced activation. KEY FINDINGS Boron-containing compounds act as inhibitors of LexA self-cleavage, as also confirmed by molecular modelling where the compounds interact with the catalytic Ser-119, via the formation of an acyl-enzyme intermediate. A new equation for the description of the inhibition potency in an autoproteolytic enzyme is also disclosed. Bacterial filamentation assays strongly support the interference of our compounds with the SOS response activation through inhibition of septum formation. SIGNIFICANCE The obtained results demonstrated that phenylboronic compounds could be exploited in a hit-to-lead optimization process toward effective LexA self-cleavage inhibitors. They would sustain the rehabilitation in therapy of several dismissed antibiotics.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Alisia Mancini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Letizia Di Pietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Salvatore Cracchiolo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nicola Franceschini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Samantha Reale
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesco de Angelis
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Torino, Torino, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
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33
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Keyamura K, Hishida T. Topological DNA-binding of structural maintenance of chromosomes-like RecN promotes DNA double-strand break repair in Escherichia coli. Commun Biol 2019; 2:413. [PMID: 31754643 PMCID: PMC6856136 DOI: 10.1038/s42003-019-0655-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/16/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial RecN, closely related to the structural maintenance of chromosomes (SMC) family of proteins, functions in the repair of DNA double-strand breaks (DSBs) by homologous recombination. Here we show that the purified Escherichia coli RecN protein topologically loads onto both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) that has a preference for ssDNA. RecN topologically bound to dsDNA slides off the end of linear dsDNA, but this is prevented by RecA nucleoprotein filaments on ssDNA, thereby allowing RecN to translocate to DSBs. Furthermore, we found that, once RecN is recruited onto ssDNA, it can topologically capture a second dsDNA substrate in an ATP-dependent manner, suggesting a role in synapsis. Indeed, RecN stimulates RecA-mediated D-loop formation and subsequent strand exchange activities. Our findings provide mechanistic insights into the recruitment of RecN to DSBs and sister chromatid interactions by RecN, both of which function in RecA-mediated DSB repair.
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Affiliation(s)
- Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
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34
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Structural Insights into Bacteriophage GIL01 gp7 Inhibition of Host LexA Repressor. Structure 2019; 27:1094-1102.e4. [PMID: 31056420 DOI: 10.1016/j.str.2019.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 11/20/2022]
Abstract
Bacteria identify and respond to DNA damage using the SOS response. LexA, a central repressor in the response, has been implicated in the regulation of lysogeny in various temperate bacteriophages. During infection of Bacillus thuringiensis with GIL01 bacteriophage, LexA represses the SOS response and the phage lytic cycle by binding DNA, an interaction further stabilized upon binding of a viral protein, gp7. Here we report the crystallographic structure of phage-borne gp7 at 1.7-Å resolution, and characterize the 4:2 stoichiometry and potential interaction with LexA using surface plasmon resonance, static light scattering, and small-angle X-ray scattering. These data suggest that gp7 stabilizes LexA binding to operator DNA via coordination of the N- and C-terminal domains of LexA. Furthermore, we have found that gp7 can interact with LexA from Staphylococcus aureus, a significant human pathogen. Our results provide structural evidence as to how phage factors can directly associate with LexA to modulate the SOS response.
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35
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Maslowska KH, Makiela‐Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:368-384. [PMID: 30447030 PMCID: PMC6590174 DOI: 10.1002/em.22267] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Katarzyna H. Maslowska
- Cancer Research Center of Marseille, CNRS, UMR7258Inserm, U1068; Institut Paoli‐Calmettes, Aix‐Marseille UniversityMarseilleFrance
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | | | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
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36
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Prasad D, Muniyappa K. The Anionic Phospholipids in the Plasma Membrane Play an Important Role in Regulating the Biochemical Properties and Biological Functions of RecA Proteins. Biochemistry 2019; 58:1295-1310. [PMID: 30726069 DOI: 10.1021/acs.biochem.8b01147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli RecA (EcRecA) forms discrete foci that cluster at cell poles during normal growth, which are redistributed along the filamented cell axis upon induction of the SOS response. The plasma membrane is thought to act as a scaffold for EcRecA foci, thereby playing an important role in RecA-dependent homologous recombination. In addition, in vivo and in vitro studies demonstrate that EcRecA binds strongly to the anionic phospholipids. However, there have been almost no data on the association of mycobacterial RecA proteins with the plasma membrane and the effects of membrane components on their function. Here, we show that mycobacterial RecA proteins specifically interact with phosphatidylinositol and cardiolipin among other anionic phospholipids; however, they had no effect on the ability of RecA proteins to bind single-stranded DNA. Interestingly, phosphatidylinositol and cardiolipin impede the DNA-dependent ATPase activity of RecA proteins, although ATP binding is not affected. Furthermore, the ability of RecA proteins to promote DNA strand exchange is not affected by anionic phospholipids. Strikingly, anionic phospholipids suppress the RecA-stimulated autocatalytic cleavage of the LexA repressor. The Mycobacterium smegmatis RecA foci localize to the cell poles during normal growth, and these structures disassemble and reassemble into several foci along the cell after the induction of DNA damage. Taken together, these data support the notion that the interaction of RecA with cardiolipin and phosphatidylinositol, the major anionic phospholipids of the mycobacterial plasma membrane, may be physiologically relevant, as they provide a scaffold for RecA storage and may regulate recombinational DNA repair and the SOS response.
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Affiliation(s)
- Deepika Prasad
- Department of Biochemistry , Indian Institute of Science , Bengaluru 560012 , India
| | - K Muniyappa
- Department of Biochemistry , Indian Institute of Science , Bengaluru 560012 , India
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37
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Ghodke H, Paudel BP, Lewis JS, Jergic S, Gopal K, Romero ZJ, Wood EA, Woodgate R, Cox MM, van Oijen AM. Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response. eLife 2019; 8:42761. [PMID: 30717823 PMCID: PMC6363387 DOI: 10.7554/elife.42761] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/22/2019] [Indexed: 12/14/2022] Open
Abstract
The RecA protein orchestrates the cellular response to DNA damage via its multiple roles in the bacterial SOS response. Lack of tools that provide unambiguous access to the various RecA states within the cell have prevented understanding of the spatial and temporal changes in RecA structure/function that underlie control of the damage response. Here, we develop a monomeric C-terminal fragment of the λ repressor as a novel fluorescent probe that specifically interacts with RecA filaments on single-stranded DNA (RecA*). Single-molecule imaging techniques in live cells demonstrate that RecA is largely sequestered in storage structures during normal metabolism. Upon DNA damage, the storage structures dissolve and the cytosolic pool of RecA rapidly nucleates to form early SOS-signaling complexes, maturing into DNA-bound RecA bundles at later time points. Both before and after SOS induction, RecA* largely appears at locations distal from replisomes. Upon completion of repair, RecA storage structures reform.
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Affiliation(s)
- Harshad Ghodke
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Bishnu P Paudel
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Kamya Gopal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Zachary J Romero
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Elizabeth A Wood
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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Chandran AV, Srikalaivani R, Paul A, Vijayan M. Biochemical characterization of Mycobacterium tuberculosisLexA and structural studies of its C-terminal segment. Acta Crystallogr D Struct Biol 2019; 75:41-55. [DOI: 10.1107/s2059798318016066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/13/2018] [Indexed: 03/21/2023] Open
Abstract
LexA is a protein that is involved in the SOS response. The protein fromMycobacterium tuberculosisand its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified. The wild-type protein autocleaves at basic pH, while the mutants do not. The wild-type and the mutant proteins dimerize and bind DNA with equal facility. The C-terminal segment also dimerizes, and it also shows a tendency to form tetramers. The C-terminal segment readily crystallized. The crystals obtained from attempts involving the full-length protein and its mutants contained only the C-terminal segment including the catalytic core and a few residues preceding it, in a dimeric or tetrameric form, indicating protein cleavage during the long period involved in crystal formation. Modes of tetramerization of the full-length protein similar to those observed for the catalytic core are feasible. A complex ofM. tuberculosisLexA and the cognate SOS box could be modeled in which the mutual orientation of the two N-terminal domains differs from that in theEscherichia coliLexA–DNA complex. These results represent the first thorough characterization ofM. tuberculosisLexA and provide definitive information on its structure and assembly. They also provide leads for further exploration of this important protein.
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Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP. Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response. Front Microbiol 2018; 9:2961. [PMID: 30619111 PMCID: PMC6305444 DOI: 10.3389/fmicb.2018.02961] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022] Open
Abstract
Many antibiotics, either directly or indirectly, cause DNA damage thereby activating the bacterial DNA damage (SOS) response. SOS activation results in expression of genes involved in DNA repair and mutagenesis, and the regulation of the SOS response relies on two key proteins, LexA and RecA. Genetic studies have indicated that inactivating the regulatory proteins of this response sensitizes bacteria to antibiotics and slows the appearance of resistance. However, advancement of small molecule inhibitors of the SOS response has lagged, despite their clear promise in addressing the threat of antibiotic resistance. Previously, we had addressed this deficit by performing a high throughput screen of ∼1.8 million compounds that monitored for inhibition of RecA-mediated auto-proteolysis of Escherichia coli LexA, the reaction that initiates the SOS response. In this report, the refinement of the 5-amino-1-(carbamoylmethyl)-1H-1,2,3-triazole-4-carboxamide scaffold identified in the screen is detailed. After development of a modular synthesis, a survey of key activity determinants led to the identification of an analog with improved potency and increased breadth, targeting auto-proteolysis of LexA from both E. coli and Pseudomonas aeruginosa. Comparison of the structure of this compound to those of others in the series suggests structural features that may be required for activity and cross-species breadth. In addition, the feasibility of small molecule modulation of the SOS response was demonstrated in vivo by the suppression of the appearance of resistance. These structure activity relationships thus represent an important step toward producing Drugs that Inhibit SOS Activation to Repress Mechanisms Enabling Resistance (DISARMERs).
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Affiliation(s)
- Trevor Selwood
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian J Larsen
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
| | - Charlie Y Mo
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew J Culyba
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Zachary M Hostetler
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
| | - Simon D P Baugh
- Fox Chase Chemical Diversity Center, Inc., Doylestown, PA, United States
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40
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Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure 2018; 27:6-26. [PMID: 30393050 DOI: 10.1016/j.str.2018.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 11/27/2022]
Abstract
The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.
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Affiliation(s)
- Philippe Youkharibache
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Stella Veretnik
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| | - Qingliang Li
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
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41
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Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM. Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. ACS Infect Dis 2018; 4:349-359. [PMID: 29275629 DOI: 10.1021/acsinfecdis.7b00122] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RecA/LexA axis of the bacterial DNA damage (SOS) response is a promising, yet nontraditional, drug target. The SOS response is initiated upon genotoxic stress, when RecA, a DNA damage sensor, induces LexA, the SOS repressor, to undergo autoproteolysis, thereby derepressing downstream genes that can mediate DNA repair and accelerate mutagenesis. As genetic inhibition of the SOS response sensitizes bacteria to DNA damaging antibiotics and decreases acquired resistance, inhibitors of the RecA/LexA axis could potentiate our current antibiotic arsenal. Compounds targeting RecA, which has many mammalian homologues, have been reported; however, small-molecules targeting LexA autoproteolysis, a reaction unique to the prokaryotic SOS response, have remained elusive. Here, we describe the logistics and accomplishments of an academic-industry partnership formed to pursue inhibitors against the RecA/LexA axis. A novel fluorescence polarization assay reporting on RecA-induced self-cleavage of LexA enabled the screening of 1.8 million compounds. Follow-up studies on select leads show distinct activity patterns in orthogonal assays, including several with activity in cell-based assays reporting on SOS activation. Mechanistic assays demonstrate that we have identified first-in-class small molecules that specifically target the LexA autoproteolysis step in SOS activation. Our efforts establish a realistic example for navigating academic-industry partnerships in pursuit of anti-infective drugs and offer starting points for dedicated lead optimization of SOS inhibitors that could act as adjuvants for current antibiotics.
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Affiliation(s)
- Charlie Y. Mo
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Matthew J. Culyba
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Trevor Selwood
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M. Kubiak
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Anthony J. Jurewicz
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul M. Keller
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Andrew J. Pope
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Amy Quinn
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jessica Schneck
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Katherine L. Widdowson
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rahul M. Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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42
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Biochemical characterization of Borrelia burgdorferi's RecA protein. PLoS One 2017; 12:e0187382. [PMID: 29088268 PMCID: PMC5663514 DOI: 10.1371/journal.pone.0187382] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/18/2017] [Indexed: 12/03/2022] Open
Abstract
RecA plays key roles in DNA recombination, replication and repair. Mutation of recA in the Lyme disease spirochete, Borrelia burgdorferi, fails to produce some of the phenotypes expected from study of recA mutation in other organisms. ‘Missing’ recA phenotypes include a lack of growth or viability effects, including in the presence of DNA damage, and a lack of a role in vlsE antigenic variation and infectivity. We present a purification and biochemical characterization of recombinant B. burgdorferi RecA protein. We find that B. burgdorferi RecA displays the expected properties of being a DNA-dependent ATPase, of having an intrinsic binding preference for ssDNA over dsDNA enhanced by ATP binding, of promoting DNA pairing and strand exchange reactions and of having a detectable coprotease activity with E. coli LexA repressor. DNA pairing and strand exchange reactions promoted by B. burgdorferi RecA show an unusually strong dependence upon the presence of the cognate ssDNA binding protein (SSB) but are very sensitive to inhibition by SSB when the ssDNA was prebound by SSB. This indicates B. burgdorferi RecA may have an enhanced requirement for recombinational mediators to promote RecA-SSB exchange, despite the absence of homologues of the RecF pathway proteins that normally play this role in eubacteria. Finally, we do not find any unusual, intrinsic properties of B. burgdorferi’s RecA protein to explain the unusual phenotype of recA mutation and suggest that there may be alternative recombinase functions that could explain the ‘missing’ phenotypes.
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43
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Intracellular d-Serine Accumulation Promotes Genetic Diversity via Modulated Induction of RecA in Enterohemorrhagic Escherichia coli. J Bacteriol 2016; 198:3318-3328. [PMID: 27698085 DOI: 10.1128/jb.00548-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/27/2016] [Indexed: 01/28/2023] Open
Abstract
We recently discovered that exposure of enterohemorrhagic Escherichia coli (EHEC) to d-serine resulted in accumulation of this unusual amino acid, induction of the SOS regulon, and downregulation of the type III secretion system that is essential for efficient colonization of the host. Here, we have investigated the physiological relevance of this elevated SOS response, which is of particular interest given the presence of Stx toxin-carrying lysogenic prophages on the EHEC chromosome that are activated during the SOS response. We found that RecA elevation in response to d-serine, while being significant, was heterogeneous and not capable of activating stx expression or stx phage transduction to a nonlysogenic recipient. This "SOS-like response" was, however, capable of increasing the mutation frequency associated with low-level RecA activity, thus promoting genetic diversity. Furthermore, this response was entirely dependent on RecA and enhanced in the presence of a DNA-damaging agent, indicating a functional SOS response, but did not result in observable cleavage of the LexA repressor alone, indicating a controlled mechanism of induction. This work demonstrates that environmental factors not usually associated with DNA damage are capable of promoting an SOS-like response. We propose that this modulated induction of RecA allows EHEC to adapt to environmental insults such as d-serine while avoiding unwanted phage-induced lysis. IMPORTANCE The SOS response is a global stress network that is triggered by the presence of DNA damage due to breakage or stalled replication forks. Activation of the SOS response can trigger the replication of lytic bacteriophages and promote genetic diversification through error-prone polymerases. We have demonstrated that the host-associated metabolite d-serine contributes to Escherichia coli niche specification and accumulates inside cells that cannot catabolize it. This results in a modulated activation of the SOS antirepressor RecA that is insufficient to trigger lytic bacteriophage but capable of increasing the SOS-associated mutation frequency. These findings describe how relevant signals not normally associated with DNA damage can hijack the SOS response, promoting diversity as E. coli strains adapt while avoiding unwanted phage lysis.
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44
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Choi H, Paton RS, Park H, Schofield CJ. Investigations on recyclisation and hydrolysis in avibactam mediated serine β-lactamase inhibition. Org Biomol Chem 2016; 14:4116-28. [PMID: 27072755 PMCID: PMC4847122 DOI: 10.1039/c6ob00353b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/04/2016] [Indexed: 01/13/2023]
Abstract
β-Lactams inhibit penicillin-binding proteins (PBPs) and serine β-lactamases by acylation of a nucleophilic active site serine. Avibactam is approved for clinical use in combination with ceftazidime, and is a breakthrough non β-lactam β-lactamase inhibitor also reacting via serine acylation. Molecular dynamics (MD) and quantum chemical calculations on avibactam-mediated inhibition of a clinically relevant cephalosporinase reveal that recyclisation of the avibactam derived carbamoyl complex is favoured over hydrolysis. In contrast, we show that analogous recyclisation in β-lactam mediated inhibition is disfavoured. Avibactam recyclisation is promoted by a proton shuttle, a 'structural' water protonating the nucleophilic serine, and stabilization of the negative charge developed on aminocarbonyl oxygen. The results imply the potential of calculations for distinguishing between bifurcating pathways during inhibition and in generating hypotheses for predicting resistance. The inability of β-lactams to undergo recyclisation may be an Achilles heel, but one that can be addressed by suitably functionalized reversibly binding inhibitors.
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Affiliation(s)
- Hwanho Choi
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea. and Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Robert S Paton
- Chemical Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 143-747, Korea.
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45
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Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor. Proc Natl Acad Sci U S A 2016; 113:E2480-8. [PMID: 27099293 DOI: 10.1073/pnas.1602618113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92-198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.
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46
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Fornelos N, Browning DF, Butala M. The Use and Abuse of LexA by Mobile Genetic Elements. Trends Microbiol 2016; 24:391-401. [PMID: 26970840 DOI: 10.1016/j.tim.2016.02.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 11/15/2022]
Abstract
The SOS response is an essential process for responding to DNA damage in bacteria. The expression of SOS genes is under the control of LexA, a global transcription factor that undergoes self-cleavage during stress to allow the expression of DNA repair functions and delay cell division until the damage is rectified. LexA also regulates genes that are not part of this cell rescue program, and the induction of bacteriophages, the movement of pathogenicity islands, and the expression of virulence factors and bacteriocins are all controlled by this important transcription factor. Recently it has emerged that when regulating the expression of genes from mobile genetic elements (MGEs), LexA often does so in concert with a corepressor. This accessory regulator can either be a host-encoded global transcription factor, which responds to various metabolic changes, or a factor that is encoded for by the MGE itself. Thus, the coupling of LexA-mediated regulation to a secondary transcription factor not only detaches LexA from its primary SOS role, but also fine-tunes gene expression from the MGE, enabling it to respond to multiple stresses. Here we discuss the mechanisms of such coordinated regulation and its implications for cells carrying such MGEs.
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Affiliation(s)
- Nadine Fornelos
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, PO Box 35, F-40014 Jyvaskyla, Finland.
| | - Douglas F Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia.
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47
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Fornelos N, Butala M, Hodnik V, Anderluh G, Bamford JK, Salas M. Bacteriophage GIL01 gp7 interacts with host LexA repressor to enhance DNA binding and inhibit RecA-mediated auto-cleavage. Nucleic Acids Res 2015; 43:7315-29. [PMID: 26138485 PMCID: PMC4551915 DOI: 10.1093/nar/gkv634] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023] Open
Abstract
The SOS response in Eubacteria is a global response to DNA damage and its activation is increasingly associated with the movement of mobile genetic elements. The temperate phage GIL01 is induced into lytic growth using the host's SOS response to genomic stress. LexA, the SOS transcription factor, represses bacteriophage transcription by binding to a set of SOS boxes in the lysogenic promoter P1. However, LexA is unable to efficiently repress GIL01 transcription unless the small phage-encoded protein gp7 is also present. We found that gp7 forms a stable complex with LexA that enhances LexA binding to phage and cellular SOS sites and interferes with RecA-mediated auto-cleavage of LexA, the key step in the initiation of the SOS response. Gp7 did not bind DNA, alone or when complexed with LexA. Our findings suggest that gp7 induces a LexA conformation that favors DNA binding but disfavors LexA auto-cleavage, thereby altering the dynamics of the cellular SOS response. This is the first account of an accessory factor interacting with LexA to regulate transcription.
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Affiliation(s)
- Nadine Fornelos
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Centre of Excellence in Biological Interactions, PO Box 35, F-40014 Jyvaskyla, Finland Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Centro de Biología Molecular 'Severo Ochoa' (CSIC-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Jaana K Bamford
- Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, Centre of Excellence in Biological Interactions, PO Box 35, F-40014 Jyvaskyla, Finland
| | - Margarita Salas
- Instituto de Biología Molecular 'Eladio Viñuela' (CSIC), Centro de Biología Molecular 'Severo Ochoa' (CSIC-Universidad Autónoma de Madrid), Cantoblanco, 28049 Madrid, Spain
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48
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A self-lysis pathway that enhances the virulence of a pathogenic bacterium. Proc Natl Acad Sci U S A 2015; 112:8433-8. [PMID: 26100878 DOI: 10.1073/pnas.1506299112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In mammalian cells, programmed cell death (PCD) plays important roles in development, in the removal of damaged cells, and in fighting bacterial infections. Although widespread among multicellular organisms, there are relatively few documented instances of PCD in bacteria. Here we describe a potential PCD pathway in Pseudomonas aeruginosa that enhances the ability of the bacterium to cause disease in a lung infection model. Activation of the system can occur in a subset of cells in response to DNA damage through cleavage of an essential transcription regulator we call AlpR. Cleavage of AlpR triggers a cell lysis program through de-repression of the alpA gene, which encodes a positive regulator that activates expression of the alpBCDE lysis cassette. Although this is lethal to the individual cell in which it occurs, we find it benefits the population as a whole during infection of a mammalian host. Thus, host and pathogen each may use PCD as a survival-promoting strategy. We suggest that activation of the Alp cell lysis pathway is a disease-enhancing response to bacterial DNA damage inflicted by the host immune system.
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49
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Abstract
![]()
Bacteria
possess a remarkable ability to rapidly adapt and evolve
in response to antibiotics. Acquired antibiotic resistance can arise
by multiple mechanisms but commonly involves altering the target site
of the drug, enzymatically inactivating the drug, or preventing the
drug from accessing its target. These mechanisms involve new genetic
changes in the pathogen leading to heritable resistance. This recognition
underscores the importance of understanding how such
genetic changes can arise. Here, we review recent advances in our
understanding of the processes that contribute to the evolution of
antibiotic resistance, with a particular focus on hypermutation mediated
by the SOS pathway and horizontal gene transfer. We explore the molecular
mechanisms involved in acquired resistance and discuss their viability
as potential targets. We propose that additional studies into these
adaptive mechanisms not only can provide insights into evolution but
also can offer a strategy for potentiating our current antibiotic
arsenal.
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50
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Resveratrol antibacterial activity against Escherichia coli is mediated by Z-ring formation inhibition via suppression of FtsZ expression. Sci Rep 2015; 5:10029. [PMID: 25942564 PMCID: PMC4419592 DOI: 10.1038/srep10029] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 03/06/2015] [Indexed: 01/14/2023] Open
Abstract
Resveratrol exhibits a potent antimicrobial activity. However, the mechanism underlying its antibacterial activity has not been shown. In this study, the antibacterial mechanism of resveratrol was investigated. To investigate induction of the SOS response, a strain containing the lacZ+gene under the control of an SOS-inducible sulA promoter was constructed. DNA damage was measured by pulse-field gel electrophoresis (PFGE). After resveratrol treatment, the cells were observed by confocal microscopy. For the RNA silencing assay, ftsZ-specific antisense peptide nucleic acid (PNA) was used. Reactive oxygen species (ROS) production increased in Escherichia coli after resveratrol treatment; however, cell growth was not recovered by ROS quenching, indicating that, in this experiment, ROS formation and cell death following resveratrol treatment were not directly correlated. Resveratrol treatment increased DNA fragmentation in cells, while SOS response-related gene expression levels increased in a dose-dependent manner. Cell elongation was observed after resveratrol treatment. Elongation was induced by inhibiting FtsZ, an essential cell-division protein in prokaryotes, and resulted in significant inhibition of Z-ring the formation in E. coli. The expression of ftsZ mRNA was suppressed by resveratrol. Our results indicate that resveratrol inhibits bacterial cell growth by suppressing FtsZ expression and Z-ring formation.
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