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Carrasco B, Torres R, Moreno-del Álamo M, Ramos C, Ayora S, Alonso JC. Processing of stalled replication forks in Bacillus subtilis. FEMS Microbiol Rev 2024; 48:fuad065. [PMID: 38052445 PMCID: PMC10804225 DOI: 10.1093/femsre/fuad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
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2
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Wu Y, Kawabata H, Kita K, Ishikawa S, Tanaka K, Yoshida KI. Constitutive glucose dehydrogenase elevates intracellular NADPH levels and luciferase luminescence in Bacillus subtilis. Microb Cell Fact 2022; 21:266. [PMID: 36539761 PMCID: PMC9768902 DOI: 10.1186/s12934-022-01993-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genetic modifications in Bacillus subtilis have allowed the conversion of myo-inositol into scyllo-inositol, which is proposed as a therapeutic agent for Alzheimer's disease. This conversion comprises two reactions catalyzed by two distinct inositol dehydrogenases, IolG and IolW. The IolW-mediated reaction requires the intracellular regeneration of NADPH, and there appears to be a limit to the endogenous supply of NADPH, which may be one of the rate-determining factors for the conversion of inositol. The primary mechanism of NADPH regeneration in this bacterium remains unclear. RESULTS The gdh gene of B. subtilis encodes a sporulation-specific glucose dehydrogenase that can use NADP+ as a cofactor. When gdh was modified to be constitutively expressed, the intracellular NADPH level was elevated, increasing the conversion of inositol. In addition, the bacterial luciferase derived from Photorhabdus luminescens became more luminescent in cells in liquid culture and colonies on culture plates. CONCLUSION The results indicated that the luminescence of luciferase was representative of intracellular NADPH levels. Luciferase can therefore be employed to screen for mutations in genes involved in NADPH regeneration in B. subtilis, and artificial manipulation to enhance NADPH regeneration can promote the production of substances such as scyllo-inositol.
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Affiliation(s)
- Yuzheng Wu
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Honami Kawabata
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kyosuke Kita
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kan Tanaka
- grid.32197.3e0000 0001 2179 2105Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan ,grid.419082.60000 0004 1754 9200Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Ken-ichi Yoshida
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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3
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Martin HA, Sundararajan A, Ermi TS, Heron R, Gonzales J, Lee K, Anguiano-Mendez D, Schilkey F, Pedraza-Reyes M, Robleto EA. Mfd Affects Global Transcription and the Physiology of Stressed Bacillus subtilis Cells. Front Microbiol 2021; 12:625705. [PMID: 33603726 PMCID: PMC7885715 DOI: 10.3389/fmicb.2021.625705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found 1,997 genes differentially expressed in Mfd– cells in the absence of diamide. Using gene knockouts, we investigated the effect of genetic interactions between Mfd and the genes in its regulon on the response to disulfide stress. Interestingly, we found that Mfd interactions were complex and identified additive, epistatic, and suppressor effects in the response to disulfide stress. Pathway enrichment analysis of our RNASeq assay indicated that major biological functions, including translation, endospore formation, pyrimidine metabolism, and motility, were affected by the loss of Mfd. Further, our RNASeq findings correlated with phenotypic changes in growth in minimal media, motility, and sensitivity to antibiotics that target the cell envelope, transcription, and DNA replication. Our results suggest that Mfd has profound effects on the modulation of the transcriptome and on bacterial physiology, particularly in cells experiencing nutritional and oxidative stress.
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Affiliation(s)
- Holly Anne Martin
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | | | - Tatiana S Ermi
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Robert Heron
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Jason Gonzales
- West Career and Technical Academy, Las Vegas, NV, United States
| | - Kaiden Lee
- The College of Idaho, Caldwell, ID, United States
| | - Diana Anguiano-Mendez
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Faye Schilkey
- National Center for Genome Resources, Santa Fe, NM, United States
| | - Mario Pedraza-Reyes
- Division of Natural and Exact Sciences, Department of Biology, University of Guanajuato, Guanajuato, Mexico
| | - Eduardo A Robleto
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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4
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Joseph AM, Badrinarayanan A. Visualizing mutagenic repair: novel insights into bacterial translesion synthesis. FEMS Microbiol Rev 2020; 44:572-582. [PMID: 32556198 PMCID: PMC7476773 DOI: 10.1093/femsre/fuaa023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
DNA repair is essential for cell survival. In all domains of life, error-prone and error-free repair pathways ensure maintenance of genome integrity under stress. Mutagenic, low-fidelity repair mechanisms help avoid potential lethality associated with unrepaired damage, thus making them important for genome maintenance and, in some cases, the preferred mode of repair. However, cells carefully regulate pathway choice to restrict activity of these pathways to only certain conditions. One such repair mechanism is translesion synthesis (TLS), where a low-fidelity DNA polymerase is employed to synthesize across a lesion. In bacteria, TLS is a potent source of stress-induced mutagenesis, with potential implications in cellular adaptation as well as antibiotic resistance. Extensive genetic and biochemical studies, predominantly in Escherichia coli, have established a central role for TLS in bypassing bulky DNA lesions associated with ongoing replication, either at or behind the replication fork. More recently, imaging-based approaches have been applied to understand the molecular mechanisms of TLS and how its function is regulated. Together, these studies have highlighted replication-independent roles for TLS as well. In this review, we discuss the current status of research on bacterial TLS, with emphasis on recent insights gained mostly through microscopy at the single-cell and single-molecule level.
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Affiliation(s)
- Asha Mary Joseph
- National Centre for Biological Sciences (Tata Institute of Fundamental Research), Bangalore, Karnataka 560065, India
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences (Tata Institute of Fundamental Research), Bangalore, Karnataka 560065, India
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5
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Hernández-Tamayo R, Oviedo-Bocanegra LM, Fritz G, Graumann PL. Symmetric activity of DNA polymerases at and recruitment of exonuclease ExoR and of PolA to the Bacillus subtilis replication forks. Nucleic Acids Res 2019; 47:8521-8536. [PMID: 31251806 PMCID: PMC6895272 DOI: 10.1093/nar/gkz554] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/06/2019] [Accepted: 06/24/2019] [Indexed: 11/14/2022] Open
Abstract
DNA replication forks are intrinsically asymmetric and may arrest during the cell cycle upon encountering modifications in the DNA. We have studied real time dynamics of three DNA polymerases and an exonuclease at a single molecule level in the bacterium Bacillus subtilis. PolC and DnaE work in a symmetric manner and show similar dwell times. After addition of DNA damage, their static fractions and dwell times decreased, in agreement with increased re-establishment of replication forks. Only a minor fraction of replication forks showed a loss of active polymerases, indicating relatively robust activity during DNA repair. Conversely, PolA, homolog of polymerase I and exonuclease ExoR were rarely present at forks during unperturbed replication but were recruited to replications forks after induction of DNA damage. Protein dynamics of PolA or ExoR were altered in the absence of each other during exponential growth and during DNA repair, indicating overlapping functions. Purified ExoR displayed exonuclease activity and preferentially bound to DNA having 5′ overhangs in vitro. Our analyses support the idea that two replicative DNA polymerases work together at the lagging strand whilst only PolC acts at the leading strand, and that PolA and ExoR perform inducible functions at replication forks during DNA repair.
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Affiliation(s)
- Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße 6, 35043 Marburg, Germany
| | - Luis M Oviedo-Bocanegra
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße 6, 35043 Marburg, Germany
| | - Georg Fritz
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Department of Physics, Philipps Universität Marburg, Renthof 5, 35032 Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße 6, 35043 Marburg, Germany
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6
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Timinskas K, Venclovas Č. New insights into the structures and interactions of bacterial Y-family DNA polymerases. Nucleic Acids Res 2019; 47:4393-4405. [PMID: 30916324 PMCID: PMC6511836 DOI: 10.1093/nar/gkz198] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/09/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022] Open
Abstract
Bacterial Y-family DNA polymerases are usually classified into DinB (Pol IV), UmuC (the catalytic subunit of Pol V) and ImuB, a catalytically dead essential component of the ImuA-ImuB-DnaE2 mutasome. However, the true diversity of Y-family polymerases is unknown. Furthermore, for most of them the structures are unavailable and interactions are poorly characterized. To gain a better understanding of bacterial Y-family DNA polymerases, we performed a detailed computational study. It revealed substantial diversity, far exceeding traditional classification. We found that a large number of subfamilies feature a C-terminal extension next to the common Y-family region. Unexpectedly, in most C-terminal extensions we identified a region homologous to the N-terminal oligomerization motif of RecA. This finding implies a universal mode of interaction between Y-family members and RecA (or ImuA), in the case of Pol V strongly supported by experimental data. In gram-positive bacteria, we identified a putative Pol V counterpart composed of a Y-family polymerase, a YolD homolog and RecA. We also found ImuA-ImuB-DnaE2 variants lacking ImuA, but retaining active or inactive Y-family polymerase, a standalone ImuB C-terminal domain and/or DnaE2. In summary, our analyses revealed that, despite considerable diversity, bacterial Y-family polymerases share previously unanticipated similarities in their structural domains/motifs and interactions.
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Affiliation(s)
- Kęstutis Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
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7
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Roles of Bacillus subtilis RecA, Nucleotide Excision Repair, and Translesion Synthesis Polymerases in Counteracting Cr(VI)-Promoted DNA Damage. J Bacteriol 2019; 201:JB.00073-19. [PMID: 30745368 DOI: 10.1128/jb.00073-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 11/20/2022] Open
Abstract
Bacteria deploy global programs of gene expression, including components of the SOS response, to counteract the cytotoxic and genotoxic effects of environmental DNA-damaging factors. Here we report that genetic damage promoted by hexavalent chromium elicited the SOS response in Bacillus subtilis, as evidenced by the induction of transcriptional uvrA-lacZ, recA-lacZ, and P recA-gfp fusions. Accordingly, B. subtilis strains deficient in homologous recombination (RecA) and nucleotide excision repair (NER) (UvrA), components of the SOS response, were significantly more sensitive to Cr(VI) treatment than were cells of the wild-type strain. These results strongly suggest that Cr(VI) induces the formation in growing B. subtilis cells of cytotoxic and genotoxic bulky DNA lesions that are processed by RecA and/or the NER pathways. In agreement with this notion, Cr(VI) significantly increased the formation of DNA-protein cross-links (DPCs) and induced mutagenesis in recA- and uvrA-deficient B. subtilis strains, through a pathway that required YqjH/YqjW-mediated translesion synthesis. We conclude that Cr(VI) promotes mutagenesis and cell death in B. subtilis by a mechanism that involves the formation of DPCs and that such deleterious effects are counteracted by both the NER and homologous recombination pathways, belonging to the RecA-dependent SOS system.IMPORTANCE It has been shown that, following permeation of cell barriers, Cr(VI) kills B. subtilis cells following a mechanism of reactive oxygen species-promoted DNA damage, which is counteracted by the guanine oxidized repair system. Here we report a distinct mechanism of Cr(VI)-promoted DNA damage that involves production of DPCs capable of eliciting the bacterial SOS response. We also report that the NER and homologous recombination (RecA) repair pathways, as well as low-fidelity DNA polymerases, counteract this metal-induced mechanism of killing in B. subtilis Hence, our results contribute to an understanding of how environmental pollutants activate global programs of gene expression that allow bacteria to contend with the cytotoxic and genotoxic effects of heavy metals.
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8
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Romero H, Torres R, Hernández-Tamayo R, Carrasco B, Ayora S, Graumann PL, Alonso JC. Bacillus subtilis RarA acts at the interplay between replication and repair-by-recombination. DNA Repair (Amst) 2019; 78:27-36. [PMID: 30954900 DOI: 10.1016/j.dnarep.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 02/20/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Bacterial RarA is thought to play crucial roles in the cellular response to blocked replication forks. We show that lack of Bacillus subtilis RarA renders cells very sensitive to H2O2, but not to methyl methane sulfonate or 4-nitroquinoline-1-oxide. RarA is epistatic to RecA in response to DNA damage. Inactivation of rarA partially suppressed the DNA repair defect of mutants lacking translesion synthesis polymerases. RarA may contribute to error-prone DNA repair as judged by the reduced frequency of rifampicin-resistant mutants in ΔrarA and in ΔpolY1 ΔrarA cells. The absence of RarA strongly reduced the viability of dnaD23ts and dnaB37ts cells upon partial thermal inactivation, suggesting that ΔrarA cells are deficient in replication fork assembly. A ΔrarA mutation also partially reduced the viability of dnaC30ts and dnaX51ts cells and slightly improved the viability of dnaG40ts cells at semi-permissive temperature. These results suggest that RarA links re-initiation of DNA replication with repair-by-recombination by controlling the access of the replication machinery to a collapsed replication fork.
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Affiliation(s)
- Hector Romero
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain; SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043, Marburg, Germany; Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Madrid, Spain.
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9
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Romero H, Rösch TC, Hernández-Tamayo R, Lucena D, Ayora S, Alonso JC, Graumann PL. Single molecule tracking reveals functions for RarA at replication forks but also independently from replication during DNA repair in Bacillus subtilis. Sci Rep 2019; 9:1997. [PMID: 30760776 PMCID: PMC6374455 DOI: 10.1038/s41598-018-38289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/18/2018] [Indexed: 12/19/2022] Open
Abstract
RarA is a widely conserved protein proposed to be involved in recombination-dependent replication. We present a cell biological approach to identify functional connections between RarA and other proteins using single molecule tracking. We found that 50% of RarA molecules were static, mostly close to replication forks and likely DNA-bound, while the remaining fraction was highly dynamic throughout the cells. RarA alternated between static and dynamic states. Exposure to H2O2 increased the fraction of dynamic molecules, but not treatment with mitomycin C or with methyl methanesulfonate, which was exacerbated by the absence of RecJ, RecD2, RecS and RecU proteins. The ratio between static and dynamic RarA also changed in replication temperature-sensitive mutants, but in opposite manners, dependent upon inhibition of DnaB or of DnaC (pre)primosomal proteins, revealing an intricate function related to DNA replication restart. RarA likely acts in the context of collapsed replication forks, as well as in conjunction with a network of proteins that affect the activity of the RecA recombinase. Our novel approach reveals intricate interactions of RarA, and is widely applicable for in vivo protein studies, to underpin genetic or biochemical connections, and is especially helpful for investigating proteins whose absence does not lead to any detectable phenotype.
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Affiliation(s)
- Hector Romero
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Thomas C Rösch
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Daniella Lucena
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany
| | - Silvia Ayora
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain
| | - Juan C Alonso
- Department Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St., 28049, Cantoblanco, Madrid, Spain.
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Hans-Meerwein-Straße, Mehrzweckgebäude, 35043, Marburg, Germany.
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.
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10
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Li Y, Chen Z, Matthews LA, Simmons LA, Biteen JS. Dynamic Exchange of Two Essential DNA Polymerases during Replication and after Fork Arrest. Biophys J 2019; 116:684-693. [PMID: 30686488 DOI: 10.1016/j.bpj.2019.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/23/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023] Open
Abstract
The replisome is a multiprotein machine responsible for the faithful replication of chromosomal and plasmid DNA. Using single-molecule super-resolution imaging, we characterized the dynamics of three replisomal proteins in live Bacillus subtilis cells: the two replicative DNA polymerases, PolC and DnaE, and a processivity clamp loader subunit, DnaX. We quantified the protein mobility and dwell times during normal replication and following replication fork stress using damage-independent and damage-dependent conditions. With these results, we report the dynamic and cooperative process of DNA replication based on changes in the measured diffusion coefficients and dwell times. These experiments show that the replication proteins are all highly dynamic and that the exchange rate depends on whether DNA synthesis is active or arrested. Our results also suggest coupling between PolC and DnaX in the DNA replication process and indicate that DnaX provides an important role in synthesis during repair. Furthermore, our results suggest that DnaE provides a limited contribution to chromosomal replication and repair in vivo.
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Affiliation(s)
- Yilai Li
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Ziyuan Chen
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Lindsay A Matthews
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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11
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Patlán AG, Corona SU, Ayala-García VM, Pedraza-Reyes M. Non-canonical processing of DNA photodimers with Bacillus subtilis UV-endonuclease YwjD, 5'→3' exonuclease YpcP and low-fidelity DNA polymerases YqjH and YqjW. DNA Repair (Amst) 2018; 70:1-9. [PMID: 30096406 DOI: 10.1016/j.dnarep.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022]
Abstract
It has been shown that mutation frequency decline (Mfd) and nucleotide excision repair (NER) deficiencies promote UV-induced mutagenesis in B. subtilis sporangia. As replication is halted in sporulating B. subtilis cells, in this report, we investigated if this response may result from an error-prone repair event involving the UV-endonuclease YwjD and low fidelity (LF) DNA synthesis. Accordingly, disruption of YwjD generated B. subtilis sporangia that were more susceptible to UV-C radiation than sporangia of the WT strain and such susceptibility increased even more after the single or simultaneous inactivation of the LF DNA polymerases YqjH and YqjW. To further explore this concept, functional His6-tagged YwjD and Y-DNA polymerases YqjH and YqjW were produced and purified to homogeneity. In vitro repair assays showed that YwjD hydrolyzed the phosphodiester bond immediately located 5´-end of a ds-DNA substrate bearing either, cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PD) or Dewar isomers (DWI). Notably, the 6-4 PD and DWI but not the CPDs repair intermediaries of YwjD were efficiently processed by the LF polymerase YqjH suggesting that an additional 5'→3' exonuclease event was necessary to process PD. Accordingly, the LF polymerase YqjW efficiently processed the incision-excision repair products derived from YwjD and exonuclease YpcP attack over CPD-containing DNA. In summary, our results unveiled a novel non-canonical repair pathway that employs YwjD to incise PD-containing DNA and low fidelity synthesis contributing thus to mutagenesis, survival and spore morphogenesis in B. subtilis.
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Affiliation(s)
- Adriana G Patlán
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Saúl U Corona
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Víctor M Ayala-García
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico.
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12
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Specialised DNA polymerases in Escherichia coli: roles within multiple pathways. Curr Genet 2018; 64:1189-1196. [PMID: 29700578 DOI: 10.1007/s00294-018-0840-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 01/15/2023]
Abstract
In many bacterial species, DNA damage triggers the SOS response; a pathway that regulates the production of DNA repair and damage tolerance proteins, including error-prone DNA polymerases. These specialised polymerases are capable of bypassing lesions in the template DNA, a process known as translesion synthesis (TLS). Specificity for lesion types varies considerably between the different types of TLS polymerases. TLS polymerases are mainly described as working in the context of replisomes that are stalled at lesions or in lesion-containing gaps left behind the replisome. Recently, a series of single-molecule fluorescence microscopy studies have revealed that two TLS polymerases, pol IV and pol V, rarely colocalise with replisomes in Escherichia coli cells, suggesting that most TLS activity happens in a non-replisomal context. In this review, we re-visit the evidence for the involvement of TLS polymerases in other pathways. A series of genetic and biochemical studies indicates that TLS polymerases could participate in nucleotide excision repair, homologous recombination and transcription. In addition, oxidation of the nucleotide pool, which is known to be induced by multiple stressors, including many antibiotics, appears to favour TLS polymerase activity and thus increases mutation rates. Ultimately, participation of TLS polymerases within non-replisomal pathways may represent a major source of mutations in bacterial cells and calls for more extensive investigation.
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13
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Schroeder JW, Yeesin P, Simmons LA, Wang JD. Sources of spontaneous mutagenesis in bacteria. Crit Rev Biochem Mol Biol 2017; 53:29-48. [PMID: 29108429 DOI: 10.1080/10409238.2017.1394262] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mutations in an organism's genome can arise spontaneously, that is, in the absence of exogenous stress and prior to selection. Mutations are often neutral or deleterious to individual fitness but can also provide genetic diversity driving evolution. Mutagenesis in bacteria contributes to the already serious and growing problem of antibiotic resistance. However, the negative impacts of spontaneous mutagenesis on human health are not limited to bacterial antibiotic resistance. Spontaneous mutations also underlie tumorigenesis and evolution of drug resistance. To better understand the causes of genetic change and how they may be manipulated in order to curb antibiotic resistance or the development of cancer, we must acquire a mechanistic understanding of the major sources of mutagenesis. Bacterial systems are particularly well-suited to studying mutagenesis because of their fast growth rate and the panoply of available experimental tools, but efforts to understand mutagenic mechanisms can be complicated by the experimental system employed. Here, we review our current understanding of mutagenic mechanisms in bacteria and describe the methods used to study mutagenesis in bacterial systems.
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Affiliation(s)
- Jeremy W Schroeder
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Ponlkrit Yeesin
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
| | - Lyle A Simmons
- b Department of Molecular, Cellular, and Developmental Biology , University of Michigan , Ann Arbor , MI , USA
| | - Jue D Wang
- a Department of Bacteriology , University of Wisconsin - Madison , Madison , WI , USA
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14
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Raguse M, Torres R, Seco EM, Gándara C, Ayora S, Moeller R, Alonso JC. Bacillus subtilis DisA helps to circumvent replicative stress during spore revival. DNA Repair (Amst) 2017; 59:57-68. [PMID: 28961460 DOI: 10.1016/j.dnarep.2017.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/24/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
The mechanisms that allow to circumvent replicative stress, and to resume DNA synthesis are poorly understood in Bacillus subtilis. To study the role of the diadenylate cyclase DisA and branch migration translocase (BMT) RadA/Sms in restarting a stalled replication fork, we nicked and broke the circular chromosome of an inert mature haploid spore, damaged the bases, and measured survival of reviving spores. During undisturbed ripening, nicks and breaks should be repaired by pathways that do not invoke long-range end resection or genetic exchange by homologous recombination, after which DNA replication might be initiated. We found that DNA damage reduced the viability of spores that lacked DisA, BMT (RadA/Sms, RuvAB or RecG), the Holliday junction resolvase RecU, or the translesion synthesis DNA polymerases (PolY1 or PolY2). DisA and RadA/Sms, in concert with RuvAB, RecG, RecU, PolY1 or PolY2, are needed to bypass replication-blocking lesions. DisA, which binds to stalled or reversed forks, did not apparently affect initiation of PriA-dependent DNA replication in vitro. We propose that DisA is necessary to coordinate responses to replicative stress; it could help to circumvent damaged template bases that otherwise impede fork progression.
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Affiliation(s)
- Marina Raguse
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany
| | - Rubén Torres
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Elena M Seco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Carolina Gándara
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Ayora
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Ralf Moeller
- German Aerospace Center (DLReV), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Linder Hoehe, D-51147 Cologne (Köln), Germany.
| | - Juan C Alonso
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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15
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Paschalis V, Le Chatelier E, Green M, Nouri H, Képès F, Soultanas P, Janniere L. Interactions of the Bacillus subtilis DnaE polymerase with replisomal proteins modulate its activity and fidelity. Open Biol 2017; 7:170146. [PMID: 28878042 PMCID: PMC5627055 DOI: 10.1098/rsob.170146] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/01/2017] [Indexed: 01/09/2023] Open
Abstract
During Bacillus subtilis replication two replicative polymerases function at the replisome to collectively carry out genome replication. In a reconstituted in vitro replication assay, PolC is the main polymerase while the lagging strand DnaE polymerase briefly extends RNA primers synthesized by the primase DnaG prior to handing-off DNA synthesis to PolC. Here, we show in vivo that (i) the polymerase activity of DnaE is essential for both the initiation and elongation stages of DNA replication, (ii) its error rate varies inversely with PolC concentration, and (iii) its misincorporations are corrected by the mismatch repair system post-replication. We also found that the error rates in cells encoding mutator forms of both PolC and DnaE are significantly higher (up to 15-fold) than in PolC mutants. In vitro, we showed that (i) the polymerase activity of DnaE is considerably stimulated by DnaN, SSB and PolC, (ii) its error-prone activity is strongly inhibited by DnaN, and (iii) its errors are proofread by the 3' > 5' exonuclease activity of PolC in a stable template-DnaE-PolC complex. Collectively our data show that protein-protein interactions within the replisome modulate the activity and fidelity of DnaE, and confirm the prominent role of DnaE during B. subtilis replication.
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Affiliation(s)
- Vasileios Paschalis
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Emmanuelle Le Chatelier
- Institut National de la Recherche Agronomique, Génétique Microbienne, 78350 Jouy-en-Josas, France
| | - Matthew Green
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Hamid Nouri
- iSSB, Genopole, CNRS, Univ EVRY, Université Paris-Saclay, Génopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 Evry, France
| | - François Képès
- iSSB, Genopole, CNRS, Univ EVRY, Université Paris-Saclay, Génopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 Evry, France
| | - Panos Soultanas
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Laurent Janniere
- iSSB, Genopole, CNRS, Univ EVRY, Université Paris-Saclay, Génopole Campus 1, Genavenir 6, 5 rue Henri Desbruères, 91030 Evry, France
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16
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Stationary-Phase Mutagenesis in Stressed Bacillus subtilis Cells Operates by Mfd-Dependent Mutagenic Pathways. Genes (Basel) 2016; 7:genes7070033. [PMID: 27399782 PMCID: PMC4962003 DOI: 10.3390/genes7070033] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/22/2016] [Accepted: 06/24/2016] [Indexed: 12/15/2022] Open
Abstract
In replication-limited cells of Bacillus subtilis, Mfd is mutagenic at highly transcribed regions, even in the absence of bulky DNA lesions. However, the mechanism leading to increased mutagenesis through Mfd remains currently unknown. Here, we report that Mfd may promote mutagenesis in nutritionally stressed B. subtilis cells by coordinating error-prone repair events mediated by UvrA, MutY and PolI. Using a point-mutated gene conferring leucine auxotrophy as a genetic marker, it was found that the absence of UvrA reduced the Leu+ revertants and that a second mutation in mfd reduced mutagenesis further. Moreover, the mfd and polA mutants presented low but similar reversion frequencies compared to the parental strain. These results suggest that Mfd promotes mutagenic events that required the participation of NER pathway and PolI. Remarkably, this Mfd-dependent mutagenic pathway was found to be epistatic onto MutY; however, whereas the MutY-dependent Leu+ reversions required Mfd, a direct interaction between these proteins was not apparent. In summary, our results support the concept that Mfd promotes mutagenesis in starved B. subtilis cells by coordinating both known and previously unknown Mfd-associated repair pathways. These mutagenic processes bias the production of genetic diversity towards highly transcribed regions in the genome.
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17
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Ramírez-Guadiana FH, Barajas-Ornelas RDC, Corona-Bautista SU, Setlow P, Pedraza-Reyes M. The RecA-Dependent SOS Response Is Active and Required for Processing of DNA Damage during Bacillus subtilis Sporulation. PLoS One 2016; 11:e0150348. [PMID: 26930481 PMCID: PMC4773242 DOI: 10.1371/journal.pone.0150348] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/29/2016] [Indexed: 12/24/2022] Open
Abstract
The expression of and role played by RecA in protecting sporulating cells of Bacillus subtilis from DNA damage has been determined. Results showed that the DNA-alkylating agent Mitomycin-C (M-C) activated expression of a PrecA-gfpmut3a fusion in both sporulating cells’ mother cell and forespore compartments. The expression levels of a recA-lacZ fusion were significantly lower in sporulating than in growing cells. However, M-C induced levels of ß-galactosidase from a recA-lacZ fusion ~6- and 3-fold in the mother cell and forespore compartments of B. subtilis sporangia, respectively. Disruption of recA slowed sporulation and sensitized sporulating cells to M-C and UV-C radiation, and the M-C and UV-C sensitivity of sporangia lacking the transcriptional repair-coupling factor Mfd was significantly increased by loss of RecA. We postulate that when DNA damage is encountered during sporulation, RecA activates the SOS response thus providing sporangia with the repair machinery to process DNA lesions that may compromise the spatio-temporal expression of genes that are essential for efficient spore formation.
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Affiliation(s)
- Fernando H. Ramírez-Guadiana
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Gto. 36050, México
| | | | - Saúl U. Corona-Bautista
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Gto. 36050, México
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, 06030–3305, Farmington, Connecticut, United States of America
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Gto. 36050, México
- * E-mail:
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18
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Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H. An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:E1096-105. [PMID: 25713353 PMCID: PMC4364195 DOI: 10.1073/pnas.1416651112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand in Bacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require the B. subtilis Y-family polymerase, PolY1 (yqjH). We find that without PolY1, association of the replicative helicase, DnaC, and the recombination protein, RecA, with lagging-strand genes increases in a transcription-dependent manner. These data suggest that PolY1 promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci. Y-family polymerases can alleviate potential obstacles to replisome progression by facilitating DNA lesion bypass, extension of D-loops, or excision repair. We find that the nucleotide excision repair (NER) proteins UvrA, UvrB, and UvrC, but not RecA, are required for transcription-dependent asymmetry in mutation rates of genes in the two orientations. Furthermore, we find that the transcription-coupling repair factor Mfd functions in the same pathway as PolY1 and is also required for increased mutagenesis of lagging-strand genes. Experimental and SNP analyses of B. subtilis genomes show mutational footprints consistent with these findings. We propose that the interplay between replication and transcription increases lesion susceptibility of, specifically, lagging-strand genes, activating an Mfd-dependent error-prone NER mechanism. We propose that this process, at least partially, underlies the accelerated evolution of lagging-strand genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ivan Liachko
- Genome Sciences, University of Washington, Seattle, WA 98195
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19
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Role of Bacillus subtilis error prevention oxidized guanine system in counteracting hexavalent chromium-promoted oxidative DNA damage. Appl Environ Microbiol 2014; 80:5493-502. [PMID: 24973075 DOI: 10.1128/aem.01665-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromium pollution is potentially detrimental to bacterial soil communities, compromising carbon and nitrogen cycles that are essential for life on earth. It has been proposed that intracellular reduction of hexavalent chromium [Cr(VI)] to trivalent chromium [Cr(III)] may cause bacterial death by a mechanism that involves reactive oxygen species (ROS)-induced DNA damage; the molecular basis of the phenomenon was investigated in this work. Here, we report that Bacillus subtilis cells lacking a functional error prevention oxidized guanine (GO) system were significantly more sensitive to Cr(VI) treatment than cells of the wild-type (WT) strain, suggesting that oxidative damage to DNA is involved in the deleterious effects of the oxyanion. In agreement with this suggestion, Cr(VI) dramatically increased the ROS concentration and induced mutagenesis in a GO-deficient B. subtilis strain. Alkaline gel electrophoresis (AGE) analysis of chromosomal DNA of WT and ΔGO mutant strains subjected to Cr(VI) treatment revealed that the DNA of the ΔGO strain was more susceptible to DNA glycosylase Fpg attack, suggesting that chromium genotoxicity is associated with 7,8-dihydro-8-oxodeoxyguanosine (8-oxo-G) lesions. In support of this notion, specific monoclonal antibodies detected the accumulation of 8-oxo-G lesions in the chromosomes of B. subtilis cells subjected to Cr(VI) treatment. We conclude that Cr(VI) promotes mutagenesis and cell death in B. subtilis by a mechanism that involves radical oxygen attack of DNA, generating 8-oxo-G, and that such effects are counteracted by the prevention and repair GO system.
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20
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Abstract
DNA helicases have important roles in genome maintenance. The RecD helicase has been well studied as a component of the heterotrimeric RecBCD helicase-nuclease enzyme important for double-strand break repair in Escherichia coli. Interestingly, many bacteria lack RecBC and instead contain a RecD2 helicase, which is not known to function as part of a larger complex. Depending on the organism studied, RecD2 has been shown to provide resistance to a broad range of DNA-damaging agents while also contributing to mismatch repair (MMR). Here we investigated the importance of Bacillus subtilis RecD2 helicase to genome integrity. We show that deletion of recD2 confers a modest increase in the spontaneous mutation rate and that the mutational signature in ΔrecD2 cells is not consistent with an MMR defect, indicating a new function for RecD2 in B. subtilis. To further characterize the role of RecD2, we tested the deletion strain for sensitivity to DNA-damaging agents. We found that loss of RecD2 in B. subtilis sensitized cells to several DNA-damaging agents that can block or impair replication fork movement. Measurement of replication fork progression in vivo showed that forks collapse more frequently in ΔrecD2 cells, supporting the hypothesis that RecD2 is important for normal replication fork progression. Biochemical characterization of B. subtilis RecD2 showed that it is a 5'-3' helicase and that it directly binds single-stranded DNA binding protein. Together, our results highlight novel roles for RecD2 in DNA replication which help to maintain replication fork integrity during normal growth and when forks encounter DNA damage.
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21
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Vlašić I, Mertens R, Seco EM, Carrasco B, Ayora S, Reitz G, Commichau FM, Alonso JC, Moeller R. Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break. Nucleic Acids Res 2013; 42:2295-307. [PMID: 24285298 PMCID: PMC3936729 DOI: 10.1093/nar/gkt1194] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacillus subtilis RecA is important for spore resistance to DNA damage, even though spores contain a single non-replicating genome. We report that inactivation of RecA or its accessory factors, RecF, RecO, RecR and RecX, drastically reduce survival of mature dormant spores to ultrahigh vacuum desiccation and ionizing radiation that induce single strand (ss) DNA nicks and double-strand breaks (DSBs). The presence of non-cleavable LexA renders spores less sensitive to DSBs, and spores impaired in DSB recognition or end-processing show sensitivities to X-rays similar to wild-type. In vitro RecA cannot compete with SsbA for nucleation onto ssDNA in the presence of ATP. RecO is sufficient, at least in vitro, to overcome SsbA inhibition and stimulate RecA polymerization on SsbA-coated ssDNA. In the presence of SsbA, RecA slightly affects DNA replication in vitro, but addition of RecO facilitates RecA-mediated inhibition of DNA synthesis. We propose that repairing of the DNA lesions generates a replication stress to germinating spores, and the RecA·ssDNA filament might act by preventing potentially dangerous forms of DNA repair occurring during replication. RecA might stabilize a stalled fork or prevent or promote dissolution of reversed forks rather than its cleavage that should require end-processing.
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Affiliation(s)
- Ignacija Vlašić
- Radiation Biology Department, German Aerospace Center, Institute of Aerospace Medicine, Linder Höhe, D-51147 Cologne (Köln), Germany, Division of Molecular Biology, Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain and Department of General Microbiology, University of Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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22
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Ramírez-Guadiana FH, Del Carmen Barajas-Ornelas R, Ayala-García VM, Yasbin RE, Robleto E, Pedraza-Reyes M. Transcriptional coupling of DNA repair in sporulating Bacillus subtilis cells. Mol Microbiol 2013; 90:1088-99. [PMID: 24118570 DOI: 10.1111/mmi.12417] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2013] [Indexed: 11/28/2022]
Abstract
In conditions of halted or limited genome replication, like those experienced in sporulating cells of Bacillus subtilis, a more immediate detriment caused by DNA damage is altering the transcriptional programme that drives this developmental process. Here, we report that mfd, which encodes a conserved bacterial protein that mediates transcription-coupled DNA repair (TCR), is expressed together with uvrA in both compartments of B. subtilis sporangia. The function of Mfd was found to be important for processing the genetic damage during B. subtilis sporulation. Disruption of mfd sensitized developing spores to mitomycin-C (M-C) treatment and UV-C irradiation. Interestingly, in non-growing sporulating cells, Mfd played an anti-mutagenic role as its absence promoted UV-induced mutagenesis through a pathway involving YqjH/YqjW-mediated translesion synthesis (TLS). Two observations supported the participation of Mfd-dependent TCR in spore morphogenesis: (i) disruption of mfd notoriously affected the efficiency of B. subtilis sporulation and (ii) in comparison with the wild-type strain, a significant proportion of Mfd-deficient sporangia that survived UV-C treatment developed an asporogenous phenotype. We propose that the Mfd-dependent repair pathway operates during B. subtilis sporulation and that its function is required to eliminate genetic damage from transcriptionally active genes.
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23
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Bidnenko V, Shi L, Kobir A, Ventroux M, Pigeonneau N, Henry C, Trubuil A, Noirot-Gros MF, Mijakovic I. Bacillus subtilis serine/threonine protein kinase YabT is involved in spore development via phosphorylation of a bacterial recombinase. Mol Microbiol 2013; 88:921-35. [PMID: 23634894 PMCID: PMC3708118 DOI: 10.1111/mmi.12233] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2013] [Indexed: 01/20/2023]
Abstract
We characterized YabT, a serine/threonine kinase of the Hanks family, from Bacillus subtilis. YabT is a putative transmembrane kinase that lacks the canonical extracellular signal receptor domain. We demonstrate that YabT possesses a DNA-binding motif essential for its activation. In vivo YabT is expressed during sporulation and localizes to the asymmetric septum. Cells devoid of YabT sporulate more slowly and exhibit reduced resistance to DNA damage during sporulation. We established that YabT phosphorylates DNA-recombinase RecA at the residue serine 2. A non-phosphorylatable mutant of RecA exhibits the same phenotype as the ΔyabT mutant, and a phosphomimetic mutant of RecA complements ΔyabT, suggesting that YabT acts via RecA phosphorylation in vivo. During spore development, phosphorylation facilitates the formation of transient and mobile RecA foci that exhibit a scanning-like movement associated to the nucleoid in the mother cell. In some cells these foci persist at the end of spore development. We show that persistent RecA foci, which presumably coincide with irreparable lesions, are mutually exclusive with the completion of spore morphogenesis. Our results highlight similarities between the bacterial serine/threonine kinase YabT and eukaryal kinases C-Abl and Mec1, which are also activated by DNA, and phosphorylate proteins involved in DNA damage repair.
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24
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MacLean RC, Torres-Barceló C, Moxon R. Evaluating evolutionary models of stress-induced mutagenesis in bacteria. Nat Rev Genet 2013; 14:221-7. [PMID: 23400102 DOI: 10.1038/nrg3415] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Increased mutation rates under stress allow bacterial populations to adapt rapidly to stressors, including antibiotics. Here we evaluate existing models for the evolution of stress-induced mutagenesis and present a new model arguing that it evolves as a result of a complex interplay between direct selection for increased stress tolerance, second-order selection for increased evolvability and genetic drift. Further progress in our understanding of the evolutionary biology of stress and mutagenesis will require a more detailed understanding both of the patterns of stress encountered by bacteria in nature and of the mutations that are produced under stress.
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Affiliation(s)
- R Craig MacLean
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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25
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Abstract
From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutagenesis. Such a balance is important for maintaining viability while providing an opportunity for the advantageous selection of mutations when faced with a changing environment. Over the last decade, studies of DNA repair pathways in bacteria have demonstrated considerable differences between Gram-positive and Gram-negative organisms. Here we review and discuss the DNA repair, genome maintenance, and DNA damage checkpoint pathways of the Gram-positive bacterium Bacillus subtilis. We present their molecular mechanisms and compare the functions and regulation of several pathways with known information on other organisms. We also discuss DNA repair during different growth phases and the developmental program of sporulation. In summary, we present a review of the function, regulation, and molecular mechanisms of DNA repair and mutagenesis in Gram-positive bacteria, with a strong emphasis on B. subtilis.
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PolA1, a putative DNA polymerase I, is coexpressed with PerR and contributes to peroxide stress defenses of group A Streptococcus. J Bacteriol 2012. [PMID: 23204468 DOI: 10.1128/jb.01847-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The peroxide stress response regulator PerR coordinates the oxidative-stress defenses of group A Streptococcus (GAS). We now show that PerR is expressed from an operon encoding a putative DNA polymerase I (PolA1), among other GAS products. A polA1 deletion mutant exhibited wild-type growth but showed reduced capacity to repair DNA damage caused by UV light or ciprofloxacin. Mutant bacteria were hypersensitive to H(2)O(2), compared with the wild type or a complemented mutant strain, and remained severely attenuated even after adaptation at sublethal H(2)O(2) levels, whereas wild-type bacteria could adapt to withstand peroxide challenge under identical conditions. The hypersensitivity of the mutant was reversed when bacteria were grown in iron-depleted medium and challenged in the presence of a hydroxyl radical scavenger, results that indicated sensitivity to hydroxyl radicals generated by Fenton chemistry. The peroxide resistance of a perR polA1 double mutant following adaptation at sublethal H(2)O(2) levels was decreased 9-fold relative to a perR single mutant, thus implicating PolA1 in PerR-mediated defenses against peroxide stress. Cultures of the polA1 mutant grown with or without prior H(2)O(2) exposure yielded considerably lower numbers of rifampin-resistant mutants than cultures of the wild type or the complemented mutant strain, a finding consistent with PolA1 lacking proofreading activity. We conclude that PolA1 promotes genome sequence diversity while playing an essential role in oxidative DNA damage repair mechanisms of GAS, dual functions predicted to confer optimal adaptive capacity and fitness in the host. Together, our studies reveal a unique genetic and functional relationship between PerR and PolA1 in streptococci.
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Martin HA, Pedraza-Reyes M, Yasbin RE, Robleto EA. Transcriptional de-repression and Mfd are mutagenic in stressed Bacillus subtilis cells. J Mol Microbiol Biotechnol 2012; 21:45-58. [PMID: 22248542 DOI: 10.1159/000332751] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In recent years, it has been proposed that conflicts between transcription and active chromosomal replication engender genome instability events. Furthermore, transcription elongation factors have been reported to prevent conflicts between transcription and replication and avoid genome instability. Here, we examined transcriptional de-repression as a genetic diversity-producing agent and showed, through the use of physiological and genetic means, that transcriptional de-represssion of a leuC defective allele leads to accumulation of Leu(+) mutations. We also showed, by using riboswitches that activate transcription in conditions of tyrosine or methionine starvation, that the effect of transcriptional de-repression of the leuC construct on the accumulation of Leu(+) mutations was independent of selection. We examined the role of Mfd, a transcription elongation factor involved in DNA repair, in this process and showed that proficiency of this factor promotes mutagenic events. These results are in stark contrast to previous reports in Escherichia coli, which showed that Mfd prevents replication fork collapses. Because our assays place cells under non-growing conditions, by starving them for two amino acids, we surmised that the Mfd mutagenic process associated with transcriptional de-repression does not result from conflicts with chromosomal replication. These results raise the interesting concept that transcription elongation factors may serve two functions in cells. In growing conditions, these factors prevent the generation of mutations, while in stress or non-growing conditions they mediate the production of genetic diversity.
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Costes A, Lecointe F, McGovern S, Quevillon-Cheruel S, Polard P. The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks. PLoS Genet 2010; 6:e1001238. [PMID: 21170359 PMCID: PMC3000357 DOI: 10.1371/journal.pgen.1001238] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 11/04/2010] [Indexed: 11/18/2022] Open
Abstract
We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB(Cter)) as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB(Cter) interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB(Cter) deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssbΔCter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB(Cter) acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.
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Affiliation(s)
- Audrey Costes
- Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
| | - François Lecointe
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, Jouy-en-Josas, France
| | - Stephen McGovern
- INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, Jouy-en-Josas, France
| | - Sophie Quevillon-Cheruel
- Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université de Paris-Sud, Centre National de la Recherche Scientifique, UMR8619, IFR115, Orsay, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Centre National de la Recherche Scientifique, LMGM-UMR5100, Toulouse, France
- * E-mail:
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Mutations in the Bacillus subtilis beta clamp that separate its roles in DNA replication from mismatch repair. J Bacteriol 2010; 192:3452-63. [PMID: 20453097 DOI: 10.1128/jb.01435-09] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The beta clamp is an essential replication sliding clamp required for processive DNA synthesis. The beta clamp is also critical for several additional aspects of DNA metabolism, including DNA mismatch repair (MMR). The dnaN5 allele of Bacillus subtilis encodes a mutant form of beta clamp containing the G73R substitution. Cells with the dnaN5 allele are temperature sensitive for growth due to a defect in DNA replication at 49 degrees C, and they show an increase in mutation frequency caused by a partial defect in MMR at permissive temperatures. We selected for intragenic suppressors of dnaN5 that rescued viability at 49 degrees C to determine if the DNA replication defect could be separated from the MMR defect. We isolated three intragenic suppressors of dnaN5 that restored growth at the nonpermissive temperature while maintaining an increase in mutation frequency. All three dnaN alleles encoded the G73R substitution along with one of three novel missense mutations. The missense mutations isolated were S22P, S181G, and E346K. Of these, S181G and E346K are located near the hydrophobic cleft of the beta clamp, a common site occupied by proteins that bind the beta clamp. Using several methods, we show that the increase in mutation frequency resulting from each dnaN allele is linked to a defect in MMR. Moreover, we found that S181G and E346K allowed growth at elevated temperatures and did not have an appreciable effect on mutation frequency when separated from G73R. Thus, we found that specific residue changes in the B. subtilis beta clamp separate the role of the beta clamp in DNA replication from its role in MMR.
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Abstract
Adaptive (stationary phase) mutagenesis is a phenomenon by which nondividing cells acquire beneficial mutations as a response to stress. Although the generation of adaptive mutations is essentially stochastic, genetic factors are involved in this phenomenon. We examined how defects in a transcriptional factor, previously reported to alter the acquisition of adaptive mutations, affected mutation levels in a gene under selection. The acquisition of mutations was directly correlated to the level of transcription of a defective leuC allele placed under selection. To further examine the correlation between transcription and adaptive mutation, we placed a point-mutated allele, leuC427, under the control of an inducible promoter and assayed the level of reversion to leucine prototrophy under conditions of leucine starvation. Our results demonstrate that the level of Leu(+) reversions increased significantly in parallel with the induced increase in transcription levels. This mutagenic response was not observed under conditions of exponential growth. Since transcription is a ubiquitous biological process, transcription-associated mutagenesis may influence evolutionary processes in all organisms.
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Abstract
The environment encountered by Mycobacterium tuberculosis during infection is genotoxic. Most bacteria tolerate DNA damage by engaging specialized DNA polymerases that catalyze translesion synthesis (TLS) across sites of damage. M. tuberculosis possesses two putative members of the DinB class of Y-family DNA polymerases, DinB1 (Rv1537) and DinB2 (Rv3056); however, their role in damage tolerance, mutagenesis, and survival is unknown. Here, both dinB1 and dinB2 are shown to be expressed in vitro in a growth phase-dependent manner, with dinB2 levels 12- to 40-fold higher than those of dinB1. Yeast two-hybrid analyses revealed that DinB1, but not DinB2, interacts with the beta-clamp, consistent with its canonical C-terminal beta-binding motif. However, knockout of dinB1, dinB2, or both had no effect on the susceptibility of M. tuberculosis to compounds that form N(2)-dG adducts and alkylating agents. Similarly, deletion of these genes individually or in combination did not affect the rate of spontaneous mutation to rifampin resistance or the spectrum of resistance-conferring rpoB mutations and had no impact on growth or survival in human or mouse macrophages or in mice. Moreover, neither gene conferred a mutator phenotype when expressed ectopically in Mycobacterium smegmatis. The lack of the effect of altering the complements or expression levels of dinB1 and/or dinB2 under conditions predicted to be phenotypically revealing suggests that the DinB homologs from M. tuberculosis do not behave like their counterparts from other organisms.
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van der Veen S, van Schalkwijk S, Molenaar D, de Vos WM, Abee T, Wells-Bennik MHJ. The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis. Microbiology (Reading) 2010; 156:374-384. [DOI: 10.1099/mic.0.035196-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The SOS response is a conserved pathway that is activated under certain stress conditions and is regulated by the repressor LexA and the activator RecA. The food-borne pathogen Listeria monocytogenes contains RecA and LexA homologues, but their roles in Listeria have not been established. In this study, we identified the SOS regulon in L. monocytogenes by comparing the transcription profiles of a wild-type strain and a ΔrecA mutant strain after exposure to the DNA-damaging agent mitomycin C. In agreement with studies in other bacteria, we identified an imperfect palindrome AATAAGAACATATGTTCGTTT as the SOS operator sequence. The SOS regulon of L. monocytogenes consists of 29 genes in 16 LexA-regulated operons, encoding proteins with functions in translesion DNA synthesis and DNA repair. We furthermore identified a role for the product of the LexA-regulated gene yneA in cell elongation and inhibition of cell division. As anticipated, RecA of L. monocytogenes plays a role in mutagenesis; ΔrecA cultures showed considerably lower rifampicin- and streptomycin-resistant fractions than the wild-type cultures. The SOS response is activated after stress exposure as shown by recA- and yneA-promoter reporter studies. Stress-survival studies showed ΔrecA mutant cells to be less resistant to heat, H2O2 and acid exposure than wild-type cells. Our results indicate that the SOS response of L. monocytogenes contributes to survival upon exposure to a range of stresses, thereby likely contributing to its persistence in the environment and in the host.
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Affiliation(s)
- Stijn van der Veen
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Bomenweg 2, 6703 HD Wageningen, The Netherlands
- Division of Health and Safety, NIZO Food Research, Kernhemseweg 2, 6718 ZB Ede, The Netherlands
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
| | - Saskia van Schalkwijk
- Division of Health and Safety, NIZO Food Research, Kernhemseweg 2, 6718 ZB Ede, The Netherlands
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
| | - Douwe Molenaar
- Division of Health and Safety, NIZO Food Research, Kernhemseweg 2, 6718 ZB Ede, The Netherlands
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
| | - Willem M. de Vos
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
| | - Tjakko Abee
- Laboratory of Food Microbiology, Wageningen University and Research Centre, Bomenweg 2, 6703 HD Wageningen, The Netherlands
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
| | - Marjon H. J. Wells-Bennik
- Division of Health and Safety, NIZO Food Research, Kernhemseweg 2, 6718 ZB Ede, The Netherlands
- Top Institute Food and Nutrition (TIFN), Nieuwe Kanaal 9A, 6709 PA Wageningen, The Netherlands
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Role of the Y-family DNA polymerases YqjH and YqjW in protecting sporulating Bacillus subtilis cells from DNA damage. Curr Microbiol 2009; 60:263-7. [PMID: 19924481 DOI: 10.1007/s00284-009-9535-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 10/28/2009] [Indexed: 10/20/2022]
Abstract
The role played by the Y-family DNA polymerases YqjH and YqjW in protecting sporulating cells of Bacillus subtilis from DNA damage was determined. The absence of either yqjH and/or yqjW not only reduced sporulation efficiency but also sensitized the sporulating cells to hydrogen peroxide, tert-butylhydroperoxide (t-BHP), mitomycin-C (M-C), and UV-C radiation. Moreover, these DNA-damaging agents increased the mutation frequency of wild-type sporulating cells to 4-azaleucine, but the production of mutants was YqjH- and YqjW-dependent. In conclusion, the results presented here indicate that YqjH/YqjW-dependent-translesion synthesis (TLS) operates in sporulating B. subtilis cells and contributes in processing spontaneous and artificially induced genetic damage, which is apparently required for an efficient sporulation process.
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Translesion DNA polymerases remodel the replisome and alter the speed of the replicative helicase. Proc Natl Acad Sci U S A 2009; 106:6031-8. [PMID: 19279203 DOI: 10.1073/pnas.0901403106] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All cells contain specialized translesion DNA polymerases that replicate past sites of DNA damage. We find that Escherichia coli translesion DNA polymerase II (Pol II) and polymerase IV (Pol IV) function with DnaB helicase and regulate its rate of unwinding, slowing it to as little as 1 bp/s. Furthermore, Pol II and Pol IV freely exchange with the polymerase III (Pol III) replicase on the beta-clamp and function with DnaB helicase to form alternative replisomes, even before Pol III stalls at a lesion. DNA damage-induced levels of Pol II and Pol IV dominate the clamp, slowing the helicase and stably maintaining the architecture of the replication machinery while keeping the fork moving. We propose that these dynamic actions provide additional time for normal excision repair of lesions before the replication fork reaches them and also enable the appropriate translesion polymerase to sample each lesion as it is encountered.
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Uchida K, Furukohri A, Shinozaki Y, Mori T, Ogawara D, Kanaya S, Nohmi T, Maki H, Akiyama M. Overproduction ofEscherichia coliDNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol 2008; 70:608-22. [DOI: 10.1111/j.1365-2958.2008.06423.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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36
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Robleto EA, Yasbin R, Ross C, Pedraza-Reyes M. Stationary phase mutagenesis in B. subtilis: a paradigm to study genetic diversity programs in cells under stress. Crit Rev Biochem Mol Biol 2008; 42:327-39. [PMID: 17917870 DOI: 10.1080/10409230701597717] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
One of the experimental platforms to study programs increasing genetic diversity in cells under stressful or nondividing conditions is adaptive mutagenesis, also called stationary phase mutagenesis or stress-induced mutagenesis. In some model systems, there is evidence that mutagenesis occurs in genes that are actively transcribed. Some of those genes may be actively transcribed as a result of environmental stress giving the appearance of directed mutation. That is, cells under conditions of starvation or other stresses accumulate mutations in transcribed genes, including those transcribed because of the selective pressure. An important question concerns how, within the context of stochastic processes, a cell biases mutation to genes under selection pressure? Because the mechanisms underlying DNA transactions in prokaryotic cells are well conserved among the three domains of life, these studies are likely to apply to the examination of genetic programs in eukaryotes. In eukaryotes, increasing genetic diversity in differentiated cells has been implicated in neoplasia and cell aging. Historically, Escherichia coli has been the paradigm used to discern the cellular processes driving the generation of adaptive mutations; however, examining adaptive mutation in Bacillus subtilis has contributed new insights. One noteworthy contribution is that the B. subtilis' ability to accumulate chromosomal mutations under conditions of starvation is influenced by cell differentiation and transcriptional derepression, as well as by proteins homologous to transcription and repair factors. Here we revise and discuss concepts pertaining to genetic programs that increase diversity in B. subtilis cells under nutritional stress.
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Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Eswara Moorthy P, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One 2007; 2:e928. [PMID: 17895969 PMCID: PMC1976550 DOI: 10.1371/journal.pone.0000928] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 08/31/2007] [Indexed: 11/25/2022] Open
Abstract
Background Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, γ-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. Principal Findings The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. Significance This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.
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Affiliation(s)
- Jason Gioia
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Okezie C. Igboeli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alicia Hawes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lesette Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huyen Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sandra Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter Blyth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Indrani Dasgupta
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Lina Bokhetache
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Fathi Karouia
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Prahathees Eswara Moorthy
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Johnathan Siefert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Akif Uzman
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Prince Buzumbo
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Avani Verma
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Hiba Zwiya
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Brian D. McWilliams
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adeola Olowu
- University of St. Thomas, Houston Texas, United States of America
| | - Kenneth D. Clinkenbeard
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - David Newcombe
- University of Idaho Coeur d'Alene, Coeur d'Alene, Idaho, United States of America
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Lisa Golebiewski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wayne L. Nicholson
- Department of Microbiology and Cell Science, University of Florida Space Life Sciences Laboratory, Kennedy Space Center, Florida, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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Varhimo E, Savijoki K, Jalava J, Kuipers OP, Varmanen P. Identification of a novel streptococcal gene cassette mediating SOS mutagenesis in Streptococcus uberis. J Bacteriol 2007; 189:5210-22. [PMID: 17513475 PMCID: PMC1951879 DOI: 10.1128/jb.00473-07] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 05/08/2007] [Indexed: 11/20/2022] Open
Abstract
Streptococci have been considered to lack the classical SOS response, defined by increased mutation after UV exposure and regulation by LexA. Here we report the identification of a potential self-regulated SOS mutagenesis gene cassette in the Streptococcaceae family. Exposure to UV light was found to increase mutations to antibiotic resistance in Streptococcus uberis cultures. The mutational spectra revealed mainly G:C-->A:T transitions, and Northern analyses demonstrated increased expression of a Y-family DNA polymerase resembling UmuC under DNA-damaging conditions. In the absence of the Y-family polymerase, S. uberis cells were sensitive to UV light and to mitomycin C. Furthermore, the UV-induced mutagenesis was almost completely abolished in cells deficient in the Y-family polymerase. The gene encoding the Y-family polymerase was localized in a four-gene operon including two hypothetical genes and a gene encoding a HdiR homolog. Electrophoretic mobility shift assays demonstrated that S. uberis HdiR binds specifically to an inverted repeat sequence in the promoter region of the four-gene operon. Database searches revealed conservation of the gene cassette in several Streptococcus species, including at least one genome each of Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus mitis, Streptococcus sanguinis, and Streptococcus thermophilus strains. In addition, the umuC operon was localized in several mobile DNA elements of Streptococcus and Lactococcus species. We conclude that the hdiR-umuC-ORF3-ORF4 operon represents a novel gene cassette capable of mediating SOS mutagenesis among members of the Streptococcaceae.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Blotting, Northern
- Ciprofloxacin/pharmacology
- DNA Damage
- Drug Resistance, Bacterial/genetics
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Bacterial/drug effects
- Gene Expression Regulation, Bacterial/radiation effects
- Genes, Bacterial
- Mitomycin/pharmacology
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis
- Mutation
- Operon
- Rifampin/pharmacology
- SOS Response, Genetics/drug effects
- SOS Response, Genetics/genetics
- SOS Response, Genetics/radiation effects
- Sequence Homology, Nucleic Acid
- Streptococcus/drug effects
- Streptococcus/genetics
- Streptococcus/radiation effects
- Ultraviolet Rays
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Affiliation(s)
- Emilia Varhimo
- University of Helsinki, Department of Basic Veterinary Sciences, P.O. Box 66, FIN-00014, Finland
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39
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Claverys JP, Prudhomme M, Martin B. Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol 2006; 60:451-75. [PMID: 16771651 DOI: 10.1146/annurev.micro.60.080805.142139] [Citation(s) in RCA: 295] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacterial transformation, a programmed mechanism for genetic exchange originally discovered in Streptococcus pneumoniae, is widespread in bacteria. It is based on the uptake and integration of exogenous DNA into the recipient genome. This review examines whether induction of competence for genetic transformation is a general response to stress in gram-positive bacteria. It compares data obtained with bacteria chosen for their different lifestyles, the soil-dweller Bacillus subtilis and the major human pathogen S. pneumoniae. The review focuses on the relationship between competence and other global responses in B. subtilis, as well as on recent evidence for competence induction in response to DNA damage or antibiotics and for the ability of S. pneumoniae to use competence as a substitute for SOS. This comparison reveals that the two species use different fitness-enhancing strategies in response to stress conditions. Whereas B. subtilis combines competence and SOS induction, S. pneumoniae relies only on competence to generate genetic diversity through transformation.
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Affiliation(s)
- Jean-Pierre Claverys
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR 5100 CNRS-Université Paul Sabatier, 31062 Toulouse Cedex 9, France.
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40
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Cirz RT, Jones MB, Gingles NA, Minogue TD, Jarrahi B, Peterson SN, Romesberg FE. Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin. J Bacteriol 2006; 189:531-9. [PMID: 17085555 PMCID: PMC1797410 DOI: 10.1128/jb.01464-06] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Staphylococcus aureus infections can be difficult to treat due to both multidrug resistance and the organism's remarkable ability to persist in the host. Persistence and the evolution of resistance may be related to several complex regulatory networks, such as the SOS response, which modifies transcription in response to environmental stress. To understand how S. aureus persists during antibiotic therapy and eventually emerges resistant, we characterized its global transcriptional response to ciprofloxacin. We found that ciprofloxacin induces prophage mobilization as well as significant alterations in metabolism, most notably the up-regulation of the tricarboxylic acid cycle. In addition, we found that ciprofloxacin induces the SOS response, which we show, by comparison of a wild-type strain and a non-SOS-inducible lexA mutant strain, includes the derepression of 16 genes. While the SOS response of S. aureus is much more limited than those of Escherichia coli and Bacillus subtilis, it is similar to that of Pseudomonas aeruginosa and includes RecA, LexA, several hypothetical proteins, and a likely error-prone Y family polymerase whose homologs in other bacteria are required for induced mutation. We also examined induced mutation and found that either the inability to derepress the SOS response or the lack of the LexA-regulated polymerase renders S. aureus unable to evolve antibiotic resistance in vitro in response to UV damage. The data suggest that up-regulation of the tricarboxylic acid cycle and induced mutation facilitate S. aureus persistence and evolution of resistance during antibiotic therapy.
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Affiliation(s)
- Ryan T Cirz
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Goranov AI, Kuester-Schoeck E, Wang JD, Grossman AD. Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. J Bacteriol 2006; 188:5595-605. [PMID: 16855250 PMCID: PMC1540033 DOI: 10.1128/jb.00342-06] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA damage and perturbations in DNA replication can induce global transcriptional responses that can help organisms repair the damage and survive. RecA is known to mediate transcriptional responses to DNA damage in several bacterial species by inactivating the repressor LexA and phage repressors. To gain insight into how Bacillus subtilis responds to various types of DNA damage, we measured the effects of DNA damage and perturbations in replication on mRNA levels by using DNA microarrays. We perturbed replication either directly with p-hydroxyphenylazo-uracil (HPUra), an inhibitor of DNA polymerase, or indirectly with the DNA-damaging reagents mitomycin C (MMC) and UV irradiation. Our results indicate that the transcriptional responses to HPUra, MMC, and UV are only partially overlapping. recA is the major transcriptional regulator under all of the tested conditions, and LexA appears to directly repress the expression of 63 genes in 26 operons, including the 18 operons previously identified as LexA targets. MMC and HPUra treatments caused induction of an integrative and conjugative element (ICEBs1) and resident prophages (PBSX and SPbeta), which affected the expression of many host genes. Consistent with previous results, the induction of these mobile elements required recA. Induction of the phage appeared to require inactivation of LexA. Unrepaired UV damage and treatment with MMC also affected the expression of some of the genes that are controlled by DnaA. Furthermore, MMC treatment caused an increase in origin-proximal gene dosage. Our results indicate that different types of DNA damage have different effects on replication and on the global transcriptional profile.
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Affiliation(s)
- Alexi I Goranov
- Department of Biology, Building 68-530, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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42
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Duigou S, Ehrlich SD, Noirot P, Noirot-Gros MF. DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis. Mol Microbiol 2005; 57:678-90. [PMID: 16045613 DOI: 10.1111/j.1365-2958.2005.04725.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Translesion synthesis (TLS) across damaged DNA bases is most often carried out by the ubiquitous error-prone DNA polymerases of the Y-family. Bacillus subtilis encodes two Y-polymerases, Pol Y1 and Pol Y2, that mediate TLS resulting in spontaneous and ultraviolet light (UV)-induced mutagenesis respectively. Here we show that TLS is a bipartite dual polymerase process in B. subtilis, involving not only the Y-polymerases but also the A-family polymerase, DNA polymerase I (Pol I). Both the spontaneous and the UV-induced mutagenesis are abolished in Pol I mutants affected solely in the polymerase catalytic site. Physical interactions between Pol I and either of the Pol Y polymerases, as well as formation of a ternary complex between Pol Y1, Pol I and the beta-clamp, were detected by yeast two- and three-hybrid assays, supporting the model of a functional coupling between the A- and Y-family polymerases in TLS. We suggest that the Pol Y carries the synthesis across the lesion, and Pol I takes over to extend the synthesis until the functional replisome resumes replication. This key role of Pol I in TLS uncovers a new function of the A-family DNA polymerases.
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Affiliation(s)
- Stéphane Duigou
- Laboratoire de Génétique Microbienne, Domaine de Vilvert, INRA, 78352 Jouy en Josas Cedex, France
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43
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Galhardo RS, Rocha RP, Marques MV, Menck CFM. An SOS-regulated operon involved in damage-inducible mutagenesis in Caulobacter crescentus. Nucleic Acids Res 2005; 33:2603-14. [PMID: 15886391 PMCID: PMC1092274 DOI: 10.1093/nar/gki551] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
DNA polymerases of the Y-family, such as Escherichia coli UmuC and DinB, are specialized enzymes induced by the SOS response, which bypass lesions allowing the continuation of DNA replication. umuDC orthologs are absent in Caulobacter crescentus and other bacteria, raising the question about the existence of SOS mutagenesis in these organisms. Here, we report that the C.crescentus dinB ortholog is not involved in damage-induced mutagenesis. However, an operon composed of two hypothetical genes and dnaE2, encoding a second copy of the catalytic subunit of Pol III, is damage inducible in a recA-dependent manner, and is responsible for most ultraviolet (UV) and mitomycin C-induced mutations in C.crescentus. The results demonstrate that the three genes are required for the error-prone processing of DNA lesions. The two hypothetical genes were named imuA and imuB, after inducible mutagenesis. ImuB is similar to proteins of the Y-family of polymerases, and possibly cooperates with DnaE2 in lesion bypass. The mutations arising as a consequence of the activity of the imuAB dnaE2 operon are rather unusual for UV irradiation, including G:C to C:G transversions.
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Affiliation(s)
| | | | | | - Carlos F. M. Menck
- To whom correspondence should be addressed at Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Avenue Professor Lineu Prestes, 1374, São Paulo, SP 05508-900, Brazil. Tel: +55 11 3091 7499; Fax: +55 11 3091 7354;
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