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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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RetS Regulates Phage Infection in Pseudomonas aeruginosa via Modulating the GacS/GacA Two-Component System. J Virol 2022; 96:e0019722. [PMID: 35348363 DOI: 10.1128/jvi.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In Pseudomonas aeruginosa, the complex multisensing regulatory networks RetS-GacS/GacA have been demonstrated to play key roles in controlling the switch between planktonic and sessile lifestyles. However, whether this multisensing system is involved in the regulation of phage infection has not been investigated. Here, we provide a link between the sensors RetS/GacS and infection of phages vB_Pae_QDWS and vB_Pae_W3. Our data suggest that the sensors kinases RetS and GacS in Pseudomonas aeruginosa play opposite regulatory functions on phage infection. Mutation in retS increased phage resistance. Cellular levels of RsmY and RsmZ increased in PaΔretS and were positively correlated with phage resistance. Further analysis demonstrated that RetS regulated phage infection by affecting the type IV pilus (T4P)-mediated adsorption. The regulation of RetS on phage infection depends on the GacS/GacA two-component system and is likely a dynamic process in response to environmental signals. The findings offer additional support for the rapid emergence of phage resistance. IMPORTANCE Our knowledge on the molecular mechanisms behind bacterium-phage interactions remains limited. Our study reported that the complex multisensing regulatory networks RetS-GacS/GacA of Pseudomonas aeruginosa PAO1 play key roles in controlling phage infection. The main observation was that the mutation in RetS could result in increased phage resistance by reducing the type IV pilus-mediated phage adsorption. The bacterial defense strategy is generally applicable to various phages since many P. aeruginosa phages can use type IV pilus as their receptors. The results also suggest that the phage infection is likely to be regulated dynamically, which depends on the environmental stimuli. Reduction of the signals that RetS favors would increase phage resistance. Our study is particularly remarkable for uncovering a signal transduction system that was involved in phage infection, which may help in filling some knowledge gaps in this field.
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3
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Ramos C, Hernández-Tamayo R, López-Sanz M, Carrasco B, Serrano E, Alonso JC, Graumann PL, Ayora S. The RecD2 helicase balances RecA activities. Nucleic Acids Res 2022; 50:3432-3444. [PMID: 35234892 PMCID: PMC8989531 DOI: 10.1093/nar/gkac131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
DNA helicases of the RecD2 family are ubiquitous. Bacillus subtilis RecD2 in association with the single-stranded binding protein SsbA may contribute to replication fork progression, but its detailed action remains unknown. In this work, we explore the role of RecD2 during DNA replication and its interaction with the RecA recombinase. RecD2 inhibits replication restart, but this effect is not observed in the absence of SsbA. RecD2 slightly affects replication elongation. RecA inhibits leading and lagging strand synthesis, and RecD2, which physically interacts with RecA, counteracts this negative effect. In vivo results show that recD2 inactivation promotes RecA–ssDNA accumulation at low mitomycin C levels, and that RecA threads persist for a longer time after induction of DNA damage. In vitro, RecD2 modulates RecA-mediated DNA strand-exchange and catalyzes branch migration. These findings contribute to our understanding of how RecD2 may contribute to overcome a replicative stress, removing RecA from the ssDNA and, thus, it may act as a negative modulator of RecA filament growth.
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Affiliation(s)
- Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
| | - Peter L Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße 6, 35043 Marburg, Germany.,Fachbereich Chemie, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049Madrid, Spain
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4
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Khemici V, Prudhomme M, Polard P. Tight Interplay between Replication Stress and Competence Induction in Streptococcus pneumoniae. Cells 2021; 10:cells10081938. [PMID: 34440707 PMCID: PMC8394987 DOI: 10.3390/cells10081938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 11/18/2022] Open
Abstract
Cells respond to genome damage by inducing restorative programs, typified by the SOS response of Escherichia coli. Streptococcus pneumoniae (the pneumococcus), with no equivalent to the SOS system, induces the genetic program of competence in response to many types of stress, including genotoxic drugs. The pneumococcal competence regulon is controlled by the origin-proximal, auto-inducible comCDE operon. It was previously proposed that replication stress induces competence through continued initiation of replication in cells with arrested forks, thereby increasing the relative comCDE gene dosage and expression and accelerating the onset of competence. We have further investigated competence induction by genome stress. We find that absence of RecA recombinase stimulates competence induction, in contrast to SOS response, and that double-strand break repair (RexB) and gap repair (RecO, RecR) initiation effectors confer a similar effect, implying that recombinational repair removes competence induction signals. Failure of replication forks provoked by titrating PolC polymerase with the base analogue HPUra, over-supplying DnaA initiator, or under-supplying DnaE polymerase or DnaC helicase stimulated competence induction. This induction was not correlated with concurrent changes in origin-proximal gene dosage. Our results point to arrested and unrepaired replication forks, rather than increased comCDE dosage, as a basic trigger of pneumococcal competence.
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Affiliation(s)
- Vanessa Khemici
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Integrative (CBI), Centre National de la Recherche Scientifique (CNRS), 31062 Toulouse, France; (V.K.); (M.P.)
- Université de Toulouse, Université Paul Sabatier, 31062 Toulouse, France
| | - Marc Prudhomme
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Integrative (CBI), Centre National de la Recherche Scientifique (CNRS), 31062 Toulouse, France; (V.K.); (M.P.)
- Université de Toulouse, Université Paul Sabatier, 31062 Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Integrative (CBI), Centre National de la Recherche Scientifique (CNRS), 31062 Toulouse, France; (V.K.); (M.P.)
- Université de Toulouse, Université Paul Sabatier, 31062 Toulouse, France
- Correspondence:
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5
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Labarde A, Jakutyte L, Billaudeau C, Fauler B, López-Sanz M, Ponien P, Jacquet E, Mielke T, Ayora S, Carballido-López R, Tavares P. Temporal compartmentalization of viral infection in bacterial cells. Proc Natl Acad Sci U S A 2021; 118:e2018297118. [PMID: 34244425 PMCID: PMC8285916 DOI: 10.1073/pnas.2018297118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virus infection causes major rearrangements in the subcellular architecture of eukaryotes, but its impact in prokaryotic cells was much less characterized. Here, we show that infection of the bacterium Bacillus subtilis by bacteriophage SPP1 leads to a hijacking of host replication proteins to assemble hybrid viral-bacterial replisomes for SPP1 genome replication. Their biosynthetic activity doubles the cell total DNA content within 15 min. Replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. This large nucleoprotein complex is a self-contained compartment whose boundaries are delimited neither by a membrane nor by a protein cage. Later during infection, SPP1 procapsids localize at the periphery of the viral DNA compartment for genome packaging. The resulting DNA-filled capsids do not remain associated to the DNA transactions compartment. They bind to phage tails to build infectious particles that are stored in warehouse compartments spatially independent from the viral DNA. Free SPP1 structural proteins are recruited to the dynamic phage-induced compartments following an order that recapitulates the viral particle assembly pathway. These findings show that bacteriophages restructure the crowded host cytoplasm to confine at different cellular locations the sequential processes that are essential for their multiplication.
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Affiliation(s)
- Audrey Labarde
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lina Jakutyte
- Laboratoire de Virologie Moléculaire et Structurale, CNRS Unité Propre de Recherche 3296 and Institut Fédératif de Recherche 115, 91198 Gif-sur-Yvette, France
| | - Cyrille Billaudeau
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Beatrix Fauler
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Maria López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Prishila Ponien
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Eric Jacquet
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195, Berlin, Germany
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Rut Carballido-López
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Paulo Tavares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France;
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Single-Molecule Dynamics at a Bacterial Replication Fork after Nutritional Downshift or Chemically Induced Block in Replication. mSphere 2021; 6:6/1/e00948-20. [PMID: 33504660 PMCID: PMC7885319 DOI: 10.1128/msphere.00948-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Replication forks must respond to changes in nutrient conditions, especially in bacterial cells. By investigating the single-molecule dynamics of replicative helicase DnaC, DNA primase DnaG, and lagging-strand polymerase DnaE in the model bacterium Bacillus subtilis, we show that proteins react differently to stress conditions in response to transient replication blocks due to DNA damage, to inhibition of the replicative polymerase, or to downshift of serine availability. DnaG appears to be recruited to the forks by a diffusion and capture mechanism, becomes more statically associated after the arrest of polymerase, but binds less frequently after fork blocks due to DNA damage or to nutritional downshift. These results indicate that binding of the alarmone (p)ppGpp due to stringent response prevents DnaG from binding to forks rather than blocking bound primase. Dissimilar behavior of DnaG and DnaE suggests that both proteins are recruited independently to the forks rather than jointly. Turnover of all three proteins was increased during replication block after nutritional downshift, different from the situation due to DNA damage or polymerase inhibition, showing high plasticity of forks in response to different stress conditions. Forks persisted during all stress conditions, apparently ensuring rapid return to replication extension.IMPORTANCE All cells need to adjust DNA replication, which is achieved by a well-orchestrated multiprotein complex, in response to changes in physiological and environmental conditions. For replication forks, it is extremely challenging to meet with conditions where amino acids are rapidly depleted from cells, called the stringent response, to deal with the inhibition of one of the centrally involved proteins or with DNA modifications that arrest the progression of forks. By tracking helicase (DnaC), primase (DnaG), and polymerase (DnaE), central proteins of Bacillus subtilis replication forks, at a single molecule level in real time, we found that interactions of the three proteins with replication forks change in different manners under different stress conditions, revealing an intriguing plasticity of replication forks in dealing with replication obstacles. We have devised a new tool to determine rates of exchange between static movement (binding to a much larger complex) and free diffusion, showing that during stringent response, all proteins have highly increased exchange rates, slowing down overall replication, while inactivation of polymerase or replication roadblocks leaves forks largely intact, allowing rapid restart once obstacles are removed.
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7
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Peng Y, Han X, Xu P, Tao F. Next‐Generation Microbial Workhorses: Comparative Genomic Analysis of Fast‐GrowingVibrioStrains Reveals Their Biotechnological Potential. Biotechnol J 2020; 15:e1900499. [DOI: 10.1002/biot.201900499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Yuan Peng
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Xiao Han
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Fei Tao
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong University Shanghai 200240 P. R. China
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8
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Serrano E, Ramos C, Ayora S, Alonso JC. Viral SPP1 DNA is infectious in naturally competent Bacillus subtilis cells: inter- and intramolecular recombination pathways. Environ Microbiol 2020; 22:714-725. [PMID: 31876108 DOI: 10.1111/1462-2920.14908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 01/09/2023]
Abstract
A proteolyzed bacteriophage (phage) might release its DNA into the environment. Here, we define the recombination functions required to resurrect an infective lytic phage from inactive environmental viral DNA in naturally competent Bacillus subtilis cells. Using phage SPP1 DNA, a model that accounts for the obtained data is proposed (i) the DNA uptake apparatus takes up environmental SPP1 DNA, fragments it, and incorporates into the cytosol different linear single-stranded (ss) DNA molecules shorter than genome-length; (ii) the SsbA-DprA mediator loads RecA onto any fragmented linear SPP1 ssDNA, but negative modulators (RecX and RecU) promote a net RecA disassembly from these ssDNAs not homologous to the host genome; (iii) single strand annealing (SSA) proteins, DprA and RecO, anneal the SsbA- or SsbB-coated complementary strands, yielding tailed SPP1 duplex intermediates; (iv) RecA polymerized on these tailed intermediates invades a homologous region in another incomplete molecule, and in concert with RecD2 helicase, reconstitutes a complete linear phage genome with redundant regions at the ends of the molecule; and (v) DprA, RecO or viral G35P SSA, may catalyze the annealing of these terminally redundant regions, alone or with the help of an exonuclease, to produce a circular unit-length duplex viral genome ready to initiate replication.
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Affiliation(s)
- Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049, Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049, Madrid, Spain
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9
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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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10
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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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11
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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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12
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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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13
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Oliveira Paiva AM, Friggen AH, Qin L, Douwes R, Dame RT, Smits WK. The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile. J Mol Biol 2019; 431:653-672. [PMID: 30633871 DOI: 10.1016/j.jmb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022]
Abstract
The maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA and modulate its conformation, and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of Clostridium difficile have been characterized to date. Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10-kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G + C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo. The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.
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Affiliation(s)
- Ana M Oliveira Paiva
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Annemieke H Friggen
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Liang Qin
- Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Roxanne Douwes
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands
| | - Remus T Dame
- Faculty of Science, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, the Netherlands; Center for Microbial Cell Biology, Leiden, the Netherlands.
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14
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The Revisited Genome of Bacillus subtilis Bacteriophage SPP1. Viruses 2018; 10:v10120705. [PMID: 30544981 PMCID: PMC6316719 DOI: 10.3390/v10120705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/06/2018] [Accepted: 12/06/2018] [Indexed: 02/05/2023] Open
Abstract
Bacillus subtilis bacteriophage SPP1 is a lytic siphovirus first described 50 years ago [1]. Its complete DNA sequence was reported in 1997 [2]. Here we present an updated annotation of the 44,016 bp SPP1 genome and its correlation to different steps of the viral multiplication process. Five early polycistronic transcriptional units encode phage DNA replication proteins and lysis functions together with less characterized, mostly non-essential, functions. Late transcription drives synthesis of proteins necessary for SPP1 viral particles assembly and for cell lysis, together with a short set of proteins of unknown function. The extensive genetic, biochemical and structural biology studies on the molecular mechanisms of SPP1 DNA replication and phage particle assembly rendered it a model system for tailed phages research. We propose SPP1 as the reference species for a new SPP1-like viruses genus of the Siphoviridae family.
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15
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Carrasco B, Seco EM, López-Sanz M, Alonso JC, Ayora S. Bacillus subtilis RarA modulates replication restart. Nucleic Acids Res 2018; 46:7206-7220. [PMID: 29947798 PMCID: PMC6101539 DOI: 10.1093/nar/gky541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 02/01/2023] Open
Abstract
The ubiquitous RarA/Mgs1/WRNIP protein plays a crucial, but poorly understood role in genome maintenance. We show that Bacillus subtilis RarA, in the apo form, preferentially binds single-stranded (ss) over double-stranded (ds) DNA. SsbA bound to ssDNA loads RarA, and for such recruitment the amphipathic C-terminal domain of SsbA is required. RarA is a DNA-dependent ATPase strongly stimulated by ssDNA–dsDNA junctions and SsbA, or by dsDNA ends. RarA, which may interact with PriA, does not stimulate PriA DNA unwinding. In a reconstituted PriA-dependent DNA replication system, RarA inhibited initiation, but not chain elongation. The RarA effect was not observed in the absence of SsbA, or when the host-encoded preprimosome and the DNA helicase are replaced by proteins from the SPP1 phage with similar function. We propose that RarA assembles at blocked forks to maintain genome integrity. Through its interaction with SsbA and with a preprimosomal component, RarA might impede the assembly of the replicative helicase, to prevent that recombination intermediates contribute to pathological DNA replication restart.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Elena M Seco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, (CNB-CSIC), Cantoblanco 28049, Madrid, Spain
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16
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Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa. Nat Commun 2018; 9:1846. [PMID: 29748556 PMCID: PMC5945682 DOI: 10.1038/s41467-018-04232-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Our understanding of the molecular mechanisms behind bacteria-phage interactions remains limited. Here we report that a small protein, SrpA, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa. We show that SrpA is essential for efficient genome replication of phage K5, and controls transcription by binding to a palindromic sequence upstream of the phage RNA polymerase gene. We identify potential SrpA-binding sites in 66 promoter regions across the P. aeruginosa genome, and experimentally validate direct binding of SrpA to some of these sites. Using transcriptomics and further experiments, we show that SrpA, directly or indirectly, regulates many cellular processes including cell motility, chemotaxis, biofilm formation, pyocyanin synthesis and protein secretion, as well as virulence in a Caenorhabditis elegans model of infection. Further research on SrpA and similar proteins, which are widely present in many other bacteria, is warranted. You et al. show that SrpA, a small protein widely conserved among bacteria, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa, including cell motility, chemotaxis, biofilm formation, and virulence.
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17
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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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18
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Valero-Rello A, López-Sanz M, Quevedo-Olmos A, Sorokin A, Ayora S. Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1. Front Microbiol 2017; 8:1816. [PMID: 29018417 PMCID: PMC5615212 DOI: 10.3389/fmicb.2017.01816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/06/2017] [Indexed: 01/02/2023] Open
Abstract
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5′→3′ exonuclease (G34.1P), the single-stranded DNA binding protein (G36P) and the Holliday junction resolvase (G44P). Correspondingly, the accumulation of linear concatemeric plasmid DNA, and the formation of transducing particles were blocked in the absence of G35P, G38P, G39P, and G40P, greatly reduced in the G34.1P, G36P mutants, and slightly reduced in G44P mutants. In contrast, establishment of injected linear plasmid DNA in the recipient host was independent of viral-encoded functions. DNA homology between SPP1 and the plasmid, rather than a viral packaging signal, enhanced the accumulation of packagable plasmid DNA. The transfer efficiency was also dependent on plasmid copy number, and rolling-circle plasmids were encapsidated at higher frequencies than theta-type replicating plasmids.
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Affiliation(s)
- Ana Valero-Rello
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain.,Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alvaro Quevedo-Olmos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alexei Sorokin
- Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
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