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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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Stoll J, Zegarra V, Bange G, Graumann PL. Single-molecule dynamics suggest that ribosomes assemble at sites of translation in Bacillus subtilis. Front Microbiol 2022; 13:999176. [PMID: 36406443 PMCID: PMC9670183 DOI: 10.3389/fmicb.2022.999176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 04/07/2024] Open
Abstract
Eukaryotic cells transcribe ribosomal RNA and largely assemble ribosomes in a structure called the nucleolus, where chromosomal regions containing rRNA operons are clustered. In bacteria, many rRNA operons cluster close to the origin regions that are positioned on the outer borders of nucleoids, close to polar areas, where translating 70S ribosomes are located. Because outer regions of the nucleoids contain the highest accumulation of RNA polymerase, it has been hypothesized that bacteria contain "nucleolus-like" structures. However, ribosome subunits freely diffuse through the entire cells, and could thus be assembled and matured throughout the non-compartmentalized cell. By tracking single molecules of two GTPases that play an essential role in ribosomal folding and processing in Bacillus subtilis, we show that this process takes place at sites of translation, i.e., predominantly at the cell poles. Induction of the stringent response led to a change in the population of GTPases assumed to be active in maturation, but did not abolish nucleoid occlusion of ribosomes or of GTPases. Our findings strongly support the idea of the conceptualization of nucleolus-like structures in bacteria, i.e., rRNA synthesis, ribosomal protein synthesis and subunit assembly occurring in close proximity at the cell poles, facilitating the efficiency of ribosome maturation even under conditions of transient nutrient deprivation.
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Affiliation(s)
| | | | | | - Peter L. Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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Moreno-Del Alamo M, Torres R, Manfredi C, Ruiz-Masó JA, Del Solar G, Alonso JC. Bacillus subtilis PcrA Couples DNA Replication, Transcription, Recombination and Segregation. Front Mol Biosci 2020; 7:140. [PMID: 32793628 PMCID: PMC7385302 DOI: 10.3389/fmolb.2020.00140] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/10/2020] [Indexed: 01/08/2023] Open
Abstract
Bacillus subtilis PcrA abrogates replication-transcription conflicts in vivo and disrupts RecA nucleoprotein filaments in vitro. Inactivation of pcrA is lethal. We show that PcrA depletion lethality is suppressed by recJ (involved in end resection), recA (the recombinase), or mfd (transcription-coupled repair) inactivation, but not by inactivating end resection (addAB or recQ), positive and negative RecA modulators (rarA or recX and recU), or genes involved in the reactivation of a stalled RNA polymerase (recD2, helD, hepA, and ywqA). We also report that B. subtilis mutations previously designated as recL16 actually map to the recO locus, and confirm that PcrA depletion lethality is suppressed by recO inactivation. The pcrA gene is epistatic to recA or mfd, but it is not epistatic to addAB, recJ, recQ, recO16, rarA, recX, recU, recD2, helD, hepA, or ywqA in response to DNA damage. PcrA depletion led to the accumulation of unsegregated chromosomes, and this defect is increased by recQ, rarA, or recU inactivation. We propose that PcrA, which is crucial to maintain cell viability, is involved in different DNA transactions.
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Affiliation(s)
- María Moreno-Del Alamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Candela Manfredi
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - José A Ruiz-Masó
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Gloria Del Solar
- Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
| | - Juan Carlos Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
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Romero H, Serrano E, Hernández-Tamayo R, Carrasco B, Cárdenas PP, Ayora S, Graumann PL, Alonso JC. Bacillus subtilis RarA Acts as a Positive RecA Accessory Protein. Front Microbiol 2020; 11:92. [PMID: 32117122 PMCID: PMC7031210 DOI: 10.3389/fmicb.2020.00092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/16/2020] [Indexed: 01/15/2023] Open
Abstract
Ubiquitous RarA AAA+ ATPases play crucial roles in the cellular response to blocked replication forks in pro- and eukaryotes. Here, we provide evidence that absence of RarA reduced the viability of ΔrecA, ΔrecO, and recF15 cells during unperturbed growth. The rarA gene was epistatic to recO and recF genes in response to H2O2- or MMS-induced DNA damage. Conversely, the inactivation of rarA partially suppressed the HR defect of mutants lacking end-resection (ΔaddAB, ΔrecJ, ΔrecQ, ΔrecS) or branch migration (ΔruvAB, ΔrecG, ΔradA) activity. RarA contributes to RecA thread formation, that are thought to be the active forms of RecA during homology search. The absence of RarA reduced RecA accumulation, and the formation of visible RecA threads in vivo upon DNA damage. When ΔrarA was combined with mutations in genuine RecA accessory genes, RecA accumulation was further reduced in ΔrarA ΔrecU and ΔrarA ΔrecX double mutant cells, and was blocked in ΔrarA recF15 cells. These results suggest that RarA contributes to the assembly of RecA nucleoprotein filaments onto single-stranded DNA, and possibly antagonizes RecA filament disassembly.
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Affiliation(s)
- Hector Romero
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Paula P. Cárdenas
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Peter L. Graumann
- SYNMIKRO, LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Juan C. Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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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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Hernández-Tamayo R, Graumann PL. Bacillus subtilis RarA forms damage-inducible foci that scan the entire cell. BMC Res Notes 2019; 12:219. [PMID: 30971308 PMCID: PMC6458690 DOI: 10.1186/s13104-019-4252-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Little is known about the activity and dynamics of ATPase RarA in B. subtilis, proposed to act at stalled DNA replication forks due to DNA damage. We performed fluorescence microscopy time lapse experiments with a functional RarA-mVenus fusion to visualize the dynamics of RarA during conditions that generate DNA damage. DATA DESCRIPTION In exponentially growing cells, we observed that 15% of the cells contained single RarA-mV (mVenus fluorescent fusion) foci moving throughout the entire cell between 3 min intervals. This percentage remained constant at different time points, indicating that focus formation during unperturbed growth is maintained at about a constant rate. When cells were exposed to stress conditions, the population of cells containing RarA-mV foci tripled after 60 min. Cells exposed to two DNA-damaging drugs, to 5 mM MMS or to 0.5 mM H2O2, showed a similar type of response, with RarA-mVenus foci moving more slowly than during unperturbed growth. It is likely that RarA-mV contributes to the repair of H2O2-induced lesions, and to a minor extent to MMS-induced lesions. The presence of foci in growing cells suggests that RarA also plays a role during the cell cycle, at least in a fraction of cells, possibly contributing to heterogeneity of response to DNA damage.
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Affiliation(s)
- Rogelio Hernández-Tamayo
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße 6, 35032, Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Straße 6, 35032, Marburg, Germany.
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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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