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Van Duyne GD, Landy A. Bacteriophage lambda site-specific recombination. Mol Microbiol 2024; 121:895-911. [PMID: 38372210 PMCID: PMC11096046 DOI: 10.1111/mmi.15241] [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: 08/29/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The site-specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage-encoded Int and Xis proteins and the host-encoded integration host factor and factor for inversion stimulation proteins. Structures of higher-order protein-DNA complexes of the four-way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site-specific recombination, with an emphasis on key studies completed over the last decade.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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2
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Kurasz JE, Crawford MC, Porwollik S, Gregory O, Tadlock KR, Balding EC, Weinert EE, McClelland M, Karls AC. Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium. J Bacteriol 2023; 205:e0026222. [PMID: 36622230 PMCID: PMC9879122 DOI: 10.1128/jb.00262-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
The adaptation of Salmonella enterica serovar Typhimurium to stress conditions involves expression of genes within the regulon of the alternative sigma factor RpoN (σ54). RpoN-dependent transcription requires an activated bacterial enhancer binding protein (bEBP) that hydrolyzes ATP to remodel the RpoN-holoenzyme-promoter complex for transcription initiation. The bEBP RtcR in S. Typhimurium strain 14028s is activated by genotoxic stress to direct RpoN-dependent expression of the RNA repair operon rsr-yrlBA-rtcBA. The molecular signal for RtcR activation is an oligoribonucleotide with a 3'-terminal 2',3'-cyclic phosphate. We show in S. Typhimurium 14028s that the molecular signal is not a direct product of nucleic acid damage, but signal generation is dependent on a RecA-controlled SOS-response pathway, specifically, induction of prophage Gifsy-1. A genome-wide mutant screen and utilization of Gifsy prophage-cured strains indicated that the nucleoid-associated protein Fis and the Gifsy-1 prophage significantly impact RtcR activation. Directed-deletion analysis and genetic mapping by transduction demonstrated that a three-gene region (STM14_3218-3220) in Gifsy-1, which is variable between S. Typhimurium strains, is required for RtcR activation in strain 14028s and that the absence of STM14_3218-3220 in the Gifsy-1 prophages of S. Typhimurium strains LT2 and 4/74, which renders these strains unable to activate RtcR during genotoxic stress, can be rescued by complementation in cis by the region encompassing STM14_3218-3220. Thus, even though RtcR and the RNA repair operon are highly conserved in Salmonella enterica serovars, RtcR-dependent expression of the RNA repair operon in S. Typhimurium is controlled by a variable region of a prophage present in only some strains. IMPORTANCE The transcriptional activator RtcR and the RNA repair proteins whose expression it regulates, RtcA and RtcB, are widely conserved in Proteobacteria. In Salmonella Typhimurium 14028s, genotoxic stress activates RtcR to direct RpoN-dependent expression of the rsr-yrlBA-rtcBA operon. This work identifies key elements of a RecA-dependent pathway that generates the signal for RtcR activation in strain 14028s. This signaling pathway requires the presence of a specific region within the prophage Gifsy-1, yet this region is absent in most other wild-type Salmonella strains. Thus, we show that the activity of a widely conserved regulatory protein can be controlled by prophages with narrow phylogenetic distributions. This work highlights an underappreciated phenomenon where bacterial physiological functions are altered due to genetic rearrangement of prophages.
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Affiliation(s)
| | | | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Oliver Gregory
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Eve C. Balding
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California–Irvine School of Medicine, Irvine, California, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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3
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Gagarinova A, Hosseinnia A, Rahmatbakhsh M, Istace Z, Phanse S, Moutaoufik MT, Zilocchi M, Zhang Q, Aoki H, Jessulat M, Kim S, Aly KA, Babu M. Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli. Nat Commun 2022; 13:4085. [PMID: 35835781 PMCID: PMC9283627 DOI: 10.1038/s41467-022-31819-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits. The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.
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Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Zoe Istace
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Mara Zilocchi
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Qingzhou Zhang
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Matthew Jessulat
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada.
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4
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Kivisaar M. Mutation and Recombination Rates Vary Across Bacterial Chromosome. Microorganisms 2019; 8:microorganisms8010025. [PMID: 31877811 PMCID: PMC7023495 DOI: 10.3390/microorganisms8010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteria evolve as a result of mutations and acquisition of foreign DNA by recombination processes. A growing body of evidence suggests that mutation and recombination rates are not constant across the bacterial chromosome. Bacterial chromosomal DNA is organized into a compact nucleoid structure which is established by binding of the nucleoid-associated proteins (NAPs) and other proteins. This review gives an overview of recent findings indicating that the mutagenic and recombination processes in bacteria vary at different chromosomal positions. Involvement of NAPs and other possible mechanisms in these regional differences are discussed. Variations in mutation and recombination rates across the bacterial chromosome may have implications in the evolution of bacteria.
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Affiliation(s)
- Maia Kivisaar
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, 51010 Tartu, Estonia
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5
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Wien F, Martinez D, Le Brun E, Jones NC, Vrønning Hoffmann S, Waeytens J, Berbon M, Habenstein B, Arluison V. The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment. Microorganisms 2019; 7:microorganisms7120639. [PMID: 31816864 PMCID: PMC6956100 DOI: 10.3390/microorganisms7120639] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
The Hfq protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoprotein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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Affiliation(s)
- Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Etienne Le Brun
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
| | - Nykola C. Jones
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark; (N.C.J.); (S.V.H.)
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, B1050 Bruxelles, Belgique;
- Laboratoire de Chimie Physique d’Orsay, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay 91400 Orsay, France
| | - Melanie Berbon
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nano-objects, CBMN UMR5248 CNRS Université de Bordeaux INP, 33607 Pessac, France; (D.M.); (M.B.); (B.H.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France;
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (F.W.); (V.A.); Tel.: +33-(0)1-69-35-96-65 (F.W.); +33-(0)1-69-08-32-82 (V.A.)
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Integration Host Factor IHF facilitates homologous recombination and mutagenic processes in Pseudomonas putida. DNA Repair (Amst) 2019; 85:102745. [PMID: 31715424 DOI: 10.1016/j.dnarep.2019.102745] [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: 07/19/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/14/2022]
Abstract
Nucleoid-associated proteins (NAPs) such as IHF, HU, Fis, and H-NS alter the topology of bound DNA and may thereby affect accessibility of DNA to repair and recombination processes. To examine this possibility, we investigated the effect of IHF on the frequency of homologous recombination (HR) and point mutations in soil bacterium Pseudomonas putida by using plasmidial and chromosomal assays. We observed positive effect of IHF on the frequency of HR, whereas this effect varied depending both on the chromosomal location of the HR target and the type of plasmid used in the assay. The occurrence of point mutations in plasmid was also facilitated by IHF, whereas in the chromosome the positive effect of IHF appeared only at certain DNA sequences and/or chromosomal positions. We did not observe any significant effects of IHF on the spectrum of mutations. However, despite of the presence or absence of IHF, different mutational hot spots appeared both in plasmid and in chromosome. Additionally, the frequency of frameshift mutations in the chromosome was also strongly affected by the location of the mutational target sequence. Taking together, our results indicate that IHF facilitates the occurrence of genetic changes in P. putida, whereas the location of the target sequence affects both the IHF-dependent and IHF-independent mechanisms.
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An optogenetic toolbox of LOV-based photosensitizers for light-driven killing of bacteria. Sci Rep 2018; 8:15021. [PMID: 30301917 PMCID: PMC6177443 DOI: 10.1038/s41598-018-33291-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 09/26/2018] [Indexed: 01/04/2023] Open
Abstract
Flavin-binding fluorescent proteins (FPs) are genetically encoded in vivo reporters, which are derived from microbial and plant LOV photoreceptors. In this study, we comparatively analyzed ROS formation and light-driven antimicrobial efficacy of eleven LOV-based FPs. In particular, we determined singlet oxygen (1O2) quantum yields and superoxide photosensitization activities via spectroscopic assays and performed cell toxicity experiments in E. coli. Besides miniSOG and SOPP, which have been engineered to generate 1O2, all of the other tested flavoproteins were able to produce singlet oxygen and/or hydrogen peroxide but exhibited remarkable differences in ROS selectivity and yield. Accordingly, most LOV-FPs are potent photosensitizers, which can be used for light-controlled killing of bacteria. Furthermore, the two variants Pp2FbFP and DsFbFP M49I, exhibiting preferential photosensitization of singlet oxygen or singlet oxygen and superoxide, respectively, were shown to be new tools for studying specific ROS-induced cell signaling processes. The tested LOV-FPs thus further expand the toolbox of optogenetic sensitizers usable for a broad spectrum of microbiological and biomedical applications.
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Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D. Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics 2018; 19:373. [PMID: 29783948 PMCID: PMC5963079 DOI: 10.1186/s12864-018-4716-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/23/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V. cholerae. We performed extensive transcription start site (TSS) mapping as well as detection/quantification of the coding and non-coding RNA (ncRNA) repertoire in strain N16961. To improve TSS detection, we developed a new technique to treat RNA extracted from cells grown in various conditions. This allowed for identification of 3078 TSSs with an average 5'UTR of 116 nucleotides, and peak distribution between 16 and 64 nucleotides; as well as 629 ncRNAs. Mitomycin C treatment induced transcription of 737 genes and 28 ncRNAs at least 2 fold, while it repressed 231 genes and 17 ncRNAs. Data analysis revealed that in addition to the core genes known to integrate the SOS regulon, several metabolic pathways were induced. This study allowed for expansion of the Vibrio SOS regulon, as twelve genes (ubiEJB, tatABC, smpA, cep, VC0091, VC1190, VC1369-1370) were found to be co-induced with their adjacent canonical SOS regulon gene(s), through transcriptional read-through. Characterization of UV and mitomycin C susceptibility for mutants of these newly identified SOS regulon genes and other highly induced genes and ncRNAs confirmed their role in DNA damage rescue and protection. CONCLUSIONS We show that genotoxic stress induces a pervasive transcriptional response, affecting almost 20% of the V. cholerae genes. We also demonstrate that the SOS regulon is larger than previously known, and its syntenic organization is conserved among Vibrio species. Furthermore, this specific co-localization is found in other γ-proteobacteria for genes recN-smpA and rmuC-tatABC, suggesting SOS regulon conservation in this phylum. Finally, we comment on the limitations of widespread NGS approaches for identification of all RNA species in bacteria.
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Affiliation(s)
- Evelyne Krin
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Sebastian Aguilar Pierlé
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
| | - Odile Sismeiro
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Bernd Jagla
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Biomarker Discovery Platform, UtechS CB and Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Marie-Agnès Dillies
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
- Present adress: Institut Pasteur, Hub Bioinformatique et Biostatistique – C3BI, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Oihane Irazoki
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Susana Campoy
- grid.7080.fDepartament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Bellaterra, Spain
| | - Zoé Rouy
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Stéphane Cruveiller
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Claudine Médigue
- 0000 0001 2180 5818grid.8390.2UMR 8030, CNRS, CEA, Institut de Biologie François Jacob - Genoscope, Laboratoire d’Analyses Bioinformatiques pour la Génomique et le Métabolisme, Université Evry-Val-d’Essonne, Evry, France
| | - Jean-Yves Coppée
- 0000 0001 2353 6535grid.428999.7Institut Pasteur, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, Paris, France
| | - Didier Mazel
- 0000 0001 2353 6535grid.428999.7Département Génomes et Génétique, Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France
- 0000 0001 2112 9282grid.4444.0CNRS, UMR 3525, Paris, France
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Oxygen and RNA in stress-induced mutation. Curr Genet 2018; 64:769-776. [PMID: 29294174 PMCID: PMC6028306 DOI: 10.1007/s00294-017-0801-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 01/29/2023]
Abstract
Mechanisms of mutation upregulated by stress responses have been described in several organisms from bacteria to human. These mechanisms might accelerate genetic change specifically when cells are maladapted to their environment. Stress-induced mutation mechanisms differ in their genetic requirements from mutation in growing cells, occurring by different mechanisms in different assay systems, but having in common a requirement for the induction of stress-responses. Here, we review progress in two areas relevant to stress-response-dependent mutagenic DNA break repair mechanisms in Escherichia coli. First, we review evidence that relates mutation to transcription. This connection might allow mutagenesis in transcribed regions, including those relevant to any stress being experienced, opening the possibility that mutations could be targeted to regions where mutation might be advantageous under conditions of a specific stress. We review the mechanisms by which replication initiated by transcription can lead to mutation. Second, we review recent findings that, although stress-induced mutation does not require exogenous DNA-damaging agents, it does require the presence of damaged bases in DNA. For starved E. coli, endogenous oxygen radicals cause these altered bases. We postulate that damaged bases stall the replisome, which, we suggest, is required for DNA-polymerase exchange, allowing the action of low-fidelity DNA polymerases that promote mutation.
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10
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Xiong L, Liao D, Lu X, Yan H, Shi L, Mo Z. Proteomic analysis reveals that a global response is induced by subinhibitory concentrations of ampicillin. Bioengineered 2017; 8:732-741. [PMID: 28881168 DOI: 10.1080/21655979.2017.1373532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In this study, a recipient-donor co-culture system was used to research the effect of subinhibitory concentrations of antibiotics on horizontal transmission in bacteria and the influence of antibiotics on protein expression. We employed two-dimensional gel electrophoresis combined with mass spectrometry to compare the protein expression profiles in systems with or without 0.5 × the minimum inhibitory concentration of ampicillin. RT-PCR was used to assess the transcriptional levels of the differentially expressed genes. Fifty-seven different proteins were induced or suppressed. The upregulated proteins were involved in transcription and translation, cell wall synthesis, bacterial SOS response, and detoxifying functions, and the downregulated proteins were involved in metabolism. These results indicated that a global response was induced in the recipient-donor co-culture system by the subinhibitory concentration of ampicillin. Further analysis revealed that a global regulatory network based on key pathways was induced in the system in response to the antibiotic pressure. These findings provide a new, more comprehensive view for research on antibiotic-resistance mechanisms in recipient-donor co-culture.
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Affiliation(s)
- Lina Xiong
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China.,b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Dongjiang Liao
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - Xinpeng Lu
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
| | - He Yan
- c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Lei Shi
- b Jinan University , Guangzhou , China.,c School of Food Sciences and Technology , South China University of Technology , Guangzhou , China
| | - Ziyao Mo
- a The First Affiliated Hospital of Guangzhou Medical University , Guangzhou Institute of Respiratory Disease, State Key Laboratory of Respiratory Disease , Guangzhou , China
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11
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Dellus-Gur E, Ram Y, Hadany L. Errors in mutagenesis and the benefit of cell-to-cell signalling in the evolution of stress-induced mutagenesis. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170529. [PMID: 29291054 PMCID: PMC5717628 DOI: 10.1098/rsos.170529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 06/07/2023]
Abstract
Stress-induced mutagenesis is a widely observed phenomenon. Theoretical models have shown that stress-induced mutagenesis can be favoured by natural selection due to the beneficial mutations it generates. These models, however, assumed an error-free regulation of mutation rate in response to stress. Here, we explore the effects of errors in the regulation of mutagenesis on the evolution of stress-induced mutagenesis, and consider the role of cell-to-cell signalling. Using theoretical models, we show (i) that stress-induced mutagenesis can be disadvantageous if errors are common; and (ii) that cell-to-cell signalling can allow stress-induced mutagenesis to be favoured by selection even when error rates are high. We conclude that cell-to-cell signalling can facilitate the evolution of stress-induced mutagenesis in microbes through second-order selection.
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12
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Moore JM, Correa R, Rosenberg SM, Hastings PJ. Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli. PLoS Genet 2017; 13:e1006733. [PMID: 28727736 PMCID: PMC5542668 DOI: 10.1371/journal.pgen.1006733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 08/03/2017] [Accepted: 04/03/2017] [Indexed: 12/31/2022] Open
Abstract
Bacteria, yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses. Stress-inducible mutagenesis potentially accelerates adaptation, and may provide important models for mutagenesis that drives cancers, host pathogen interactions, antibiotic resistance and possibly much of evolution generally. In Escherichia coli repair of double-strand breaks (DSBs) becomes mutagenic, using low-fidelity DNA polymerases under the control of the SOS DNA-damage response and RpoS general stress response, which upregulate and allow the action of error-prone DNA polymerases IV (DinB), II and V to make mutations during repair. Pol IV is implied to compete with and replace high-fidelity DNA polymerases at the DSB-repair replisome, causing mutagenesis. We report that up-regulated Pol IV is not sufficient for mutagenic break repair (MBR); damaged bases in the DNA are also required, and that in starvation-stressed cells, these are caused by reactive-oxygen species (ROS). First, MBR is reduced by either ROS-scavenging agents or constitutive activation of oxidative-damage responses, both of which reduce cellular ROS levels. The ROS promote MBR other than by causing DSBs, saturating mismatch repair, oxidizing proteins, or inducing the SOS response or the general stress response. We find that ROS drive MBR through oxidized guanines (8-oxo-dG) in DNA, in that overproduction of a glycosylase that removes 8-oxo-dG from DNA prevents MBR. Further, other damaged DNA bases can substitute for 8-oxo-dG because ROS-scavenged cells resume MBR if either DNA pyrimidine dimers or alkylated bases are induced. We hypothesize that damaged bases in DNA pause the replisome and allow the critical switch from high fidelity to error-prone DNA polymerases in the DSB-repair replisome, thus allowing MBR. The data imply that in addition to the indirect stress-response controlled switch to MBR, a direct cis-acting switch to MBR occurs independently of DNA breakage, caused by ROS oxidation of DNA potentially regulated by ROS regulators.
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Affiliation(s)
- Jessica M. Moore
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Raul Correa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Susan M. Rosenberg
- Department of Biochemistry and Molecular Biology, 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
- Dan L. Duncan Comprehensive Cancer 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
| | - P. J. Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
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Bergkessel M, Basta DW, Newman DK. The physiology of growth arrest: uniting molecular and environmental microbiology. Nat Rev Microbiol 2016; 14:549-62. [PMID: 27510862 PMCID: PMC10069271 DOI: 10.1038/nrmicro.2016.107] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Most bacteria spend the majority of their time in prolonged states of very low metabolic activity and little or no growth, in which electron donors, electron acceptors and/or nutrients are limited, but cells are poised to undergo rapid division cycles when resources become available. These non-growing states are far less studied than other growth states, which leaves many questions regarding basic bacterial physiology unanswered. In this Review, we discuss findings from a small but diverse set of systems that have been used to investigate how growth-arrested bacteria adjust metabolism, regulate transcription and translation, and maintain their chromosomes. We highlight major questions that remain to be addressed, and suggest that progress in answering them will be aided by recent methodological advances and by dialectic between environmental and molecular microbiology perspectives.
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14
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Dame RT, Tark-Dame M. Bacterial chromatin: converging views at different scales. Curr Opin Cell Biol 2016; 40:60-65. [PMID: 26942688 DOI: 10.1016/j.ceb.2016.02.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/13/2023]
Abstract
Bacterial genomes are functionally organized and compactly folded into a structure referred to as bacterial chromatin or the nucleoid. An important role in genome folding is attributed to Nucleoid-Associated Proteins, also referred to as bacterial chromatin proteins. Although a lot of molecular insight in the mechanisms of operation of these proteins has been generated in the test tube, knowledge on genome organization in the cellular context is still lagging behind severely. Here, we discuss important advances in the understanding of three-dimensional genome organization due to the application of Chromosome Conformation Capture and super-resolution microscopy techniques. We focus on bacterial chromatin proteins whose proposed role in genome organization is supported by these approaches. Moreover, we discuss recent insights into the interrelationship between genome organization and genome activity/stability in bacteria.
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Affiliation(s)
- Remus T Dame
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands.
| | - Mariliis Tark-Dame
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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