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Sakai M, Shimosaka T, Katsumata K, Yohda M, Narumi I. Developing a new host-vector system for Deinococcus grandis. Front Microbiol 2024; 15:1387296. [PMID: 38863757 PMCID: PMC11165121 DOI: 10.3389/fmicb.2024.1387296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/26/2024] [Indexed: 06/13/2024] Open
Abstract
Deinococcus spp. are known for their radiation resistance, toxic compound removal, and production of valuable substances. Therefore, developing gene expression systems for Deinococcus spp. is crucial in advancing genetic engineering applications. To date, plasmid vectors that express foreign genes in D. radiodurans and D. geothermalis have been limited to plasmid pI3 and its derivatives. In contrast, plasmid vectors that express foreign genes in D. grandis include plasmid pZT23 and its derivatives. In this study, we developed a new system for the stable introduction and retention of expression plasmids for D. grandis. Two cryptic plasmids were removed from the wild-type strain to generate the TY3 strain. We then constructed a shuttle vector plasmid, pGRC5, containing the replication initiation region of the smallest cryptic plasmid, pDEGR-3, replication initiation region of the E. coli vector, pACYC184, and an antibiotic resistance gene. We introduced pGRC5, pZT23-derived plasmid pZT29H, and pI3-derived plasmid pRADN8 into strain TY3, and found their coexistence in D. grandis cells. The quantitative PCR assay results found that pGRC5, pZT29H, and pRADN8 had relative copy numbers of 11, 26, and 5 per genome, respectively. Furthermore, we developed a new plasmid in which the luciferase gene was controlled by the promoter region, which contained radiation-desiccation response operator sequences for D. grandis DdrO, a stress response regulon repressor in D. grandis, hence inducing gene expression via ultraviolet-C light irradiation. These plasmids are expected to facilitate the removal and production of toxic and valuable substances, in D. grandis, respectively, particularly of those involving multiple genes.
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Affiliation(s)
- Miyabi Sakai
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Taichi Shimosaka
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
| | | | - Masafumi Yohda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Issay Narumi
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
- Graduate School of Life Sciences, Toyo University, Asaka, Japan
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2
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de Groot A, Blanchard L. DNA repair and oxidative stress defense systems in radiation-resistant Deinococcus murrayi. Can J Microbiol 2023; 69:416-431. [PMID: 37552890 DOI: 10.1139/cjm-2023-0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Deinococcus murrayi is a bacterium isolated from hot springs in Portugal, and named after Dr. Robert G.E. Murray in recognition of his research on the genus Deinococcus. Like other Deinococcus species, D. murrayi is extremely resistant to ionizing radiation. Repair of massive DNA damage and limitation of oxidative protein damage are two important factors contributing to the robustness of Deinococcus bacteria. Here, we identify, among others, the DNA repair and oxidative stress defense proteins in D. murrayi, and highlight special features of D. murrayi. For DNA repair, D. murrayi does not contain a standalone uracil-DNA glycosylase (Ung), but it encodes a protein in which Ung is fused to a DNA photolyase domain (PhrB). UvrB and UvrD contain large insertions corresponding to inteins. One of its endonuclease III enzymes lacks a [4Fe-4S] cluster. Deinococcus murrayi possesses a homolog of the error-prone DNA polymerase IV. Concerning oxidative stress defense, D. murrayi encodes a manganese catalase in addition to a heme catalase. Its organic hydroperoxide resistance protein Ohr is atypical because the redox active cysteines are present in a CXXC motif. These and other characteristics of D. murrayi show further diversity among Deinococcus bacteria with respect to resistance-associated mechanisms.
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Affiliation(s)
- Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
| | - Laurence Blanchard
- Aix Marseille Univ, CEA, CNRS, BIAM, Molecular and Environmental Microbiology Team, Saint Paul-Lez-Durance, F-13115, France
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Coexistence of SOS-Dependent and SOS-Independent Regulation of DNA Repair Genes in Radiation-Resistant Deinococcus Bacteria. Cells 2021; 10:cells10040924. [PMID: 33923690 PMCID: PMC8072749 DOI: 10.3390/cells10040924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/28/2022] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and able to repair a shattered genome in an essentially error-free manner after exposure to high doses of radiation or prolonged desiccation. An efficient, SOS-independent response mechanism to induce various DNA repair genes such as recA is essential for radiation resistance. This pathway, called radiation/desiccation response, is controlled by metallopeptidase IrrE and repressor DdrO that are highly conserved in Deinococcus. Among various Deinococcus species, Deinococcus radiodurans has been studied most extensively. Its genome encodes classical DNA repair proteins for error-free repair but no error-prone translesion DNA polymerases, which may suggest that absence of mutagenic lesion bypass is crucial for error-free repair of massive DNA damage. However, many other radiation-resistant Deinococcus species do possess translesion polymerases, and radiation-induced mutagenesis has been demonstrated. At least dozens of Deinococcus species contain a mutagenesis cassette, and some even two cassettes, encoding error-prone translesion polymerase DnaE2 and two other proteins, ImuY and ImuB-C, that are probable accessory factors required for DnaE2 activity. Expression of this mutagenesis cassette is under control of the SOS regulators RecA and LexA. In this paper, we review both the RecA/LexA-controlled mutagenesis and the IrrE/DdrO-controlled radiation/desiccation response in Deinococcus.
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Redox signaling through zinc activates the radiation response in Deinococcus bacteria. Sci Rep 2021; 11:4528. [PMID: 33633226 PMCID: PMC7907104 DOI: 10.1038/s41598-021-84026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and other DNA damage- and oxidative stress-generating conditions. An efficient SOS-independent response mechanism inducing expression of several DNA repair genes is essential for this resistance, and is controlled by metalloprotease IrrE that cleaves and inactivates transcriptional repressor DdrO. Here, we identify the molecular signaling mechanism that triggers DdrO cleavage. We show that reactive oxygen species (ROS) stimulate the zinc-dependent metalloprotease activity of IrrE in Deinococcus. Sudden exposure of Deinococcus to zinc excess also rapidly induces DdrO cleavage, but is not accompanied by ROS production and DNA damage. Further, oxidative treatment leads to an increase of intracellular free zinc, indicating that IrrE activity is very likely stimulated directly by elevated levels of available zinc ions. We conclude that radiation and oxidative stress induce changes in redox homeostasis that result in IrrE activation by zinc in Deinococcus. We propose that a part of the zinc pool coordinated with cysteine thiolates is released due to their oxidation. Predicted regulation systems involving IrrE- and DdrO-like proteins are present in many bacteria, including pathogens, suggesting that such a redox signaling pathway including zinc as a second messenger is widespread and participates in various stress responses.
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Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA. Int J Mol Sci 2020; 21:ijms21197389. [PMID: 33036395 PMCID: PMC7583915 DOI: 10.3390/ijms21197389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 11/17/2022] Open
Abstract
Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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Blanchard L, Guérin P, Roche D, Cruveiller S, Pignol D, Vallenet D, Armengaud J, de Groot A. Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria. Microbiologyopen 2017; 6. [PMID: 28397370 PMCID: PMC5552922 DOI: 10.1002/mbo3.477] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/22/2017] [Accepted: 02/28/2017] [Indexed: 12/26/2022] Open
Abstract
The extreme radiation resistance of Deinococcus bacteria requires the radiation‐stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation‐induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo‐IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM‐containing DNA or interaction of IrrE with DNA‐bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE‐dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation‐resistant Deinococcus species.
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Affiliation(s)
- Laurence Blanchard
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - Philippe Guérin
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - David Roche
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Stéphane Cruveiller
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - David Pignol
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
| | - David Vallenet
- CEA, DRF, Institut de Génomique, LABGeM, Evry, France.,UMR-CNRS 8030 Génomique Métabolique, CEA Institut de Génomique - Genoscope, Evry, France
| | - Jean Armengaud
- Laboratory "Innovative technologies for Detection and Diagnostic", CEA-Marcoule, DRF/IBITEC-S/SPI/Li2D, Bagnols-sur-Cèze, France
| | - Arjan de Groot
- Lab Bioenerget Cellulaire, CEA, DRF, BIAM, Saint-Paul-lez-Durance, France.,CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France.,Aix-Marseille Université, Saint-Paul-lez-Durance, France
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8
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Brutesco C, Prévéral S, Escoffier C, Descamps ECT, Prudent E, Cayron J, Dumas L, Ricquebourg M, Adryanczyk-Perrier G, de Groot A, Garcia D, Rodrigue A, Pignol D, Ginet N. Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:52-65. [PMID: 27234828 DOI: 10.1007/s11356-016-6952-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible Pars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.
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Affiliation(s)
- Catherine Brutesco
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Sandra Prévéral
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Camille Escoffier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elodie C T Descamps
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - Louis Dumas
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Manon Ricquebourg
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Géraldine Adryanczyk-Perrier
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Arjan de Groot
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, Villeurbanne, 69622, France
| | - David Pignol
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Nicolas Ginet
- CEA, DRF, BIAM, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, 13108, France.
- CNRS, UMR Biol Veget and Microbiol Environ, Saint-Paul-lez-Durance, 13108, France.
- Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France.
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Bouthier de la Tour C, Blanchard L, Dulermo R, Ludanyi M, Devigne A, Armengaud J, Sommer S, de Groot A. The abundant and essential HU proteins in Deinococcus deserti and Deinococcus radiodurans are translated from leaderless mRNA. MICROBIOLOGY-SGM 2015; 161:2410-22. [PMID: 26385459 DOI: 10.1099/mic.0.000186] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
HU proteins have an important architectural role in nucleoid organization in bacteria. Compared with HU of many bacteria, HU proteins from Deinococcus species possess an N-terminal lysine-rich extension similar to the eukaryotic histone H1 C-terminal domain involved in DNA compaction. The single HU gene in Deinococcus radiodurans, encoding DrHU, is required for nucleoid compaction and cell viability. Deinococcus deserti contains three expressed HU genes, encoding DdHU1, DdHU2 and DdHU3. Here, we show that either DdHU1 or DdHU2 is essential in D. deserti. DdHU1 and DdHU2, but not DdHU3, can substitute for DrHU in D. radiodurans, indicating that DdHU3 may have a non-essential function different from DdHU1, DdHU2 and DrHU. Interestingly, the highly abundant DrHU and DdHU1 proteins, and also the less expressed DdHU2, are translated in Deinococcus from leaderless mRNAs, which lack a 5'-untranslated region and, hence, the Shine-Dalgarno sequence. Unexpectedly, cloning the DrHU or DdHU1 gene under control of a strong promoter in an expression plasmid, which results in leadered transcripts, strongly reduced the DrHU and DdHU1 protein level in D. radiodurans compared with that obtained from the natural leaderless gene. We also show that the start codon position for DrHU and DdHU1 should be reannotated, resulting in proteins that are 15 and 4 aa residues shorter than initially reported. The expression level and start codon correction were crucial for functional characterization of HU in Deinococcus.
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Affiliation(s)
- Claire Bouthier de la Tour
- 1Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Bâtiment 409, F-91405 Orsay, France
| | - Laurence Blanchard
- 2CEA, DSV, IBEB, Lab Bioenerget Cellulaire, F-13108 Saint-Paul-lez-Durance, France 3CNRS, UMR 7265 Biol Veget & Microbiol Environ, F-13108 Saint-Paul-lez-Durance, France 4Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France
| | - Rémi Dulermo
- 1Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Bâtiment 409, F-91405 Orsay, France 3CNRS, UMR 7265 Biol Veget & Microbiol Environ, F-13108 Saint-Paul-lez-Durance, France 4Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France 5CEA, DSV, IBEB, Lab Ecol Microb Rhizosphere & Environ Extrem, F-13108 Saint-Paul-lez-Durance, France
| | - Monika Ludanyi
- 2CEA, DSV, IBEB, Lab Bioenerget Cellulaire, F-13108 Saint-Paul-lez-Durance, France 3CNRS, UMR 7265 Biol Veget & Microbiol Environ, F-13108 Saint-Paul-lez-Durance, France 4Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France
| | - Alice Devigne
- 1Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Bâtiment 409, F-91405 Orsay, France
| | - Jean Armengaud
- 6CEA-Marcoule, DSV/IBITEC-S/SPI/Li2D, Laboratory 'Innovative technologies for Detection and Diagnostic', BP 17171, F-30207 Bagnols-sur-Cèze, France
| | - Suzanne Sommer
- 1Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, Bâtiment 409, F-91405 Orsay, France
| | - Arjan de Groot
- 3CNRS, UMR 7265 Biol Veget & Microbiol Environ, F-13108 Saint-Paul-lez-Durance, France 2CEA, DSV, IBEB, Lab Bioenerget Cellulaire, F-13108 Saint-Paul-lez-Durance, France 4Aix-Marseille Université, F-13108 Saint-Paul-lez-Durance, France
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10
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de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L. RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti. Genome Biol Evol 2015; 6:932-48. [PMID: 24723731 PMCID: PMC4007540 DOI: 10.1093/gbe/evu069] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deinococcus deserti is a desiccation- and radiation-tolerant desert bacterium. Differential RNA sequencing (RNA-seq) was performed to explore the specificities of its transcriptome. Strikingly, for 1,174 (60%) mRNAs, the transcription start site was found exactly at (916 cases, 47%) or very close to the translation initiation codon AUG or GUG. Such proportion of leaderless mRNAs, which may resemble ancestral mRNAs, is unprecedented for a bacterial species. Proteomics showed that leaderless mRNAs are efficiently translated in D. deserti. Interestingly, we also found 173 additional transcripts with a 5′-AUG or 5′-GUG that would make them competent for ribosome binding and translation into novel small polypeptides. Fourteen of these are predicted to be leader peptides involved in transcription attenuation. Another 30 correlated with new gene predictions and/or showed conservation with annotated and nonannotated genes in other Deinococcus species, and five of these novel polypeptides were indeed detected by mass spectrometry. The data also allowed reannotation of the start codon position of 257 genes, including several DNA repair genes. Moreover, several novel highly radiation-induced genes were found, and their potential roles are discussed. On the basis of our RNA-seq and proteogenomics data, we propose that translation of many of the novel leaderless transcripts, which may have resulted from single-nucleotide changes and maintained by selective pressure, provides a new explanation for the generation of a cellular pool of small peptides important for protection of proteins against oxidation and thus for radiation/desiccation tolerance and adaptation to harsh environmental conditions.
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Affiliation(s)
- Arjan de Groot
- CEA, DSV, IBEB, Lab Bioénergétique Cellulaire, Saint-Paul-lez-Durance, France
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Ludanyi M, Blanchard L, Dulermo R, Brandelet G, Bellanger L, Pignol D, Lemaire D, de Groot A. Radiation response in Deinococcus deserti: IrrE is a metalloprotease that cleaves repressor protein DdrO. Mol Microbiol 2014; 94:434-49. [PMID: 25170972 DOI: 10.1111/mmi.12774] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2014] [Indexed: 11/28/2022]
Abstract
Deinococcus bacteria are famous for their extreme radiation tolerance. The IrrE protein was shown to be essential for radiation tolerance and, in an unelucidated manner, for induction of a number of genes in response to radiation, including recA and other DNA repair genes. Earlier studies indicated that IrrE could be a zinc peptidase, but proteolytic activity was not demonstrated. Here, using several in vivo and in vitro experiments, IrrE from Deinococcus deserti was found to interact with DdrO, a predicted regulator encoded by a radiation-induced gene that is, like irrE, highly conserved in Deinococcus. Moreover, IrrE was found to cleave DdrO in vitro and when the proteins were coexpressed in Escherichia coli. This cleavage was not observed in the presence of metal chelator EDTA or when IrrE contains a mutation in the conserved active-site motif of metallopeptidases. In D. deserti, IrrE-dependent cleavage of DdrO was observed after exposure to radiation. Furthermore, DdrO-dependent repression of the promoter of a radiation-induced gene was shown. These results demonstrate that IrrE is a metalloprotease and we propose that IrrE-mediated cleavage inactivates repressor protein DdrO, leading to transcriptional induction of various genes required for repair and survival after exposure of Deinococcus to radiation.
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Affiliation(s)
- Monika Ludanyi
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix-Marseille Université, Saint-Paul-lez-Durance, F-13108, France
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Timinskas K, Balvočiūtė M, Timinskas A, Venclovas Č. Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res 2013; 42:1393-413. [PMID: 24106089 PMCID: PMC3919608 DOI: 10.1093/nar/gkt900] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The analysis of ∼2000 bacterial genomes revealed that they all, without a single exception, encode one or more DNA polymerase III α-subunit (PolIIIα) homologs. Classified into C-family of DNA polymerases they come in two major forms, PolC and DnaE, related by ancient duplication. While PolC represents an evolutionary compact group, DnaE can be further subdivided into at least three groups (DnaE1-3). We performed an extensive analysis of various sequence, structure and surface properties of all four polymerase groups. Our analysis suggests a specific evolutionary pathway leading to PolC and DnaE from the last common ancestor and reveals important differences between extant polymerase groups. Among them, DnaE1 and PolC show the highest conservation of the analyzed properties. DnaE3 polymerases apparently represent an ‘impaired’ version of DnaE1. Nonessential DnaE2 polymerases, typical for oxygen-using bacteria with large GC-rich genomes, have a number of features in common with DnaE3 polymerases. The analysis of polymerase distribution in genomes revealed three major combinations: DnaE1 either alone or accompanied by one or more DnaE2s, PolC + DnaE3 and PolC + DnaE1. The first two combinations are present in Escherichia coli and Bacillus subtilis, respectively. The third one (PolC + DnaE1), found in Clostridia, represents a novel, so far experimentally uncharacterized, set.
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Affiliation(s)
- Kestutis Timinskas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, Vilnius LT-02241, Lithuania
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Dedieu A, Sahinovic E, Guérin P, Blanchard L, Fochesato S, Meunier B, de Groot A, Armengaud J. Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation. Proteome Sci 2013; 11:3. [PMID: 23320389 PMCID: PMC3564903 DOI: 10.1186/1477-5956-11-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/23/2012] [Indexed: 11/10/2022] Open
Abstract
UNLABELLED BACKGROUND Deinococcus deserti VCD115 has been isolated from Sahara surface sand. This radiotolerant bacterium represents an experimental model of choice to understand adaptation to harsh conditions encountered in hot arid deserts. We analysed the soluble proteome dynamics in this environmentally relevant model after exposure to 3 kGy gamma radiation, a non-lethal dose that generates massive DNA damages. For this, cells were harvested at different time lapses after irradiation and their soluble proteome contents have been analysed by 2-DE and mass spectrometry. RESULTS In the first stage of the time course we observed accumulation of DNA damage response protein DdrB (that shows the highest fold change ~11), SSB, and two different RecA proteins (RecAP and RecAC). Induction of DNA repair protein PprA, DNA damage response protein DdrD and the two gyrase subunits (GyrA and GyrB) was also detected. A response regulator of the SarP family, a type II site-specific deoxyribonuclease and a putative N-acetyltransferase are three new proteins found to be induced. In a more delayed stage, we observed accumulation of several proteins related to central metabolism and protein turn-over, as well as helicase UvrD and novel forms of both gyrase subunits differing in terms of isoelectric point and molecular weight. CONCLUSIONS Post-translational modifications of GyrA (N-terminal methionine removal and acetylation) have been evidenced and their significance discussed. We found that the Deide_02842 restriction enzyme, which is specifically found in D. deserti, is a new potential member of the radiation/desiccation response regulon, highlighting the specificities of D. deserti compared to the D. radiodurans model.
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Affiliation(s)
- Alain Dedieu
- Laboratoire de Biochimie des Systèmes Perturbés, CEA Marcoule, DSV, iBEB, SBTN, LBSP, BAGNOLS-SUR-CEZE, F-30207, France.
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14
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Multiple strategies for translesion synthesis in bacteria. Cells 2012; 1:799-831. [PMID: 24710531 PMCID: PMC3901139 DOI: 10.3390/cells1040799] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/29/2012] [Accepted: 09/30/2012] [Indexed: 12/16/2022] Open
Abstract
Damage to DNA is common and can arise from numerous environmental and endogenous sources. In response to ubiquitous DNA damage, Y-family DNA polymerases are induced by the SOS response and are capable of bypassing DNA lesions. In Escherichia coli, these Y-family polymerases are DinB and UmuC, whose activities are modulated by their interaction with the polymerase manager protein UmuD. Many, but not all, bacteria utilize DinB and UmuC homologs. Recently, a C-family polymerase named ImuC, which is similar in primary structure to the replicative DNA polymerase DnaE, was found to be able to copy damaged DNA and either carry out or suppress mutagenesis. ImuC is often found with proteins ImuA and ImuB, the latter of which is similar to Y‑family polymerases, but seems to lack the catalytic residues necessary for polymerase activity. This imuAimuBimuC mutagenesis cassette represents a widespread alternative strategy for translesion synthesis and mutagenesis in bacteria. Bacterial Y‑family and ImuC DNA polymerases contribute to replication past DNA damage and the acquisition of antibiotic resistance.
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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Zeng YH, Shen FT, Tan CC, Huang CC, Young CC. The flexibility of UV-inducible mutation in Deinococcus ficus as evidenced by the existence of the imuB-dnaE2 gene cassette and generation of superior feather degrading bacteria. Microbiol Res 2011; 167:40-7. [PMID: 21459566 DOI: 10.1016/j.micres.2011.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/23/2011] [Accepted: 02/27/2011] [Indexed: 10/18/2022]
Abstract
The lexA-imuB-dnaE2 gene cassette contributing to the TLS (translesion synthesis) polymerase activity and can easily cause mutation after DNA damage in many bacteria. But it was previously thought that TLS polymerase activity was unlikely to exist in the radio-resistant genus Deinococcus. In our preliminary studies, the lexA-imuB-dnaE2 gene cassette was found in a newly isolated feather-degrading Deinococcus ficus. Here we have attempted to determine the imuB gene sequence from another Deinococcus species namely D. grandis, by using the newly designed primers. The destroying of either imuB or dnaE2 gene in D. ficus leads to the increase in UV sensitivity and decrease in UV-induced mutations, which demonstrated the existence of TLS polymerase activity in D. ficus. In the presence of lexA-imuB-dnaE2, it is possible to obtain mutants with various keratinolytic activities after UV exposure. The keratinolytic activity of mutant strain CC-ZG207 increased by approximately twofold during growth in liquid feather medium. In contrast, the mutant strain CC-ZG227 showed only half of the keratinolytic activity compared with the wild type strain. By utilizing SDS-PAGE and zymogram profile analysis, the change in the protease activity was observed. We have proposed that the superior mutants of D. ficus can be created under UV stress, which is mediated by the lexA-imuB-dnaE2 gene cassette.
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Affiliation(s)
- You-Hong Zeng
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, Taiwan
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Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010; 107:13093-8. [PMID: 20615954 DOI: 10.1073/pnas.1002614107] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In Mycobacterium tuberculosis (Mtb), damage-induced mutagenesis is dependent on the C-family DNA polymerase, DnaE2. Included with dnaE2 in the Mtb SOS regulon is a putative operon comprising Rv3395c, which encodes a protein of unknown function restricted primarily to actinomycetes, and Rv3394c, which is predicted to encode a Y-family DNA polymerase. These genes were previously identified as components of an imuA-imuB-dnaE2-type mutagenic cassette widespread among bacterial genomes. Here, we confirm that Rv3395c (designated imuA') and Rv3394c (imuB) are individually essential for induced mutagenesis and damage tolerance. Yeast two-hybrid analyses indicate that ImuB interacts with both ImuA' and DnaE2, as well as with the beta-clamp. Moreover, disruption of the ImuB-beta clamp interaction significantly reduces induced mutagenesis and damage tolerance, phenocopying imuA', imuB, and dnaE2 gene deletion mutants. Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity. In contrast, replacement of DnaE2 catalytic residues reproduces the dnaE2 gene deletion phenotype, strongly implying a direct role for the alpha-subunit in mutagenic lesion bypass. These data implicate differential protein interactions in specialist polymerase function and identify the split imuA'-imuB/dnaE2 cassette as a compelling target for compounds designed to limit mutagenesis in a pathogen increasingly associated with drug resistance.
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