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Wang Y, Hu J, Gao X, Cao Y, Ye S, Chen C, Wang L, Xu H, Guo M, Zhang D, Zhou R, Hua Y, Zhao Y. cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans. mBio 2024; 15:e0114424. [PMID: 38916345 PMCID: PMC11253593 DOI: 10.1128/mbio.01144-24] [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: 04/14/2024] [Accepted: 05/30/2024] [Indexed: 06/26/2024] Open
Abstract
The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from Deinococcus radiodurans. Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the anti-cAMP-mediated allosteric transition. Moreover, the second syn-cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of D. radiodurans.IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of Escherichia coli (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from Deinococcus radiodurans, DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.
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Affiliation(s)
- Yudong Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xufan Gao
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuchen Cao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shumai Ye
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cheng Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dong Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ruhong Zhou
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Department of Chemistry, Columbia University, New York, New York, USA
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Rollo F, Martins GD, Gouveia AG, Ithurbide S, Servant P, Romão CV, Moe E. Insights into the role of three Endonuclease III enzymes for oxidative stress resistance in the extremely radiation resistant bacterium Deinococcus radiodurans. Front Microbiol 2023; 14:1266785. [PMID: 37771704 PMCID: PMC10523315 DOI: 10.3389/fmicb.2023.1266785] [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: 07/25/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
The extremely radiation and desiccation resistant bacterium Deinococcus radiodurans possesses three genes encoding Endonuclease III-like enzymes (DrEndoIII1, DrEndoIII2, DrEndoIII3). In vitro enzymatic activity measurements revealed that DrEndoIII2 is the main Endonuclease III in this organism, while DrEndoIII1 and 3 possess unusual and, so far, no detectable EndoIII activity, respectively. In order to understand the role of these enzymes at a cellular level, DrEndoIII knockout mutants were constructed and subjected to various oxidative stress related conditions. The results showed that the mutants are as resistant to ionizing and UV-C radiation as well as H2O2 exposure as the wild type. However, upon exposure to oxidative stress induced by methyl viologen, the knockout strains were more resistant than the wild type. The difference in resistance may be attributed to the observed upregulation of the EndoIII homologs gene expression upon addition of methyl viologen. In conclusion, our data suggest that all three EndoIII homologs are crucial for cell survival in stress conditions, since the knockout of one of the genes tend to be compensated for by overexpression of the genes encoding the other two.
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Affiliation(s)
- Filipe Rollo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Guilherme D. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - André G. Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Solenne Ithurbide
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
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3
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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] [Received: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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4
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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Villa JK, Han R, Tsai CH, Chen A, Sweet P, Franco G, Vaezian R, Tkavc R, Daly MJ, Contreras LM. A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. Sci Rep 2021; 11:12949. [PMID: 34155239 PMCID: PMC8217566 DOI: 10.1038/s41598-021-91335-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Networks of transcriptional and post-transcriptional regulators are critical for bacterial survival and adaptation to environmental stressors. While transcriptional regulators provide rapid activation and/or repression of a wide-network of genes, post-transcriptional regulators, such as small RNAs (sRNAs), are also important to fine-tune gene expression. However, the mechanisms of sRNAs remain poorly understood, especially in less-studied bacteria. Deinococcus radiodurans is a gram-positive bacterium resistant to extreme levels of ionizing radiation (IR). Although multiple unique regulatory systems (e.g., the Radiation and Desiccation Response (RDR)) have been identified in this organism, the role of post-transcriptional regulators has not been characterized within the IR response. In this study, we have characterized an sRNA, PprS (formerly Dsr2), as a post-transcriptional coordinator of IR recovery in D. radiodurans. PprS showed differential expression specifically under IR and knockdown of PprS resulted in reduced survival and growth under IR, suggesting its importance in regulating post-radiation recovery. We determined a number of potential RNA targets involved in several pathways including translation and DNA repair. Specifically, we confirmed that PprS binds within the coding region to stabilize the pprM (DR_0907) transcript, a RDR modulator. Overall, these results are the first to present an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance.
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Affiliation(s)
- Jordan K Villa
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Runhua Han
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Chen-Hsun Tsai
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Philip Sweet
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Gabriela Franco
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Respina Vaezian
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Rok Tkavc
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Department of Microbiology and Immunology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Michael J Daly
- Department of Pathology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Molecular and Cellular Biology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Lydia M Contreras
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA.
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6
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Joshi SR, Jagtap S, Basu B, Deobagkar DD, Ghosh P. Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PLoS One 2020; 15:e0234721. [PMID: 32579573 PMCID: PMC7314050 DOI: 10.1371/journal.pone.0234721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 06/02/2020] [Indexed: 01/12/2023] Open
Abstract
Systems biology based approaches have been effectively utilized to mine high throughput data. In the current study, we have performed system-level analysis for Deinococcus radiodurans R1 by constructing a gene co-expression network based on several microarray datasets available in the public domain. This condition-independent network was constructed by Weighted Gene Co-expression Network Analysis (WGCNA) with 61 microarray samples from 9 different experimental conditions. We identified 13 co-expressed modules, of which, 11 showed functional enrichments of one or more pathway/s or biological process. Comparative analysis of differentially expressed genes and proteins from radiation and desiccation stress studies with our co-expressed modules revealed the association of cyan with radiation response. Interestingly, two modules viz darkgreen and tan was associated with radiation as well as desiccation stress responses. The functional analysis of these modules showed enrichment of pathways important for adaptation of radiation or desiccation stress. To decipher the regulatory roles of these stress responsive modules, we identified transcription factors (TFs) and then calculated a Biweight mid correlation between modules hub gene and the identified TFs. We obtained 7 TFs for radiation and desiccation responsive modules. The expressions of 3 TFs were validated in response to gamma radiation using qRT-PCR. Along with the TFs, selected close neighbor genes of two important TFs, viz., DR_0997 (CRP) and DR_2287 (AsnC family transcriptional regulator) in the darkgreen module were also validated. In our network, among 13 hub genes associated with 13 modules, the functionality of 5 hub genes which are annotated as hypothetical proteins (hypothetical hub genes) in D. radiodurans genome has been revealed. Overall the study provided a better insight of pathways and regulators associated with relevant DNA damaging stress response in D. radiodurans.
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Affiliation(s)
- Suraj R. Joshi
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Surabhi Jagtap
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Deepti D. Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
- * E-mail: ,
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7
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Comparative Proteomics Analysis Reveals New Features of the Oxidative Stress Response in the Polyextremophilic Bacterium Deinococcus radiodurans. Microorganisms 2020; 8:microorganisms8030451. [PMID: 32210096 PMCID: PMC7143949 DOI: 10.3390/microorganisms8030451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Deinococcus radiodurans is known for its extreme resistance to ionizing radiation, oxidative stress, and other DNA-damaging agents. The robustness of this bacterium primarily originates from its strong oxidative resistance mechanisms. Hundreds of genes have been demonstrated to contribute to oxidative resistance in D. radiodurans; however, the antioxidant mechanisms have not been fully characterized. In this study, comparative proteomics analysis of D. radiodurans grown under normal and oxidative stress conditions was conducted using label-free quantitative proteomics. The abundances of 852 of 1700 proteins were found to significantly differ between the two groups. These differential proteins are mainly associated with translation, DNA repair and recombination, response to stresses, transcription, and cell wall organization. Highly upregulated expression was observed for ribosomal proteins such as RplB, Rpsl, RpsR, DNA damage response proteins (DdrA, DdrB), DNA repair proteins (RecN, RecA), and transcriptional regulators (members of TetR, AsnC, and GntR families, DdrI). The functional analysis of proteins in response to oxidative stress is discussed in detail. This study reveals the global protein expression profile of D. radiodurans in response to oxidative stress and provides new insights into the regulatory mechanism of oxidative resistance in D. radiodurans.
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A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans. Biomolecules 2019; 10:biom10010022. [PMID: 31877996 PMCID: PMC7022480 DOI: 10.3390/biom10010022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022] Open
Abstract
Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.
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9
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Lu H, Wang L, Li S, Pan C, Cheng K, Luo Y, Xu H, Tian B, Zhao Y, Hua Y. Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO. Nucleic Acids Res 2019; 47:9925-9933. [PMID: 31410466 PMCID: PMC6765133 DOI: 10.1093/nar/gkz720] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 12/25/2022] Open
Abstract
DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.
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Affiliation(s)
- Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Shengjie Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Chaoming Pan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuxia Luo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, China
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10
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Qi HZ, Wang WZ, He JY, Ma Y, Xiao FZ, He SY. Antioxidative system of Deinococcus radiodurans. Res Microbiol 2019; 171:45-54. [PMID: 31756434 DOI: 10.1016/j.resmic.2019.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 10/31/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022]
Abstract
Deinococcus radiodurans is famous for its extreme resistance to various stresses such as ionizing radiation (IR), desiccation and oxidative stress. The underlying mechanism of exceptional resistance of this robust bacterium still remained unclear. However, the antioxidative system of D. radiodurans has been considered to be the determinant factor for its unparalleled resistance and protects the proteome during stress, then the DNA repair system and metabolic system exert their functions to restore the cell to normal physiological state. The antioxidative system not only equipped with the common reactive oxygen species (ROS) scavenging enzymes (e.g., catalase and superoxide dismutase) but also armed with a variety of non-enzyme antioxidants (e.g., carotenoids and manganese species). And the small manganese complexes play an important role in the antioxidative system of D. radiodurans. Recent studies have characterized several regulators (e.g., PprI and PprM) in D. radiodurans, which play critical roles in the protection of the bacteria from various stresses. In this review, we offer a panorama of the progress regarding the characteristics of the antioxidative system in D. radiodurans and its application in the future.
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Affiliation(s)
- Hui-Zhou Qi
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Function Laboratory Center, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Wu-Zhou Wang
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Jun-Yan He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Yun Ma
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China
| | - Fang-Zhu Xiao
- Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China
| | - Shu-Ya He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, 421001, China; Hengyang Key Laboratory for Biological Effects of Nuclear Radiation, University of South China, Hengyang, 421001, China.
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11
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Xue D, Liu W, Chen Y, Liu Y, Han J, Geng X, Li J, Jiang S, Zhou Z, Zhang W, Chen M, Lin M, Ongena M, Wang J. RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans. Int J Mol Sci 2019; 20:ijms20225603. [PMID: 31717497 PMCID: PMC6888292 DOI: 10.3390/ijms20225603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 °C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.
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Affiliation(s)
- Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Wenzheng Liu
- School of Food and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China;
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Xiuxiu Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Jiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, China;
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
| | - Marc Ongena
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
- Correspondence: (M.O.); (J.W.)
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (D.X.); (Y.C.); (Y.L.); (J.H.); (Z.Z.); (W.Z.); (M.C.); (M.L.)
- Correspondence: (M.O.); (J.W.)
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Xue D, Chen Y, Li J, Han J, Liu Y, Jiang S, Zhou Z, Zhang W, Chen M, Lin M, Ongena M, Wang J. Targeting Hsp20 Using the Novel Small Non-coding RNA DnrH Regulates Heat Tolerance in Deinococcus radiodurans. Front Microbiol 2019; 10:2354. [PMID: 31681218 PMCID: PMC6798082 DOI: 10.3389/fmicb.2019.02354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/27/2019] [Indexed: 11/26/2022] Open
Abstract
Small non-coding RNAs (ncRNAs) are a class of regulatory molecules, which remain understudied in bacteria. In the extremophilic bacterium Deinococcus radiodurans, although hundreds of ncRNAs have been identified, few have been characterized in detail. In this study, we report the identification and characterization of a novel heat-inducible ncRNA named DnrH. Heat tolerance analysis showed that deleting DnrH significantly inhibited viability in response to high temperature conditions. Comparative phenotypic and qRT-PCR analyses of a DnrH mutant (ΔDnrH) and wild-type (WT) D. radiodurans suggested that DnrH is potentially involved in regulating the expression of the heat shock-related gene Hsp20. Microscale thermophoresis and genetic complementation showed that a 28-nucleotide (nt) sequence in the stem-loop structure of DnrH (143–170 nt) pairs with its counterpart in the coding region of Hsp20 mRNA (91–117 nt) via a 22 nt region. In vivo, mutation of the 22-nt region in the D. radiodurans genome led to a reduction in heat tolerance similar to that observed in the DnrH-mutant. Our results show that DnrH positively influences heat tolerance by increasing the transcription of Hsp20 mRNA, demonstrating, for the first time, a ncRNA that directly controls the expression of a heat stress-resistance gene. This work provides new insight into the heat stress response mechanism of D. radiodurans as well as other extremophiles that express similar Hsp20 proteins.
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Affiliation(s)
- Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shijie Jiang
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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13
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Wang W, Ma Y, He J, Qi H, Xiao F, He S. Gene regulation for the extreme resistance to ionizing radiation of Deinococcus radiodurans. Gene 2019; 715:144008. [DOI: 10.1016/j.gene.2019.144008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/24/2019] [Accepted: 07/24/2019] [Indexed: 01/05/2023]
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14
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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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