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Wang Y, Liu J, Yi Y, Zhu L, Liu M, Zhang Z, Xie Q, Jiang L. Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria. Front Microbiol 2024; 15:1447785. [PMID: 39119139 PMCID: PMC11306087 DOI: 10.3389/fmicb.2024.1447785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.
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Affiliation(s)
- Yuxian Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Jiayu Liu
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Yuanyang Yi
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
- College of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Liying Zhu
- School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, China
| | - Minghui Liu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/ Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, China
| | - Qiong Xie
- China Astronaut Research and Training Center, Beijing, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
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Park JH, Lee S, Shin E, Abdi Nansa S, Lee SJ. The Transposition of Insertion Sequences in Sigma-Factor- and LysR-Deficient Mutants of Deinococcus geothermalis. Microorganisms 2024; 12:328. [PMID: 38399731 PMCID: PMC10892881 DOI: 10.3390/microorganisms12020328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Some insertion sequence (IS) elements were actively transposed using oxidative stress conditions, including gamma irradiation and hydrogen peroxide treatment, in Deinococcus geothermalis, a radiation-resistant bacterium. D. geothermalis wild-type (WT), sigma factor gene-disrupted (∆dgeo_0606), and LysR gene-disrupted (∆dgeo_1692) mutants were examined for IS induction that resulted in non-pigmented colonies after gamma irradiation (5 kGy) exposure. The loss of pigmentation occurred because dgeo_0524, which encodes a phytoene desaturase in the carotenoid pathway, was disrupted by the transposition of IS elements. The types and loci of the IS elements were identified as ISDge2 and ISDge6 in the ∆dgeo_0606 mutant and ISDge5 and ISDge7 in the ∆dgeo_1692 mutant, but were not identified in the WT strain. Furthermore, 80 and 100 mM H2O2 treatments induced different transpositions of IS elements in ∆dgeo_0606 (ISDge5, ISDge6, and ISDge7) and WT (ISDge6). However, no IS transposition was observed in the ∆dgeo_1692 mutant. The complementary strain of the ∆dgeo_0606 mutation showed recovery effects in the viability assay; however, the growth-delayed curve did not return because the neighboring gene dgeo_0607 was overexpressed, probably acting as an anti-sigma factor. The expression levels of certain transposases, recognized as pivotal contributors to IS transposition, did not precisely correlate with active transposition in varying oxidation environments. Nevertheless, these findings suggest that specific IS elements integrated into dgeo_0524 in a target-gene-deficient and oxidation-source-dependent manner.
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Affiliation(s)
| | | | | | | | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea; (J.H.P.); (S.L.); (E.S.); (S.A.N.)
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Chen Y, Zhang Q, Wang D, Shu YG, Shi H. Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space. Microbiol Spectr 2023; 11:e0347422. [PMID: 36749041 PMCID: PMC10100890 DOI: 10.1128/spectrum.03474-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
Near space (20 to 100 km in altitude) is an extreme environment with high radiation and extreme cold, making it difficult for organisms to survive. However, many studies had shown that there were still microbes living in this extremely harsh environment. It was particularly important to study which factors affected the survival of microorganisms living in near space after exposure to irradiation, as this was related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. Survival after radiation was probably influenced by the growth condition before radiation, which is called the memory effect. In this research, we used different growth conditions to affect the growth of Deinococcus radiodurans and lyophilized bacteria in exponential phase to maintain the physiological state at this stage. Then high-altitude scientific balloon exposure experiments were carried out by using the Chinese Academy of Sciences Balloon-Borne Astrobiology Platform (CAS-BAP) at Dachaidan, Qinghai, China (37°44'N, 95°21'E). The aim was to investigate which factors influence survival after near-space exposure. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. If the differences in growth rate were caused by differences in nutrition, the survival rate and growth rate were positively correlated. Moreover, the addition of paraquat and Mn2+ during the growth phase can also increase survival. This finding may help to deepen the understanding of the mechanics of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space. IMPORTANCE Earth's near space is an extreme environment with high radiation and extreme cold. Which factors affect the survival of microbes in near space is related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. We performed several exposure experiments with Deinococcus radiodurans in near space to investigate which factors influence the survival rate after near-space exposure; that is, there was a relationship between survival after radiation and the growth condition before radiation. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. This finding may help to deepen the understanding of the mechanism of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space.
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Affiliation(s)
- Yining Chen
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Deyu Wang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yao-Gen Shu
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
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4
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Huang Y, Wurihan W, Lu B, Zou Y, Wang Y, Weldon K, Fondell JD, Lai Z, Wu X, Fan H. Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor. Front Microbiol 2022; 12:812448. [PMID: 35046926 PMCID: PMC8762339 DOI: 10.3389/fmicb.2021.812448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.
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Affiliation(s)
- Yehong Huang
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Bin Lu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Joseph D Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
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5
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Boulant E, Cambon E, Vergalli J, Bernard R, Neulat-Ripoll F, Nolent F, Gorgé O, Girleanu M, Favier AL, Leonetti JP, Bolla JM. Tolerance engineering in Deinococcus geothermalis by heterologous efflux pumps. Sci Rep 2021; 11:4280. [PMID: 33608597 PMCID: PMC7896070 DOI: 10.1038/s41598-021-83339-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/28/2021] [Indexed: 11/21/2022] Open
Abstract
Producing industrially significant compounds with more environmentally friendly represents a challenging task. The large-scale production of an exogenous molecule in a host microfactory can quickly cause toxic effects, forcing the cell to inhibit production to survive. The key point to counter these toxic effects is to promote a gain of tolerance in the host, for instance, by inducing a constant flux of the neo-synthetized compound out of the producing cells. Efflux pumps are membrane proteins that constitute the most powerful mechanism to release molecules out of cells. We propose here a new biological model, Deinococcus geothermalis, organism known for its ability to survive hostile environment; with the aim of coupling the promising industrial potential of this species with that of heterologous efflux pumps to promote engineering tolerance. In this study, clones of D. geothermalis containing various genes encoding chromosomal heterologous efflux pumps were generated. Resistant recombinants were selected using antibiotic susceptibility tests to screen promising candidates. We then developed a method to determine the efflux efficiency of the best candidate, which contains the gene encoding the MdfA of Salmonella enterica serovar Choleraesuis. We observe 1.6 times more compound in the external medium of the hit recombinant than that of the WT at early incubation time. The data presented here will contribute to better understanding of the parameters required for efficient production in D. geothermalis.
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Affiliation(s)
- Erika Boulant
- Aix Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
| | | | - Julia Vergalli
- Aix Marseille Univ, INSERM, SSA, IRBA, MCT, Marseille, France
| | - Rémi Bernard
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
- Vilmorin SA, Centre de Recherche de La Costière, Ledenon, France
| | - Fabienne Neulat-Ripoll
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Flora Nolent
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées, Département Microbiologie et Maladies Infectieuses, Unité Bactériologie, Brétigny-sur-Orge, France
| | - Maria Girleanu
- Institut de Recherche Biomédicale des Armées, Département des Plateformes et Recherche Technologique, Unité Imagerie, Brétigny-sur-Orge, France
| | - Anne-Laure Favier
- Institut de Recherche Biomédicale des Armées, Département des Plateformes et Recherche Technologique, Unité Imagerie, Brétigny-sur-Orge, France
| | - Jean-Paul Leonetti
- Deinove, Cap Sigma/ZAC Euromédecine II, Grabels, France
- Institut de Recherche en Infectiologie de Montpellier, UMR 9004-CNRS/UM, Montpellier, France
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6
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Metabolic Engineering of Extremophilic Bacterium Deinococcus radiodurans for the Production of the Novel Carotenoid Deinoxanthin. Microorganisms 2020; 9:microorganisms9010044. [PMID: 33375757 PMCID: PMC7823818 DOI: 10.3390/microorganisms9010044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
Deinoxanthin, a xanthophyll derived from Deinococcus species, is a unique organic compound that provides greater antioxidant effects compared to other carotenoids due to its superior scavenging activity against singlet oxygen and hydrogen peroxide. Therefore, it has attracted significant attention as a next-generation organic compound that has great potential as a natural ingredient in a food supplements. Although the microbial identification of deinoxanthin has been identified, mass production has not yet been achieved. Here, we report, for the first time, the development of an engineered extremophilic microorganism, Deinococcus radiodurans strain R1, that is capable of producing deinoxanthin through rational metabolic engineering and process optimization. The genes crtB and dxs were first introduced into the genome to reinforce the metabolic flux towards deinoxanthin. The optimal temperature was then identified through a comparative analysis of the mRNA expression of the two genes, while the carbon source was further optimized to increase deinoxanthin production. The final engineered D. radiodurans strain R1 was able to produce 394 ± 17.6 mg/L (102 ± 11.1 mg/g DCW) of deinoxanthin with a yield of 40.4 ± 1.2 mg/g sucrose and a productivity of 8.4 ± 0.2 mg/L/h from 10 g/L of sucrose. The final engineered strain and the strategies developed in the present study can act as the foundation for the industrial application of extremophilic microorganisms.
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7
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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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8
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Discovery and Characterization of Native Deinococcus radiodurans Promoters for Tunable Gene Expression. Appl Environ Microbiol 2019; 85:AEM.01356-19. [PMID: 31471304 DOI: 10.1128/aem.01356-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/26/2019] [Indexed: 01/28/2023] Open
Abstract
The potential utilization of extremophiles as a robust chassis for metabolic engineering applications has prompted interest in the use of Deinococcus radiodurans for bioremediation efforts, but current applications are limited by the lack of availability of genetic tools, such as promoters. In this study, we used a combined computational and experimental approach to identify and screen 30 predicted promoters for expression in D. radiodurans using a fluorescent reporter assay. The top eight candidates were further characterized, compared to currently available promoters, and optimized for engineering through minimization for use in D. radiodurans Of these top eight, two promoter regions, PDR_1261 and PrpmB, were stronger and more consistent than the most widely used promoter sequence in D. radiodurans, PgroES Furthermore, half of the top eight promoters could be minimized by at least 20% (to obtain final sequences that are approximately 24 to 177 bp), and several of the putative promoters either showed activity in Escherichia coli or were D. radiodurans specific, broadening the use of the promoters for various applications. Overall, this work introduces a suite of novel, well-characterized promoters for protein production and metabolic engineering in D. radiodurans IMPORTANCE The tolerance of the extremophile, Deinococcus radiodurans, to numerous oxidative stresses makes it ideal for bioremediation applications, but many of the tools necessary for metabolic engineering are lacking in this organism compared to model bacteria. Although native and engineered promoters have been used to drive gene expression for protein production in D. radiodurans, very few have been well characterized. Informed by bioinformatics, this study expands the repertoire of well-characterized promoters for D. radiodurans via thorough characterization of eight putative promoters with various strengths. These results will help facilitate tunable gene expression, since these promoters demonstrate strong and consistent performance compared to the current standard, PgroES This study also provides a methodology for high-throughput promoter identification and characterization using fluorescence in D. radiodurans The promoters identified in this study will facilitate metabolic engineering of D. radiodurans and enable its use in biotechnological applications ranging from bioremediation to synthesis of commodity chemicals.
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9
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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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10
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Jiang S, Wang J, Liu X, Liu Y, Guo C, Zhang L, Han J, Wu X, Xue D, Gomaa AE, Feng S, Zhang H, Chen Y, Ping S, Chen M, Zhang W, Li L, Zhou Z, Zuo K, Li X, Yang Y, Lin M. DrwH, a novel WHy domain-containing hydrophobic LEA5C protein from Deinococcus radiodurans, protects enzymatic activity under oxidative stress. Sci Rep 2017; 7:9281. [PMID: 28839181 PMCID: PMC5570939 DOI: 10.1038/s41598-017-09541-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
Water stress and hypersensitive response (WHy) domain is typically found as a component of atypical late embryogenesis abundant (LEA) proteins closely associated with resistance to multiple stresses in numerous organisms. Several putative LEA proteins have been identified in Deinococcus bacteria; however their precise function remains unclear. This work reports the characterization of a Deinococcus-specific gene encoding a novel WHy domain-containing hydrophobic LEA5C protein (named DrwH) in D. radiodurans R1. The expression of the drwH gene was induced by oxidative and salinity stresses. Inactivation of this gene resulted in increased sensitivity to oxidative and salinity stresses as well as reduced activities of antioxidant enzymes. The WHy domain of the DrwH protein differs structurally from that of a previously studied bacterial LEA5C protein, dWHy1, identified as a gene product from an Antarctic desert soil metagenome library. Further analysis indicated that in E. coli, the function of DrwH is related to oxidative stress tolerance, whereas dWHy1 is associated with freezing-thawing stress tolerance. Under oxidative stress induced by H2O2, DrwH protected the enzymatic activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH). These findings provide new insight into the evolutionary and survival strategies of Deinococcus bacteria under extreme environmental conditions.
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Affiliation(s)
- Shijie Jiang
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiahui Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoli Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahmed E Gomaa
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuai Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Heng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuzhen Ping
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengfu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kaijing Zuo
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xufeng Li
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Yi Yang
- Key Lab of Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochem J 2016; 473:4493-4505. [PMID: 27754888 DOI: 10.1042/bcj20160659] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Transcription factors of the Gre family bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus-specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn2+, but not Mg2+, ions. In contrast, we show that Gfh1 and Gfh2 moderately inhibit transcription initiation in the presence of either Mg2+ or Mn2+ ions. By using a molecular beacon assay, we demonstrate that Gfh1 and Gfh2 do not significantly change promoter complex stability or the rate of promoter escape by D. radiodurans RNAP. At the same time, Gfh factors significantly increase the apparent KM value for the 5'-initiating nucleotide, without having major effects on the affinity of metal ions for the RNAP active site. Similar inhibitory effects of Gfh factors are observed for transcription initiation on promoters recognized by the principal and an alternative σ factor. In summary, our data suggest that D. radiodurans Gfh factors impair the binding of initiating substrates independently of the metal ions bound in the RNAP active site, but have only mild overall effects on transcription initiation. Thus the mechanisms of modulation of RNAP activity by these factors are different for various steps of transcription.
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12
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Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
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Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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13
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Tripathi L, Zhang Y, Lin Z. Bacterial sigma factors as targets for engineered or synthetic transcriptional control. Front Bioeng Biotechnol 2014; 2:33. [PMID: 25232540 PMCID: PMC4153023 DOI: 10.3389/fbioe.2014.00033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/20/2014] [Indexed: 11/20/2022] Open
Abstract
Sigma (σ) factors are the predominant constituents of transcription regulation in bacteria. σ Factors recruit the core RNA polymerase to recognize promoters with specific DNA sequences. Recently, engineering of transcriptional regulators has become a significant tool for strain engineering. The present review summarizes the recent advances in σ factor based engineering or synthetic design. The manipulation of σ factors presents insights into the bacterial stress tolerance and metabolite productivity. We envision more synthetic design based on σ factors that can be used to tune the regulatory network of bacteria.
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Affiliation(s)
- Lakshmi Tripathi
- Department of Chemical Engineering, Tsinghua University , Beijing , China
| | - Yan Zhang
- Department of Chemical Engineering, Tsinghua University , Beijing , China
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University , Beijing , China
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14
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Hua X, Wang H, Wang C, Tian B, Hua Y. Global effect of an RNA polymerase β-subunit mutation on gene expression in the radiation-resistant bacterium Deinococcus radiodurans. SCIENCE CHINA-LIFE SCIENCES 2011; 54:854-62. [PMID: 21809039 DOI: 10.1007/s11427-011-4209-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 06/24/2011] [Indexed: 10/17/2022]
Abstract
The β-subunit of RNA polymerase, which is involved in rifampin binding, is highly conserved among prokaryotes, and Rifr mutants detected in many bacteria are the result of amino acid changes. Spontaneous rifampin resistance mutations resulting in amino acid replacement (L420R) and deletion (1258-66 9 bp deletion) have been previously isolated in the rpoB gene of Deinococcus radiodurans. In this study, a β-subunit mutation in D. radiodurans resulted in a unique effect on growth rate. We used DNA microarrays and biochemical assays to investigate how the Rifr mutation in the β-subunit led to changes in growth rate via altered regulation of multiple genes. The expression of genes with predicted functions in metabolism, cellular processes and signaling, and information storage and processing were significantly altered in the 9 bp-deletion rpoB mutant. The consensus promoter sequence of up-regulated genes in the 9 bp-deletion rpoB mutant was identified as an AT-rich sequence. Greater levels of reactive oxygen species accumulated in the L420R and 9 bp-deletion rpoB mutants compared with wild type. These results provide insight into the molecular mechanism of how the β-subunit Rifr mutation alters the regulation of multiple genes.
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Affiliation(s)
- Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, China
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15
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Shuryak I, Brenner DJ. Effects of radiation quality on interactions between oxidative stress, protein and DNA damage in Deinococcus radiodurans. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2010; 49:693-703. [PMID: 20574841 DOI: 10.1007/s00411-010-0305-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 06/01/2010] [Indexed: 05/29/2023]
Abstract
Ionizing radiation damages DNA and also induces oxidative stress, which can affect the function of proteins involved in DNA repair, thereby causing repair of DNA damage to become less efficient. We previously developed a mathematical model of this potentially synergistic relationship and applied it to γ-ray exposure data on the radiation-resistant prokaryote Deinococcus radiodurans. Here, we investigate the effects of radiation quality on these processes by applying the model to data on exposures of D. radiodurans to heavy ions with linear energy transfer (LET) of 18.5-11,300 keV/μm. The model adequately describes these data using three parameters combinations: radiogenic DNA damage induction, repair protein inactivation and cellular repair capacity. Although statistical uncertainties around best-fit parameter estimates are substantial, the behaviors of model parameters are consistent with current knowledge of LET effects: inactivation cross-sections for both DNA and proteins increase with increasing LET; DNA damage yield per unit of radiation dose also increases with LET; protein damage per unit dose tends to decrease with LET; DNA and especially protein damage yields are reduced when cells are irradiated in the dry state. These results suggest that synergism between oxidative stress and DNA damage may play an important role not only during γ-ray exposure, but during high-LET radiation exposure as well.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Medical Center, New York, NY 10032, USA.
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16
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Holland AD, Rothfuss HM, Lidstrom ME. Development of a defined medium supporting rapid growth for Deinococcus radiodurans and analysis of metabolic capacities. Appl Microbiol Biotechnol 2006; 72:1074-82. [PMID: 16575566 DOI: 10.1007/s00253-006-0399-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Revised: 02/26/2006] [Accepted: 03/02/2006] [Indexed: 10/24/2022]
Abstract
A morpholinepropanesulfonic acid (MOPS)-buffered rich defined medium (RDM) was optimized to support a reproducible 2.6-h doubling time at 35 degrees C for Deinococcus radiodurans R1 and used to gain insight into vitamin and carbon metabolism. D. radiodurans was shown to require biotin and niacin for growth in this medium. A glutamine-serine simple defined medium (SDM) was developed that supported a 4-h doubling time, and this medium was used to probe sulfur and methionine metabolism. Vitamin B(12) was shown to alleviate methionine auxotrophy, and under these conditions, sulfate was used as the sole sulfur source. Phenotypic characterization of a methionine synthase deletion mutant demonstrated that the B(12) alleviation of methionine auxotrophy was due to the necessity of the B(12)-dependent methionine synthase in methionine biosynthesis. Growth on ammonium as the sole nitrogen source in the presence of vitamin B(12) was demonstrated, but it was not possible to achieve reproducibly good growth in the absence of at least one amino acid as a nitrogen source. Growth on sulfate, cysteine, and methionine as sulfur sources demonstrated the function of a complete sulfur recycling pathway in this strain. These studies have demonstrated that rapid growth of D. radiodurans R1 can be achieved in a MOPS-based medium solely containing a carbon source, salts, four vitamins, and two amino acids.
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Affiliation(s)
- Alexandra D Holland
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-2180, USA
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17
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Schmid AK, Lipton MS, Mottaz H, Monroe ME, Smith RD, Lidstrom ME. Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J Proteome Res 2005; 4:709-18. [PMID: 15952717 DOI: 10.1021/pr049815n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The results of previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of more than 130 genes, including classical chaperones such as the groESL and dnaKJ operons and proteases such as clpB are induced in response to elevated temperature. In addition, previous qualitative whole-cell mass spectrometric studies conducted under heat shock conditions indicated global changes in the D. radiodurans proteome. To enable the discovery of novel heat shock inducible proteins as well as gain greater biological insight into the classical heat shock response at the protein level, we undertook the global whole-cell FTICR mass spectrometric proteomics study reported here. We have greatly increased the power of this approach by conducting a large number of replicate experiments in addition to taking a semiquantitative approach to data analysis, finding good reproducibility between replicates. Through this analysis, we have identified with high confidence a core set of classical heat shock proteins whose expression increases dramatically and reproducibly in response to elevated temperature. In addition, we have found that the heat shock proteome includes a large number of induced proteins that have not been identified previously as heat responsive, and have therefore been designated as candidate responders. Finally, our results are consistent with the hypothesis that elevated temperature stress could lead to cross-protection against other related stresses.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195-2125, USA.
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18
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Ohba H, Satoh K, Yanagisawa T, Narumi I. The radiation responsive promoter of the Deinococcus radiodurans pprA gene. Gene 2005; 363:133-41. [PMID: 16203111 DOI: 10.1016/j.gene.2005.07.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2005] [Revised: 07/05/2005] [Accepted: 07/13/2005] [Indexed: 11/27/2022]
Abstract
In a previous study, we identified a novel radiation-inducible protein PprA that plays a critical role in the radiation resistance of Deinococcus radiodurans [Narumi, I., Satoh, K., Cui, S., Funayama, T., Kitayama, S., Watanabe, H., 2004. PprA: a novel protein from Deinococcus radiodurans that stimulates DNA ligation. Mol. Microbiol. 54, 278-285.]. Despite the interest in mechanisms underlying radiation responses in D. radiodurans, little is known about the radiation responsive promoter for radiation-inducible proteins. In this study, three transcriptional start points for pprA mRNA were identified by primer extension analysis, located at positions -156, -154 and -22 upstream from the pprA translation initiation site. The amount of the three extended products increased in cells exposed to 2 kGy followed by a 0.5-h post-incubation. This suggested the existence of at least two radiation responsive promoters for pprA expression. Functional characterization of the upstream region of the pprA gene using a luciferase reporter assay revealed that the distal promoter is located between positions -208 and -156 from the translation initiation site, while the proximal promoter is located between positions -57 and -22. The region located between positions -57 and -38 was indispensable for proximal promoter activity. Site-directed mutagenesis of a thymine positioned at -33 resulted in severe impairment of promoter activity, and suggested that the thymine functions as a master base for the proximal radiation responsive promoter. The product of the D. radiodurans pprI gene is thought to be a general switch in the radiation response [Hua, Y., Narumi, I., Gao, G., Tian, B., Satoh, K., Kitayama, S., Shen, B., 2003. PprI: a general switch responsible for extreme radioresistance of Deinococcus radiodurans. Biochem. Biophys. Res. Commun. 306, 354-360.]. We examined the effect of pprI disruption on pprA promoter activity. The results suggested that up-regulation of pprA expression by the pprI gene product is triggered at the promoter level.
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Affiliation(s)
- Hirofumi Ohba
- Research Group for Biotechnology Development, Department of Ion-beam-applied Biology, Japan Atomic Energy Research Institute, 1233 Watanuki-machi, Takasaki, Gunma 370-1292, Japan
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Schmid AK, Howell HA, Battista JR, Peterson SN, Lidstrom ME. HspR is a global negative regulator of heat shock gene expression in Deinococcus radiodurans. Mol Microbiol 2005; 55:1579-90. [PMID: 15720562 DOI: 10.1111/j.1365-2958.2005.04494.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The HspR protein functions as a negative regulator of chaperone and protease gene expression in a diversity of bacteria. Here we have identified, cloned and deleted the Deinococcus radiodurans HspR homologue, DR0934. Delta hspR mutants exhibit moderate growth defects when shifted to mild heat shock temperatures, but are severely impaired for survival at 48 degrees C. Using quantitative reverse transcription polymerase chain reaction and global transcriptional analysis, we have identified 14 genes that are derepressed in the absence of stress in the delta hspR background, 11 of which encode predicted chaperones and proteases, including dnaKJgrpE, ftsH, lonB, hsp20 and clpB. Promoter mapping indicated that the transcription of these genes initiates from a promoter bearing a sigma70-type consensus, and that putative HspR binding sites (HAIR) were present in the 5'-untranslated regions. Electrophoretic mobility shift assays indicated that HspR binds to these promoters at the HAIR site in vitro. These results strongly suggest that DR0934 encodes the HspR-like global negative regulator of D. radiodurans that directly represses chaperone and protease gene expression by binding to the HAIR site in close proximity to promoter regions.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195-2180, USA
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Schmid AK, Howell HA, Battista JR, Peterson SN, Lidstrom ME. Global transcriptional and proteomic analysis of the Sig1 heat shock regulon of Deinococcus radiodurans. J Bacteriol 2005; 187:3339-51. [PMID: 15866918 PMCID: PMC1111999 DOI: 10.1128/jb.187.10.3339-3351.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sig1 gene, predicted to encode an extracytoplasmic function-type heat shock sigma factor of Deinococcus radiodurans, has been shown to play a central role in the positive regulation of the heat shock operons groESL and dnaKJ. To determine if Sig1 is required for the regulation of additional heat shock genes, we monitored the global transcriptional and proteomic profiles of a D. radiodurans R1 sig1 mutant and wild-type cells in response to elevated temperature stress. Thirty-one gene products were identified that showed heat shock induction in the wild type but not in the sig1 mutant. Quantitative real-time PCR experiments verified the transcriptional requirement of Sig1 for the heat shock induction of the mRNA of five of these genes-dnaK, groES, DR1314, pspA, and hsp20. hsp20 appears to encode a new member of the small heat shock protein superfamily, DR1314 is predicted to encode a hypothetical protein with no recognizable orthologs, and pspA is predicted to encode a protein involved in maintenance of membrane integrity. Deletion mutation analysis demonstrated the importance in heat shock protection of hsp20 and DR1314. The promoters of dnaKJE, groESL, DR1314, pspA, and hsp20 were mapped and, combined with computer-based pattern searches of the upstream regions of the 26 other Sig1 regulon members, these results suggested that Sig1 might recognize both sigma70-type and sigma(W)-type promoter consensus sequences. These results expand the D. radiodurans Sig1 heat shock regulon to include 31 potential new members, including not only factors with cytoplasmic functions, such as groES and dnaK, but also those with extracytoplasmic functions, like pspA.
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Affiliation(s)
- Amy K Schmid
- Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195-2180, USA.
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21
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Bischoff M, Dunman P, Kormanec J, Macapagal D, Murphy E, Mounts W, Berger-Bächi B, Projan S. Microarray-based analysis of the Staphylococcus aureus sigmaB regulon. J Bacteriol 2004; 186:4085-99. [PMID: 15205410 PMCID: PMC421609 DOI: 10.1128/jb.186.13.4085-4099.2004] [Citation(s) in RCA: 310] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Accepted: 03/18/2004] [Indexed: 01/30/2023] Open
Abstract
Microarray-based analysis of the transcriptional profiles of the genetically distinct Staphylococcus aureus strains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by sigmaB activity. While sigmaB was found to positively control 198 genes by a factor of > or =2 in at least two of the three genetic lineages analyzed, 53 ORFs were repressed in the presence of sigmaB. Gene products that were found to be influenced by sigmaB are putatively involved in all manner of cellular processes, including cell envelope biosynthesis and turnover, intermediary metabolism, and signaling pathways. Most of the genes and/or operons identified as upregulated by sigmaB were preceded by a nucleotide sequence that resembled the sigmaB consensus promoter sequence of Bacillus subtilis. A conspicuous number of virulence-associated genes were identified as regulated by sigmaB activity, with many adhesins upregulated and prominently represented in this group, while transcription of various exoproteins and toxins were repressed. The data presented here suggest that the sigmaB of S. aureus controls a large regulon and is an important modulator of virulence gene expression that is likely to act conversely to RNAIII, the effector molecule of the agr locus. We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments.
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Affiliation(s)
- Markus Bischoff
- Department of Medical Microbiology, University of Zurich, CH-8028 Zurich, Switzerland.
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