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Kumari K, Sharma PK, Singh RP. Unravelling the transcriptome response of Enterobacter sp. S-33 under varying temperature. Arch Microbiol 2024; 206:81. [PMID: 38294553 DOI: 10.1007/s00203-023-03792-6] [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: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
Enterobacter genus includes the bacteria occupying every aspect of environment, however, their adaptability at varying temperature is not clear. In the present study, we analyzed the transcriptome response of Enterobacter sp. S-33 and their functional genes under various temperatures (30-45 ℃) that were expressed and accumulated in cells under temperature-stress. During a temperature shift from 37 to 45 ℃, 165 genes showed differential expression including 112 up-regulated and 53 down-regulated. In particular, heat-shock genes such as CspA, 16 kDa heat shock protein A/B and transcriptional regulators such as LysR, TetR, and LuxR were differentially expressed, indicating the role of complex molecular mechanism of Enterobacter adapting to temperature stress. Similarly, genes associated to signal transduction, ABC transporters, iron homeostasis, and quorum sensing were also induced. The Gene ontology enrichment analysis of differentially expressed genes (DEGs) were categorized into "transmembrane transport", "tRNA binding", "hydrogen sulfide biosynthetic process" and "sulfate assimilation" terms. In addition, Kyoto Encyclopedia of Genes and Genomes pathways showed that ABC transporter as well as quorum sensing pathways were significantly enriched. Overall, current study has contributed to explore the adaptive molecular mechanisms of Enterobacter spp. upon temperature change, which further opens new avenues for future in-depth functional studies.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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Gao Y, Li N, Zhou Y, Zhang Z, Zhang Y, Fan P, Zhou H, Zhang T, Chang L, Gao H, Li Y, Kang X, Xie Q, Lyu Z, Xu P. iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C 6+ heavy ion irradiation. BMC Microbiol 2022; 22:264. [PMID: 36333788 PMCID: PMC9635210 DOI: 10.1186/s12866-022-02676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Deinococcus radiodurans (D. radiodurans) is best known for its extreme resistance to diverse environmental stress factors, including ionizing radiation (IR), ultraviolet (UV) irradiation, oxidative stress, and high temperatures. Robust DNA repair system and antioxidant system have been demonstrated to contribute to extreme resistance in D. radiodurans. However, practically all studies on the mechanism underlying D. radiodurans’s extraordinary resistance relied on the treated strain during the post-treatment recovery lag phase to identify the key elements involved. The direct gene or protein changes of D. radiodurans after stress have not yet been characterized. Results In this study, we performed a proteomics profiling on D. radiodurans right after the heavy ion irradiation treatment, to discover the altered proteins that were quickly responsive to IR in D. radiodurans. Our study found that D. radiodurans shown exceptional resistance to 12C6+ heavy ion irradiation, in contrast to Escherichia coli (E.coli) strains. By using iTRAQ (Isobaric Tags for Relative and Absolute Quantitation)-based quantitative mass spectrometry analysis, the kinetics of proteome changes induced by various dosages of 12C6+ heavy ion irradiation were mapped. The results revealed that 452 proteins were differentially expressed under heavy ion irradiation, with the majority of proteins being upregulated, indicating the upregulation of functional categories of translation, TCA cycle (Tricarboxylic Acid cycle), and antioxidation regulation under heavy ion irradiation. Conclusions This study shows how D. radiodurans reacts to exposure to 12C6+ heavy ion irradiation in terms of its overall protein expression profile. Most importantly, comparing the proteome profiling of D. radiodurans directly after heavy ion irradiation with research on the post-irradiation recovery phase would potentially provide a better understanding of mechanisms underlying the extreme radioresistance in D. radiodurans. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02676-x.
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Affiliation(s)
- Yuan Gao
- grid.27871.3b0000 0000 9750 7019Central Laboratory of College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China ,grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Naikang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Yanxia Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,Beijing Institute of Food Inspection and Research, Beijing Municipal Center for Food Safety Monitoring and Risk Assessment, Beijing, 102206 People’s Republic of China
| | - Zhenpeng Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Pengcheng Fan
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Hangfan Zhou
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Tao Zhang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Lei Chang
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Huiying Gao
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Yanchang Li
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China
| | - Xianjiang Kang
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Qiong Xie
- grid.418516.f0000 0004 1791 7464China Astronaut Research and Training Center, Beijing, 100094 People’s Republic of China
| | - Zhitang Lyu
- School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China
| | - Ping Xu
- grid.419611.a0000 0004 0457 9072State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing, 102206 People’s Republic of China ,School of Life Sciences, Institute of Life Science and Green DevelopmentHebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, 180 East Wusi Road, Baoding, 071002 People’s Republic of China ,grid.186775.a0000 0000 9490 772XAnhui Medical University, Hefei, 230032 People’s Republic of China ,grid.443382.a0000 0004 1804 268XMedical School of Guizhou University, Guiyang, 550025 People’s Republic of China ,grid.411866.c0000 0000 8848 7685Second Clinical Medicine Collage, Guangzhou University Chinese Medicine, Guangzhou, 510006 People’s Republic of China
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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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