1
|
Zhu C, Sun B, Liu T, Zheng H, Gu W, He W, Sun F, Wang Y, Yang M, Bei W, Peng X, She Q, Xie L, Chen L. Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival. BMC Genomics 2017; 18:436. [PMID: 28583064 PMCID: PMC5460551 DOI: 10.1186/s12864-017-3784-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 05/10/2017] [Indexed: 11/24/2022] Open
Abstract
Background Vibrio parahaemolyticus causes serious seafood-borne gastroenteritis and death in humans. Raw seafood is often subjected to post-harvest processing and low-temperature storage. To date, very little information is available regarding the biological functions of cold shock proteins (CSPs) in the low-temperature survival of the bacterium. In this study, we determined the complete genome sequence of V. parahaemolyticus CHN25 (serotype: O5:KUT). The two main CSP-encoding genes (VpacspA and VpacspD) were deleted from the bacterial genome, and comparative transcriptomic analysis between the mutant and wild-type strains was performed to dissect the possible molecular mechanisms that underlie low-temperature adaptation by V. parahaemolyticus. Results The 5,443,401-bp V. parahaemolyticus CHN25 genome (45.2% G + C) consisted of two circular chromosomes and three plasmids with 4,724 predicted protein-encoding genes. One dual-gene and two single-gene deletion mutants were generated for VpacspA and VpacspD by homologous recombination. The growth of the ΔVpacspA mutant was strongly inhibited at 10 °C, whereas the VpacspD gene deletion strongly stimulated bacterial growth at this low temperature compared with the wild-type strain. The complementary phenotypes were observed in the reverse mutants (ΔVpacspA-com, and ΔVpacspD-com). The transcriptome data revealed that 12.4% of the expressed genes in V. parahaemolyticus CHN25 were significantly altered in the ΔVpacspA mutant when it was grown at 10 °C. These included genes that were involved in amino acid degradation, secretion systems, sulphur metabolism and glycerophospholipid metabolism along with ATP-binding cassette transporters. However, a low temperature elicited significant expression changes for 10.0% of the genes in the ΔVpacspD mutant, including those involved in the phosphotransferase system and in the metabolism of nitrogen and amino acids. The major metabolic pathways that were altered by the dual-gene deletion mutant (ΔVpacspAD) radically differed from those that were altered by single-gene mutants. Comparison of the transcriptome profiles further revealed numerous differentially expressed genes that were shared among the three mutants and regulators that were specifically, coordinately or antagonistically modulated by VpaCspA and VpaCspD. Our data also revealed several possible molecular coping strategies for low-temperature adaptation by the bacterium. Conclusions This study is the first to describe the complete genome sequence of V. parahaemolyticus (serotype: O5:KUT). The gene deletions, complementary insertions, and comparative transcriptomics demonstrate that VpaCspA is a primary CSP in the bacterium, while VpaCspD functions as a growth inhibitor at 10 °C. These results have improved our understanding of the genetic basis for low-temperature survival by the most common seafood-borne pathogen worldwide. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3784-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chunhua Zhu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Boyi Sun
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Taigang Liu
- College of Information Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Centre at Shanghai, Shanghai, 201203, People's Republic of China
| | - Wenyi Gu
- Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Centre at Shanghai, Shanghai, 201203, People's Republic of China
| | - Wei He
- Shanghai Hanyu Bio-lab, 151 Ke Yuan Road, Shanghai, 201203, People's Republic of China
| | - Fengjiao Sun
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Yaping Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China
| | - Meicheng Yang
- Shanghai Institute for Food and Drug Control, 1500 Zhang Heng Road, Shanghai, 201203, People's Republic of China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, Laboratory of Animal Infectious Diseases, College of Animal Science & Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200, Copenhagen N, Denmark
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200, Copenhagen N, Denmark
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 201203, People's Republic of China.
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, People's Republic of China.
| |
Collapse
|
2
|
Reymer A, Babik S, Takahashi M, Nordén B, Beke-Somfai T. ATP Hydrolysis in the RecA-DNA Filament Promotes Structural Changes at the Protein-DNA Interface. Biochemistry 2015. [PMID: 26196253 DOI: 10.1021/acs.biochem.5b00614] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To address the mechanistic roles of ATP hydrolysis in RecA-promoted strand exchange reaction in homologous recombination, quantum mechanical calculations are performed on key parts of the RecA-DNA complex. We find that ATP hydrolysis may induce changes at the protein-DNA interface, resulting in the rearrangement of the hydrogen bond network connecting the ATP and the DNA binding sites.
Collapse
Affiliation(s)
- Anna Reymer
- †Department of Chemistry and Molecular Biology, Gothenburg University, SE-405 30 Gothenburg, Sweden
| | - Sándor Babik
- ‡Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Masayuki Takahashi
- §School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-14 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Bengt Nordén
- ‡Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Tamás Beke-Somfai
- ‡Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,∥Institute of Materials Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary
| |
Collapse
|