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Yi X, Xu X, Chen Y, Xu G, Zhu Z, Li H, Shen H, Lin M, Zhao W, Zheng J, Jiang X. Genetic analysis of Vibrio alginolyticus challenged by Fructus schisandrae reveals the mechanism of virulence genes. Gene 2023; 870:147421. [PMID: 37031882 DOI: 10.1016/j.gene.2023.147421] [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: 11/30/2022] [Revised: 03/21/2023] [Accepted: 04/04/2023] [Indexed: 04/11/2023]
Abstract
Due to the abusive use of antibiotics, bacterial resistance has become a global problem and poses severe threats to aquaculture. The drug-resistant diseases caused by Vibrio alginolyticus have caused significant economic losses to cultured marine fish. Fructus schisandrae is used to treat inflammatory diseases in China and Japan. There have been no reports of bacterial molecular mechanisms associated with F. schisandrae stress. In this study, the inhibiting effect of F. schisandrae on the growth of V. alginolyticus was detected to understand response mechanisms at the molecular level. The antibacterial tests were analyzed via next-generation deep sequencing technology (RNA sequencing, RNA-seq). Wild V. alginolyticus (CK) was compared with V. alginolyticus, F. schisandrae incubated for 2 h, and V. alginolyticus, F. schisandrae incubated for 4 h. Our results revealed that there were 582 genes (236 upregulated and 346 downregulated) and 1068 genes (376 upregulated and 692 downregulated), respectively. Differentially expressed genes (DEGs) were involved in the following functional categories: metabolic process, single-organism process, catalytic activity, cellular process, binding, membrane, cell part, cell, and localization. FS_2 h was compared with FS_4 h, and 21 genes (14 upregulated and 7 downregulated) were obtained. The RNA-seq results were validated by detecting the expression levels of 13 genes using quantitative real-time polymerase chain reaction (qRT-PCR). The qRT-PCR results matched those of the sequencing, which reinforced the reliability of the RNA-seq. The results revealed the transcriptional response of V. alginolyticus to F. schisandrae, which will provide new ideas for studying V. alginolyticus' complex virulence molecular mechanism and the possibility of developing Schisandra to prevent and treat drug-resistant diseases.
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Affiliation(s)
- Xin Yi
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - XiaoJin Xu
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China; Fujian Province Key Laboratory of Special Aquatic Formula Feed(Fujian Tianma Science and Technology Group Co., Ltd.)
| | - YuNong Chen
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China; Fujian Province Key Laboratory of Special Aquatic Formula Feed(Fujian Tianma Science and Technology Group Co., Ltd.)
| | - Genhuang Xu
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - ZhiQin Zhu
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - Huiyao Li
- Fisheries Research Institute of Fujian, Xiamen 361013, China
| | - HaoYang Shen
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - Mao Lin
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - Wenyu Zhao
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - Jiang Zheng
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China
| | - XingLong Jiang
- Fisheries College, Jimei University, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Fujian Provincial Key Laboratory of Marine Fishery Resources and Eco-environment, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fujian Province, Xiamen 361021, China.
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GcvB Regulon Revealed by Transcriptomic and Proteomic Analysis in Vibrio alginolyticus. Int J Mol Sci 2022; 23:ijms23169399. [PMID: 36012664 PMCID: PMC9409037 DOI: 10.3390/ijms23169399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 02/07/2023] Open
Abstract
Vibrio alginolyticus is a widely distributed marine bacterium that is a threat to the aquaculture industry as well as human health. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and cellular processes by modulating gene expression post-transcriptionally. GcvB is one of the most conserved sRNAs that is regarded as the master regulator of amino acid uptake and metabolism in a wide range of Gram-negative bacteria. However, little information about GcvB-mediated regulation in V. alginolyticus is available. Here we first characterized GcvB in V. alginolyticus ZJ-T and determined its regulon by integrated transcriptome and quantitative proteome analysis. Transcriptome analysis revealed 40 genes differentially expressed (DEGs) between wild-type ZJ-T and gcvB mutant ZJ-T-ΔgcvB, while proteome analysis identified 50 differentially expressed proteins (DEPs) between them, but only 4 of them displayed transcriptional differences, indicating that most DEPs are the result of post-transcriptional regulation of gcvB. Among the differently expressed proteins, 21 are supposed to be involved in amino acid biosynthesis and transport, and 11 are associated with type three secretion system (T3SS), suggesting that GcvB may play a role in the virulence besides amino acid metabolism. RNA-EMSA showed that Hfq binds to GcvB, which promotes its stability.
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Begrem S, Jérôme M, Leroi F, Delbarre-Ladrat C, Grovel O, Passerini D. Genomic diversity of Serratia proteamaculans and Serratia liquefaciens predominant in seafood products and spoilage potential analyses. Int J Food Microbiol 2021; 354:109326. [PMID: 34247024 DOI: 10.1016/j.ijfoodmicro.2021.109326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/03/2021] [Accepted: 06/29/2021] [Indexed: 11/18/2022]
Abstract
Serratia sp. cause food losses and waste due to spoilage; it is noteworthy that they represent a dominant population in seafood. The main spoilage associated species comprise S. liquefaciens, S. grimesii, S. proteamaculans and S. quinivorans, also known as S. liquefaciens-like strains. These species are difficult to discriminate since classical 16S rRNA gene-based sequences do not possess sufficient resolution. In this study, a phylogeny based on the short-length luxS gene was able to speciate 47 Serratia isolates from seafood, with S. proteamaculans being the main species from fresh salmon and tuna, cold-smoked salmon, and cooked shrimp while S. liquefaciens was only found in cold-smoked salmon. The genome of the first S. proteamaculans strain isolated from the seafood matrix (CD3406 strain) was sequenced. Pangenome analyses of S. proteamaculans and S. liquefaciens indicated high adaptation potential. Biosynthetic pathways involved in antimicrobial compounds production and in the main seafood spoilage compounds were also identified. The genetic equipment highlighted in this study contributed to gain further insights into the predominance of Serratia in seafood products and their capacity to spoil.
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Affiliation(s)
- Simon Begrem
- IFREMER, BRM, EM(3)B Laboratory, Rue de l'Île d'Yeu, BP 21105, F-44300 Nantes Cedex 3, France; Université de Nantes, MMS - EA2160, 44000 Nantes, France
| | - Marc Jérôme
- IFREMER, BRM, EM(3)B Laboratory, Rue de l'Île d'Yeu, BP 21105, F-44300 Nantes Cedex 3, France
| | - Françoise Leroi
- IFREMER, BRM, EM(3)B Laboratory, Rue de l'Île d'Yeu, BP 21105, F-44300 Nantes Cedex 3, France
| | | | - Olivier Grovel
- Université de Nantes, MMS - EA2160, 44000 Nantes, France
| | - Delphine Passerini
- IFREMER, BRM, EM(3)B Laboratory, Rue de l'Île d'Yeu, BP 21105, F-44300 Nantes Cedex 3, France.
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Nagaoka S, Sugiyama N, Yatsunami R, Nakamura S. Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica. Biosci Biotechnol Biochem 2021; 85:1986-1994. [PMID: 34215877 DOI: 10.1093/bbb/zbab122] [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: 04/11/2021] [Accepted: 06/21/2021] [Indexed: 11/12/2022]
Abstract
3-Isopropylmalate dehydrogenase (IPMDH) catalyzes oxidative decarboxylation of (2R, 3S)-3-isopropylmalate to 2-oxoisocaproate in leucine biosynthesis. In this study, recombinant IPMDH (HjIPMDH) from an extremely halophilic archaeon, Haloarcula japonica TR-1, was characterized. Activity of HjIPMDH increased as KCl concentration increased, and the maximum activity was observed at 3.0 m KCl. Analytical ultracentrifugation revealed that HjIPMDH formed a homotetramer at high KCl concentrations, and it dissociated to a monomer at low KCl concentrations. Additionally, HjIPMDH was thermally stabilized by higher KCl concentrations. This is the first report on haloarchaeal IPMDH.
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Affiliation(s)
- Shintaro Nagaoka
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Noriko Sugiyama
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Rie Yatsunami
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan.,National Institute of Technology (KOSEN), Numazu College, Numazu, Shizuoka, Japan
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