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Zhang Y, Zhang T, Qiu Y, Zhang M, Lu X, Yang W, Hu L, Zhou D, Gao B, Lu R. Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation. Curr Microbiol 2023; 80:371. [PMID: 37838636 DOI: 10.1007/s00284-023-03425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/19/2023] [Indexed: 10/16/2023]
Abstract
Vibrio parahaemolyticus, the leading cause of bacterial seafood-associated gastroenteritis, can form biofilms. In this work, the gene expression profiles of V. parahaemolyticus during biofilm formation were investigated by transcriptome sequencing. A total of 183, 503, and 729 genes were significantly differentially expressed in the bacterial cells at 12, 24 and 48 h, respectively, compared with that at 6 h. Of these, 92 genes were consistently activated or repressed from 6 to 48 h. The genes involved in polar flagellum, chemotaxis, mannose-sensitive haemagglutinin type IV pili, capsular polysaccharide, type III secretion system 1 (T3SS1), T3SS2, thermostable direct hemolysin (TDH), type VI secretion system 1 (T6SS1) and T6SS2 were downregulated, whereas those involved in V. parahaemolyticus pathogenicity island (Vp-PAI) (except for T3SS2 and TDH) and membrane fusion proteins were upregulated. Three extracellular protease genes (vppC, prtA and VPA1071) and a dozen of outer membrane protein encoding genes were also significantly differentially expressed during biofilm formation. In addition, five putative c-di-GMP metabolism-associated genes were significantly differentially expressed, which may account for the drop in c-di-GMP levels after the beginning of biofilm formation. Moreover, many putative regulatory genes were significantly differentially expressed, and more than 1000 putative small non-coding RNAs were detected, suggesting that biofilm formation was tightly regulated by complex regulatory networks. The data provided a global view of gene expression profiles during biofilm formation, showing that the significantly differentially expressed genes were involved in multiple cellular pathways, including virulence, biofilm formation, metabolism, and regulation.
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Affiliation(s)
- Yiquan Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong, 226006, Jiangsu, China
- Department of Clinical Laboratory, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Tingting Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong, 226006, Jiangsu, China
- Department of Clinical Laboratory, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Yue Qiu
- Department of Clinical Laboratory, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, 213000, Jiangsu, China
| | - Miaomiao Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong, 226006, Jiangsu, China
- Department of Clinical Laboratory, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xiuhui Lu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Bo Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Renfei Lu
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong, 226006, Jiangsu, China.
- Department of Clinical Laboratory, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China.
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Comprehensive insights into the metabolism characteristics of small RNA Qrr4 in Vibrio alginolyticus. Appl Microbiol Biotechnol 2023; 107:1887-1902. [PMID: 36795140 DOI: 10.1007/s00253-023-12435-1] [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: 11/23/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/17/2023]
Abstract
Vibrio alginolyticus is an important foodborne pathogen that can infect both humans and marine animals and cause massive economic losses in aquaculture. Small noncoding RNAs (sRNAs) are emerging posttranscriptional regulators that affect bacterial physiology and pathological processes. In the present work, a new cell density-dependent sRNA, Qrr4, was characterized in V. alginolyticus based on a previously reported RNA-seq analysis and bioinformatics approach. The effects of Qrr4 actions on the physiology, virulence, and metabolism of V. alginolyticus were comprehensively investigated based on molecular biology and metabolomics approaches. The results showed that qrr4 deletion markedly inhibited growth, motility and extracellular protease activities. Additionally, nontargeted metabolism and lipidomics analyses revealed that qrr4 deletion induced significant disturbance of multiple metabolic pathways. The key metabolic remodelling that occurred in response to qrr4 deletion was found to involve phospholipid, nucleotide, carbohydrate and amino acid metabolic pathways, providing novel clues about a potential mechanism via which mutation of qrr4 could interfere with cellular energy homeostasis, modulate membrane phospholipid composition and inhibit nucleic acid and protein syntheses to regulate the motility, growth and virulence characteristics of V. alginolyticus. Overall, this study provides a comprehensive understanding of the regulatory roles of the new cell density-dependent sRNA Qrr4 in V. alginolyticus. KEY POINTS: • A novel cell density-dependent sRNA, Qrr4, was cloned in V. alginolyticus. •Qrr4 regulated growth and virulence factors of V. alginolyticus. • Phospholipid, nucleotide and energy metabolisms were modulated obviously by Qrr4.
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Wang M, Liang Y, Li F, Shen S, Huang X, Sun Y. Enhancement of biological denitrification by the addition of novel sRNA Pda200 under antibiotic pressure. BIORESOURCE TECHNOLOGY 2022; 365:128113. [PMID: 36252762 DOI: 10.1016/j.biortech.2022.128113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Paracoccus denitrificans can adapt to complex environmental changes and sRNAs play crucial roles during this process. This work aim to identify antibiotic-induced sRNA that regulated denitrification and explored its potential for functional enhancement of this process. Target prediction indicated complementary base pairing between the denitrifying gene nosZ and the sRNA Pda200. Anaerobic culture of P. denitrificans ATCC 19367 in the presence of florfenicol (FF) resulted in significant decreases in nosZ and Pda200 gene expression (p < 0.01). Two additional denitrifiers isolated from contaminated sediment were co-cultured with ATCC 19367 to generate a consortium. And an inducible Pda200 expression strain was also added. The results revealed that Pda200 significantly enhanced napA, napB and norB expression in different types of denitrifiers under FF condition (p < 0.05 ∼ 0.001). This study identified the sRNA Pda200 as a novel positive regulator of denitrification, which may realize the efficient treatment of antibiotic-contaminated wastewater by microbial agents.
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Affiliation(s)
- Mei Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China; Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, PR China
| | - Yi Liang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Fulin Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Shuqing Shen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Xinyu Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China
| | - Yongxue Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, PR China.
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Zhang X, Sun J, Chen F, Qi H, Chen L, Sung YY, Huang Y, Lv A, Hu X. Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism. Microb Genom 2021; 7. [PMID: 33952389 PMCID: PMC8209731 DOI: 10.1099/mgen.0.000549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The virulence of Vibrio parahaemolyticus is variable depending on its virulence determinants. A V. parahaemolyticus strain, in which the virulence is governed by the pirA and pirB genes, can cause acute hepatopancreatic necrosis disease (AHPND) in shrimps. Some V. parahaemolyticus that are non-AHPND strains also cause shrimp diseases and result in huge economic losses, while their pathogenicity and pathogenesis remain unclear. In this study, a non-AHPND V. parahaemolyticus, TJA114, was isolated from diseased Penaeus vannamei associated with a high mortality. To understand its virulence and adaptation to the external environment, whole-genome sequencing of this isolate was conducted, and its phenotypic profiles including pathogenicity, growth characteristics and nutritional requirements were investigated. Shrimps following artificial infection with this isolate presented similar clinical symptoms to the naturally diseased ones and generated obvious pathological lesions. The growth characteristics indicated that the isolate TJA114 could grow well under different salinity (10–55 p.p.t.), temperature (23–37 °C) and pH (6–10) conditions. Phenotype MicroArray results showed that this isolate could utilize a variety of carbon sources, amino acids and a range of substrates to help itself adapt to the high hyperosmotic and alkaline environments. Antimicrobial-susceptibility test showed that it was a multidrug-resistant bacterium. The whole-genomic analysis showed that this V. parahaemolyticus possessed many important functional genes associated with multidrug resistance, stress response, adhesions, haemolysis, putative secreted proteases, dedicated protein secretion systems and a variety of nutritional metabolic mechanisms. These annotated functional genes were confirmed by the phenotypic profiles. The results in this study indicated that this V. parahaemolyticus isolate possesses a high pathogenicity and strong environmental adaptability.
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Affiliation(s)
- Xue Zhang
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Jingfeng Sun
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Feng Chen
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Hongli Qi
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Limei Chen
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Malaysia
| | - Yadong Huang
- Tianjin Hengqian Aquaculture Co. Ltd, Tianjin 300270, PR China
| | - Aijun Lv
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Xiucai Hu
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin 300384, PR China
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Liu H, Liu W, He X, Chen X, Yang J, Wang Y, Li Y, Ren J, Xu W, Zhao Y. Characterization of a cell density-dependent sRNA, Qrr, and its roles in the regulation of the quorum sensing and metabolism in Vibrio alginolyticus. Appl Microbiol Biotechnol 2020; 104:1707-1720. [PMID: 31907574 DOI: 10.1007/s00253-019-10278-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/08/2019] [Accepted: 11/23/2019] [Indexed: 12/25/2022]
Abstract
Vibrio alginolyticus is an important fish pathogen causing pandemic diseases in marine animals. Small noncoding RNAs (sRNAs) are important posttranscriptional modulators of gene expression and involved in the pathogenesis of bacterial pathogens. Thus far, no cell density-dependent sRNA has been reported in V. alginolyticus. In this study, a cell density-dependent sRNA, Qrr, predicted based on the previous RNA-Seq analysis of V. alginolyticus cultured at low cell density (LCD) and high cell density (HCD), was characterized. The Qrr mutant showed significantly impaired growth and decreased swimming and swarming ability, and increased biofilm formation, extracellular polysaccharide content, serine protease production, and LD50 values during zebrafish infection in contrast to the wild-type strain. Qrr modulates the master regulators LuxR and AphA in quorum sensing (QS) pathways possibly at the posttranscriptional level by base pairing with the 5'-untranslated regions (5'-UTRs). Meanwhile, both LuxR and AphA could directly bind to the promoter of qrr to activate or repress its transcription, respectively. Moreover, our unbiased metabolic approaches revealed that Qrr modulates a large quantity of metabolic and lipidomic pathways, including amino acids, purine and pyrimidine derivatives, tricarboxylic acid cycle (TCA cycle) intermediates, and lipids. Collectively, this work contributes to a systematic understanding of regulatory roles of the cell density-dependent sRNA, Qrr, in V. alginolyticus.
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Affiliation(s)
- Huan Liu
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Wang Liu
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Xiaoxian He
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Xuefeng Chen
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Jinfang Yang
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yi Wang
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Yue Li
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Jiamin Ren
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China
| | - Wensheng Xu
- Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Faculty of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, China.
| | - Yanni Zhao
- School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, China.
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Deng Y, Su Y, Liu S, Bei L, Guo Z, Li H, Chen C, Feng J. A novel sRNA srvg17985 identified in Vibrio alginolyticus involving into metabolism and stress response. Microbiol Res 2019; 229:126295. [PMID: 31450184 DOI: 10.1016/j.micres.2019.126295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 11/28/2022]
Abstract
Vibrio alginolyticus is an opportunistic pathogen that is a threat to the aquaculture industry. Evidence has revealed critical roles for small RNAs (sRNAs) in bacterial physiology and pathology by modulating gene expression post transcription. However, little information about sRNA-mediated regulation in V. alginolyticus is available. We experimentally verified the existence and characterized the function of sRNA srvg17985 in V. alginolyticus ZJ-T. We identified a 179 nt and growth-phase-dependent transcript with a σ70 promoter and a ρ-independent terminator. The transcript consisted of five stem-loops and was conserved in Vibrio spp. Phenotype microarray assays showed that deletion of srvg17985 led to less use of Gly-Glu as a carbon source but a gain in ability to use l-phenylalanine as a nitrogen source. Srvg17985 regulated the osmotic stress response with stronger tolerance to NaCl but weaker tolerance to urea. In addition, srvg17985 inhibited the deamination of l-serine at pH 9.5 and promoted the hydrolysis of X-beta-d-glucuronide, thus affecting the pH stress response. Bioinformatics by IntaRNA and TargetRNA2 identified 45 common target mRNAs, some of which probably contributed to the observed phenotypes. These results indicated that srvg17985 regulated environmental adaptation. The results provide valuable information for in-depth studies of sRNA-mediated regulation mechanisms of the complex physiological processes of V alginolyticus and provide new targets for antibacterial therapeutics or attenuated vaccines for Vibrio spp.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China
| | - Youlu Su
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lei Bei
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Zhixun Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huo Li
- Jinyang Tropical Haizhen Aquaculture Co., Ltd., Maoming, China
| | - Chang Chen
- Xisha/Nansha Ocean Observation and Research Station, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; Tropical Aquaculture Research and Development Centre, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Hainan, China.
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