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Molecular Cloning and Bioinformatics Analysis of msrA Gene from Vibrio alginolyticus Strain HY9901

Agricultural Biotechnology 2024年第4期13卷 1-5,10页

作者： Zhiqing WEI Zhihang CHEN Yingzhu WEI Na WANG huanying pang Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing 100176China

[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 *** protein had a stable structure,and it was hydrophobic *** structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane *** amino acid sequence of MsrA contained multiple signal binding *** subcellular localization showed that MsrA protein was most likely located in the *** analysis showed that MsrA of *** had high homology with other Vibrio species,and the highest homology with *** the prediction of functional domains,MsrA had the function of methionine sulfoxide *** secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the *** similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.

关键词： Vibrio alginolyticus Gene cloning MsrA Bioinformatics analysis

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Molecular Cloning and Bioinformatics Analysis of sucC Gene of Vibrio alginolyticus Strain HY9901

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Asian Agricultural Research 2024年第8期16卷 32-37页

作者： Yingzhu WEI Zhiqing WEI Xuelian LIN huanying pang Na WANG Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing 100176China

[Objectives]To clone the sucC gene of Vibrio alginolyticus strain HY9901 and conduct the bioinformatics analysis.[Methods]Based on the sucC gene of *** strain HY9901,specific primers were designed to amplify the full length sequence by PCR and make further analysis.[Results]The theoretical molecular weight of SucC protein was about 41528.45 Da,and the full length was 1167 bp,encoding 388 amino *** has no signal peptide and transmembrane region,and has a variety of functional *** is predicted that it is mainly located in the cytoplasm,and the ubiquitin and lactate modification sites overlap,and it has high gene homology with Vibrio ***α-helix,random coil and extended strand are the main secondary *** similarity between the constructed three-level structure model and the template is high.[Conclusions]This study reveals the structural characteristics and functional potential of SucC protein,and provides a theoretical basis for the study of drug resistance mechanism and prevention strategies.

关键词： Vibrio alginolyticus Gene amplification sucC gene Succinyl-Coa synthetase Protein post-translational modification Bioinformatics analysis

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Construction of Molecular Biology and Experiment Case Library for Graduate Students

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Asian Agricultural Research 2024年第8期16卷 47-49页

作者： huanying pang Miao XIE Shuanghu CAI Yu HUANG Yucong HUANG Jichang JIAN Fisheries College Guangdong Ocean UniversityZhanjiang 524088China National Fisheries Science and Technology Experimental Teaching Demonstration Center Zhanjiang 524088China

Molecular Biology and Experiment is considered fundamental for graduate students specializing in aquaculture at Guangdong Ocean *** discipline focuses on the examination of the structure and function of macromolecules,including proteins and nucleic ***,it elucidates biological phenomena and principles at the molecular level,making it an essential foundational course for students pursuing various biology *** a foundational course for the basic application of aquaculture,Molecular Biology and Experiment requires guidance through numerous examples and ***,there are several challenges to address in developing the case ***,a case library has been established to meet the course requirements of Molecular Biology and Experiment for modern graduate students,with the central goal of reforming the educational model of higher education institutions and enhancing the effectiveness and quality of talent *** strategy is designed to nurture highly skilled professionals who can address the current needs of the industry.

关键词： Case library Molecular biology and experiment Aquaculture major

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Molecular Cloning of clpX Gene from Vibrio alginolyticus HY9901 and Its Bioinformatics Analysis

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Asian Agricultural Research 2024年第8期16卷 17-22页

作者： Xiaoxin WEN Yuyan HE Jiajie MA Weijie ZHANG huanying pang Na WANG Fisheries College Guangdong Ocean UniversityZhanjiang 524088China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524088China Chinese Academy of Inspection and Quarantine Beijing 100176China

According to the clpX gene sequence of Vibrio alginolyticus HY9901,a pair of specific primers were designed,and the full length was cloned by PCR and subjected to bioinformatics *** results showed that the clpX gene was 1281 bp in length and encoded 426 amino *** molecular structure formula was C 3842 H 6405 N 1281 O 1598 S 260,with a theoretical protein molecular weight of approximately 1044473.4 kDa and a theoretical pI value of *** clpX gene was predominantly situated within the cytoplasm,exhibiting unstable and hydrophilic protein *** possessed a signal peptide cleavage site,lacked a transmembrane region,and was not associated with any KEGG metabolic ***,it possessed 2 glycine phosphorylation sites,a CAMP-dependent protein kinase phosphorylation site,a C-terminal amidation modification site,6 protein kinase C phosphorylation sites,7 microbody C-terminal target signal sites,and an ATP/GTP *** clpX phylogenetic tree was constructed using the MEGA 5.0 software via the neighbor-joining *** results demonstrated that the clpX of *** exhibited up to 100%affinity with the clpX of Vibrio *** single subunit 3D structure model of the ClpX protein was obtained using the SWISS-MODEL program.A structural and functional analysis of the protein revealed the presence of three distinct ClpX structural and functional *** the prediction of secondary structure,the proportions ofα-helix,random coil,β-sheet and extended strand were 40.38%,37.09%,5.40%and 17.14%,*** analysis of the ClpX protein through the STRING database revealed that the proteins interacting with the ClpX protein were Tig,Atpd,Hflb,Msrb-2,Rpod,Clpp,Clpa,Lon-1,Hfq,and ANP63951.1.A computational analysis of the ClpX protein identified a number of post-translational modification sites,including phosphorylation,acetylation,ubiquitination,glycosylation,methylation,S-palmitoylation,and *** significance of this st

关键词： Vibrio alginolyticus clpX gene Bioinformatics analysis

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Molecular Cloning and Bioinformatics Analysis of cyaA Gene of Vibrio alginolyticus Strain HY9901

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Agricultural Biotechnology 2024年第4期13卷 6-10页

作者： Shi WANG Peng ZHOU Yujia ZHANG Weijie ZHANG Na WANG huanying pang Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing 100176China

[Objectives]This study was conducted to explore the biological functions of cyaA gene of Vibrio alginolyticus.[Methods]With DNA of *** HY 9901 as a template,primers were designed according to the sequence of cyaA gene,and the cyaA gene was amplified by *** analysis was performed.[Results]The cyaA gene of *** HY9901 was 2529 bp in size,and encoded 842 amino *** molecular structure of CyaA protein was C_(4358)H_(6745)N_(1171)O_(1286)S_(35).Its theoretical molecular weight was 97.24167 kDa and the theoretical pI value was *** had no signal peptide and transmembrane *** protein had three N-terminal glycosylation sites,one cAMP and cGMP-dependent protein kinase phosphorylation site,nine protein kinase C phosphorylation sites,nine casein kinase II phosphorylation sites,one tyrosine kinase phosphorylation site,seven N-terminal myristoylation sites,one pentenyl binding site and ten microbody C-terminal localization signal *** localization prediction showed that CyaA protein was mainly located in the nucleus and *** multi-sequence alignment and phylogenetic tree construction,it was concluded that *** had high CyaA homology with other Vibrio *** of *** was clustered with Vibrio fluminensis and Vibrio marinisedimini,and they were closely *** secondary structure of CyaA protein consisted ofα-helixes(43.11%),random coils(38.00%)and extended strands(14.49%).In protein network interaction,it was found that the proteins adjacent to CyaA protein were Crp-2,CpdA,Crr,PtsG-2,ANP67209.1,Crp-1,PykF,Pyk,RelA and Ndk.[Conclusions]This study provides a new idea for formulating strategies for the prevention and control of vibriosis.

关键词： Vibrio alginolyticus cyaA gene Bioinformatics analysis

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Molecular Cloning of sodB Gene from Vibrio alginolyticus HY9901 and Its Bioinformatics Analysis

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Asian Agricultural Research 2024年第7期16卷 42-47页

作者： Shuai YANG Yingying JIANG Haiyun FENG Weijie ZHANG Na WANG Xiaonan LU huanying pang Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing100176China Department of Food Science and Agricultural Chemistry Faculty of Agricultural and Environmental SciencesMcGill UniversitySainte-Anne-de-Bellevue H9X 3V9Canada

Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by *** results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino *** predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of *** prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane *** amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal *** probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the *** amino acid sequence of the sodB gene of *** exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with ***,indicating a relatively close relationship between *** the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,*** similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.

关键词： Vibrio alginolyticus Gene cloning sodB gene Bioinformatics analysis

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Cloning and Bioinformatics Analysis of hcp Gene in Aeromonas hydrophila

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Asian Agricultural Research 2024年第3期16卷 36-40页

作者： Fan LI Xingjun FU Haiyun FENG Shi WANG Weijie ZHANG huanying pang Na WANG Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing 100176China

[Objectives]To explore the function of hcp gene in Aeromonas hydrophila.[Methods]A pair of specific primers was designed referring to the hcp gene sequence of *** hcp gene was amplified by PCR,and performed bioinformatics analysis.[Results]The hcp gene had a total length of 1650 bp and encoded 549 amino *** theoretical molecular weight of the protein predicted was about 59476.44 *** predicting the N-terminal signal peptide structure of the amino acid sequence,neither obvious signal peptide cleavage site nor signal peptide was found,and the protein had no transmembrane *** amino acid sequence had a N-glycosylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,9 N-myristoylation sites,4 isoprene binding sites,10 microbody C-terminal target signal sites,and an ATP/GTP binding site motif A(P-ring).The amino acid sequence of hcp gene of *** was performed homology analysis with other Aeromonas strains,and it showed higher homology with *** the secondary structure,theα-helix,β-sheet,random coil and extended strand accounted for 45.36%,6.01%,37.52%and 11.11%,*** tertiary structure model consisted of 18α-helix and 22β-*** of protein-protein network interaction demonstrated that the proteins interacting with Hcp protein were AHA_3407,nrfA,nirB-1,nirB-2 and AHA_1112.[Conclusions]Through the bioinformatics prediction results,the basic information of hcp gene of *** is preliminarily understood,and the possible function of this protein is predicted,in order to provide guidance for subsequent vaccine research.

关键词： Aeromonas hydrophila Gene amplification hcp gene Bioinformatics analysis

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Gene Cloning and Bioinformatics Analysis of phoR Gene from Vibrio alginolyticus HY9901

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Asian Agricultural Research 2024年第6期16卷 36-40页

作者： Xiangyu LIU Peng ZHOU Haiyun FENG Weijie ZHANG huanying pang Na WANG Xiaonan LU Fisheries College Guangdong Ocean UniversityZhanjiang 524025China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture&Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524025China Chinese Academy of Inspection and Quarantine Beijing100176China Department of Food Science and Agricultural Chemistry Faculty of Agricultural and Environmental SciencesMcGill UniversitySainte-Anne-de-Bellevue H9X 3V9Canada

PhoR is a histidine kinase in a two-component regulatory system that regulates phosphorus metabolic pathways and undertakes the key mission of information transmission in pathogenic *** full-length phoR gene was successfully cloned from the Vibrio alginolyticus HY9901 strain.A comprehensive analysis of the cloned gene was conducted using *** analysis revealed that the total length of the phoR gene(GenBank accession No.:KJ958404.1)is 1299 bp,with the coding region containing a total of 432 amino acid *** phylogenetic tree of PhoR revealed that it belongs to the same subclade as *** SMART program was employed for the purpose of functional domain prediction,which revealed that PhoR possesses three major functional domains:PAS(amino acids 98-166),HisKA(amino acids 205-272),and HATPase_c(amino acids 317-429).

关键词： Vibrio alginolyticus phoR gene Gene cloning Bioinformatics analysis

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Bioinformatics Analysis of DNA-binding Response Regulator PhoP in Vibrio alginolyticus

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Asian Agricultural Research 2022年第3期14卷 42-46,61页

作者： Yifan WU Junlin WANG Fuyuan ZENG Weijie ZHANG Xing XIAO huanying pang College of Fisheries Guangdong Ocean University/Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals/Key Laboratory of Control for Diseases of Aquatic Economic Animals of Guangdong Higher Education Institutes Zhanjiang 524088 China

[Objectives]To amplify the DNA-binding response regulator PhoP in Vibrio alginolyticus and analyze its sequence characteristics and subunit structure.[Methods]According to the sequence of the DNA-binding response regulator PhoP in ***,a pair of specific primers was designed for PCR amplification,and the bioinformatics of the sequence amplified was *** MEGA 5.0 software,the phoP phylogenetic tree was constructed by the neighbor-joining *** SWISS-MODEL software,the three-dimensional structural model of the PhoP subunit was simulated.[Results]The full-length phoP gene was 732 bp,encoding a total of 243 amino *** predicted theoretical molecular weight of the protein is about 27.67 kD,and the isoelectric point is *** prediction results of protein subcellular localization,SignalP 4.0,TMHMM Server 2.0 and SoftBerry-Psite show that PhoP is located in the cytoplasm,and is stable and hydrophobic;there is a signal peptide cleavage site between amino acids 29 and 30,and there is no transmembrane *** amino acid sequence contains one Asn-glycosylation site,one protein kinase C phosphorylation site,seven casein kinase II phosphorylation sites,one tyrosine kinase phosphorylation site,three myristoylation sites,and seven C-terminal microbody targeting signal *** PhoP of *** has high homology with that of Vibrio *** PhoP subunit of *** has similar configuration to the single-subunit RegX3 protein of Mycobacterium tuberculosis.[Conclusions]This study has a positive effect on the prevention and control of vibriosis and the improvement of the current aquatic economic animal breeding environment.

关键词： Vibrio alginolyticus Gene cloning PhoP Bioinformatics analysis

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Cloning and Bioinformatics Analysis of TpiA Gene of Vibrio alginolyticus HY9901

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Asian Agricultural Research 2022年第5期14卷 22-26,44页

作者： Ling ZUO Liangchuan CHEN Shuai YANG Xing XIAO Fuyuan ZENG Junlin WANG Weijie ZHANG huanying pang Fisheries College of Guangdong Ocean University Zhanjiang 524088China Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals Key Laboratory of Diseases Controlling for Aquatic Economic Animals of Guangdong Higher Education InstitutionsZhanjiang 524088China

[Objectives]To clone and analyze the TpiA gene of Vibrio alginolyticus HY9901.[Methods]According to the TpiA gene sequence of ***,a pair of specific primers was designed,and its full length was amplified by PCR.[Results]The full length of TpiA gene is 771 bp,encoding 256 amino acid residues in total,and the NCBI accession number is *** to the deduced amino acid sequence,its molecular weight was predicted to be about 26.97548 kDa,and its isoelectric point was *** amino acid sequence of the N-terminal signal peptide structure was predicted,and it was found that there was no obvious signal peptide cleavage site,no signal peptide,and no transmembrane region;the amino acid sequence contained 3 N-glycosylation sites,4 protein kinase C phosphorylation sites,2 casein kinase II phosphorylation sites,6 N-myristoylation sites,7 microbody C-terminal target signal site,and 1 triose phosphate isomerase active *** prediction results of protein subcellular localization showed that TpiA may be located in mitochondria or cytoplasm,with probability of 39.1%and 34.8%,*** amino acid sequence of the TpiA gene of *** shared 98.83%-99.61%homology with other Vibrio species,and it was clustered into the same subfamily with Vibrio parahaemolyticus and had a close *** the secondary structure prediction,the proportions ofα-helix,random coil and extended chain were 44.53%,41.41%and 14.06%,respectively,and the similarity of its tertiary structure model to template 1aw1.1.A was 85.16%.[Conclusions]This study is intended to provide a basis for further research on the role of TpiA gene in the type III secretion system and related research on antibiotic resistance.

关键词： Vibrio alginolyticus Gene amplification TpiA Bioinformatics analysis

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