三种常见假单胞菌Pel胞外多糖转运系统相关蛋白PelA-G的生物信息学比较分析

吴倩; 张昭寰; 黄振华; 刘静; 潘迎捷; 赵勇

doi:10.13417/j.gab.040.003115

三种常见假单胞菌Pel胞外多糖转运系统相关蛋白PelA-G的生物信息学比较分析

吴倩¹,
张昭寰^1,2, ,,
黄振华¹,
刘静¹,
潘迎捷^1,3,4,
赵勇^1,3,4, ,

1. 上海海洋大学食品学院;
2. 上海海洋大学水产与生命学院;
3. 农业农村部水产品贮藏保鲜质量安全风险评估实验室(上海);
4. 上海水产品加工及贮藏工程技术研究中心

基金项目:

国家自然科学基金(32001800)

国家博士后创新人才支持计划(BX20190194)共同资助

详细信息

通讯作者:
张昭寰,zh-zhang@shou.edu.cn

赵勇,yzhao@shou.edu.cn

中图分类号: Q933
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出版历程
- 刊出日期: 2021-10-24

Bioinformatics Comparative Analysis of Proteins PelA-G Associated with Exopolysaccharide Transport System in Three Common Pseudomonas

1. College of Food Science and Technology, Shanghai Ocean University;
2. College of Fisheries and Life Sciences, Shanghai Ocean University;
3. Laboratory of Quality & Safety Risk Assessment for Aquatic Product on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs;
4. Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation

摘要

摘要: 铜绿假单胞菌(Pseudomonas aeruginosa)、荧光假单胞菌(Pseudomonas fluorescens)及恶臭假单胞菌(Pseudomonas putida)是重要的致病菌与腐败菌，极易形成生物被膜，对人类健康和食品质量安全造成了严重的危害。Pel胞外多糖是假单胞菌(Pseudomonas)生物被膜的重要组成部分，通过相应的Pel系统进行合成和转运。运用生物信息学分析技术对Pel系统相关蛋白进行分析，有助于更好地理解假单胞菌生物被膜的形成机制。本研究以3种常见假单胞菌为研究对象，通过生物信息学分析技术，结合ExPASy在线工具、SignalP 4.0 Server、TMHMM-2.0、Phyre2等软件，分析了3种假单胞菌Pel胞外多糖转运系统相关蛋白PelA-G的理化性质、信号肽、跨膜区域以及三级结构和功能。结果表明，除PelE和PelG蛋白的理论等电点存在差异外，3种假单胞菌Pel系统的理化性质基本相同。荧光假单胞菌PelA蛋白不含跨膜区，铜绿假单胞菌PelE蛋白比另外两种菌多1段跨膜区，其他蛋白的跨膜区不存在明显差异。同源建模结果表明，3种菌PelA-G蛋白的折叠方式相同，三维结构能够高度重合，推测它们在Pel胞外多糖转运过程中发挥着相同的功能。本研究从生物信息学的角度揭示了3种假单胞菌Pel系统结构和功能上的共性，为该系统转运机制的进一步研究提供重要的数据基础。
- 假单胞菌 /
- Pel胞外多糖转运系统 /
- 生物信息学分析 /
- 蛋白三级结构与功能
Abstract: Pseudomonas aeruginosa, Pseudomonas fluorescens, and Pseudomonas putida are important pathogenic and spoilage bacteria that can easily form biofilms causing serious harm to human health and food safety. Pel is an important component in the Pseudomonas biofilm and translocation of it is proposed to occur via Pel exopolysaccharide transport system. Analyzing proteins by bioinformatics in the Pel system contribute to understand the formation mechanism of Pseudomonas biofilm betterly. In the study, we analyzed the physicochemical properties, signal peptides, transmembrane region and tertiary structure of PelA-G proteins of the Pel exopolysaccharides transport system in three Pseudomonas species by ExPASy, SignalP 4.0 Server, TMHMM-2.0 and Phyre2. The results showed that the physicochemical properties of PelA-G proteins were almost the same in three Pseudomonas Pel systems, except the theoretical isoelectric points of PelE and PelG proteins. P. aeruginosa PelA protein does not contain a transmembrane region, and its PelE protein has one more transmembrane region compared to the other two strains. Three strains had the same folding pattern and the three-dimensional structure could be highly overlapping by homologous modeling, suggesting that they played the same function in the transport process of Pel exopolysaccharides. This study revealed the similarities in structure and function of three Pseudomonas Pel systems by bioinformatics and provided an important data basis for the further study on this transport system.
- Pseudomonas /
- Pel exopolysaccharide transport system /
- Bioinformatics analysis /
- Tertiary structure and protein function

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参考文献(33)

[1]	Acheson J.F.,Derewenda Z.S.,and Zimmer J.,2019,Architecture of the cellulose synthase outer membrane channel and its association with the periplasmic TPR domain,Structure,27(12):1855-1861.e3.
[2]	Artimo P.,Jonnalagedda M.,Arnold K.,Baratin D.,Csardi G.,de Castro E.,Duvaud S.,Flegel V.,Fortier A.,Gasteiger E.,Grosdidier A.,Hernandez C.,Ioannidis V.,Kuznetsov D.,Liechti R.,Moretti S.,Mostaguir K.,Redaschi N.,Rossier G.,Xenarios I.,and Stockinger H.,2012,ExPASy:SIBbioinformatics resource portal,Nucleic Acids Res.,40(W1):597-603.
[3]	Baker P.,Hill P.J.,Snarr B.D.,Alnabelseya N.,Pestrak M.J.,Lee M.J.,Jennings L.K.,Tam J.,Melnyk R.A.,Parsek M.R.,Sheppard D.C.,Wozniak D.J.,and Howell P.L.,2016,Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and prevent Pseudomonas aeruginosa biofilms,Sci.Adv.,2(5):e1501632.
[4]	Snarr B.D.,Baker P.,Bamford N.C.,Sato Y.,Liu H.,Lehoux M.,Gravelat F.N.,Ostapska H.,Baistrocchi S.R.,Cerone R.P.,Filler E.E.,Parsek M.R.,Filler S.G.,Howell P.L.,and Sheppard D.C.,2017,Microbial glycoside hydrolases as antibiofilm agents with cross-kingdom activity,Proc.Natl.Acad.Sci.USA,114(27):7124-7129.
[5]	Cao X.Y.,Bao M.L.,Yao Y.,Xie W.,Jia X.E.,Jiang S.Y.,Shao G.,and Bade R.G.,2020,Bioinformatics analysis of DNAmethylated binding protein MBD family,Jiyinzuxue yu Yingyong Shengwuxue (Genomics and Applied Biology),39(8):3710-3715.(曹晓宇,鲍牧兰,姚远,谢伟,贾小娥,姜树原,邵国,巴德仁贵,2020,DNA甲基化结合蛋白MBD家族的生物信息学分析,基因组学与应用生物学,39(08):3710-3715.)
[6]	Chen Q.M.,Cheng D.J.,Liu S.P.,Ma Z.G.,Tan X.,and Zhao P.,2014,Genome-wide identification and expression profiling of the fatty acid desaturase gene family in the silkworm,Bombyx mori,Genet.Mol.Res.,13(2):3747-3760.
[7]	Costerton J.W.,Stewart P.S.,and Greenberg E.P.,1999,Bacterial biofilms:a common cause of persistent infections,Science,284(5418):1318-1322.
[8]	Colvin K.M.,Irie Y.,Tart C.S.,Urbano R.,Whitney J.C.,Ryder C.,Howell P.L.,Wozniak D.J.,and Parsek M.R.,2012,The Pel and Psl polysaccharides provide Pseudomonas aeruginosa structural redundancy within the biofilm matrix,Environ.Microbiol.,14(8):1913-1928.
[9]	Colvin K.M.,Alnabelseya N.,Baker P.,Whitney J.C.,Howell P.L.,and Parsek M.R.,2013,PelA deacetylase activity is required for Pel polysaccharide synthesis in Pseudomonas aeruginosa,J.Bacteriol.,195(10):2329-2339.
[10]	Flemming H.C.,and Wing ender J.,2010,The biofilm matrix,Nat.Rev.Microbiol.,8(9):623-633.
[11]	Franklin M.J.,Nivens D.E.,Weadge J.T.,and Howell P.L.,2011,Biosynthesis of the Pseudomonas aeruginosa extracellular polysaccharides,alginate,pel,and psl,Front.Microbiol.,2:167.
[12]	Fux C.A.,Costerton J.W.,Stewart P.S.,and Stoodley P.,2005,Survival strategies of infectious biofilms,Trends Microbiol.,13(1):34-40.
[13]	He X.,Szewczyk P.,Karyakin A.,Evin M.,Hong W.X.,Zhang Q.H.,and Chang G.,2010,Structure of a cation-bound multidrug and toxic compound extrusion transporter,Nature,467(7318):991-994.
[14]	Kelley L.A.,Mezulis S.,Yates C.M.,Wass M.N.,and Sternberg M.J.E.,2015,The Phyre2 web portal for protein modeling,prediction and analysis,Nat.Protoc.,10(6):845-858.
[15]	Kubicek J.,Block H.,Maertens B.,Spriestersbach A.,and Labahn J.,2014,Expression and purification of membrane proteins,Methods Enzymol.,541:117-140.
[16]	Jennings L.K.,Storek K.M.,Ledvina H.E.,Coulon C.,Marmont L.S.,Sadovskaya I.,Secor P.R.,Tseng B.S.,Scian M.,Filloux A.,Wozniak D.J.,Howell P.L.,and Parsek M.R.,2015,Pel is a cationic exopolysaccharide that cross-links extracellular DNA in the Pseudomonas aeruginosa biofilm matrix,Proc.Natl.Acad.Sci.USA,112(36):11353-11358.
[17]	Liu H.Z.,Li S.J.,Xie X.B.,and Shi Q.S.,2021,Pseudomonas putida actively forms biofilms to protect the population under antibiotic stress,Environ.Pollut.,270:116261.
[18]	Marmont L.S.,Rich J.D.,Whitney J.C.,Whitfield G.B.,Almblad H.,Robinson H.,Parsek M.R.,Harrison J.J.,and Howell P.L.,2017a,Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa,Proc.Natl.Acad.Sci.USA,114(11):2892-2897.
[19]	Marmont L.S.,Whitfield G.B.,Rich J.D.,Yip P.,Giesbrecht L.B.,Stremick C.A.,Whitney J.C.,Parsek M.R.,Harrison J.J.,and Howell P.L.,2017b,PelA and PelB proteins form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation in Pseudomonas aeruginosa,J.Biol.Chem.,292(47):19411-19422.
[20]	Owji H.,Nezafat N.,Negahdaripour M.,Hajiebrahimi A.,and Ghasemi Y.,2018,A comprehensive review of signal peptides:Structure,roles,and applications,Eur.J.Cell Biol.,97(6):422-441.
[21]	Ryder C.,Byrd M.,and Wozniak D.J.,2007,Role of polysaccharides in Pseudomonas aeruginosa biofilm development,Curr.Opin.Microbiol.,10(6):644-648.
[22]	Sana T.G.,Lomas R.,Gimenez M.R.,Laubier A.,Soscia C.,Chauvet C.,Conesa A.,Voulhoux R.,Ize B.,and Bleves S.,2019,Differential modulation of quorum sensing signaling through QslA in Pseudomonas aeruginosa strains PAO1 and PA14,J.Bacteriol.,201(21):e00362-19.
[23]	Shahrizal M.,Daimon Y.,Tanaka Y.,Hayashi Y.,Nakayama S.,Iwaki S.,Narita S.I.,Kamikubo H.,Akiyama Y.,and Tsukazaki T.,2019,Structural basis for the function of theβ-barrel assembly-enhancing protease BepA,J.Mol.Biol.,431(3):625-635.
[24]	Siriken B.,Öz V.,and ErolĪ.,2021,Quorum sensing systems,related virulence factors,and biofilm formation in Pseudomonas aeruginosa isolated from fish,Arch.Microbiol.,203(4):1519-1528.
[25]	Tong J.R.,Zhang Z.H.,Huang Z.H.,Liu H.Q.,Pan Y.J.,and Zhao Y.,2020,Bioinformatics analysis for structure and function of localization of lipoprotein system transporters in Vibrio parahaemolyticus,Weishengwu Xuebao (Acta Microbiologica Sinica),60(10):2242-2252.(童金蓉,张昭寰,黄振华,刘海泉,潘迎捷,赵勇,2020,副溶血性弧菌脂蛋白定位系统转运蛋白结构与功能的生物信息学分析,微生物学报,60(10):2242-2252.)
[26]	Wang S.T.,Niu Y.T.,Zhang H.,Li P.X.,Zhang N.M.,Cheng J.L.,and Lin J.S.2021,An engineered bacterium for the targeted delivery of proteins to destroy Pseudomonas aeruginosa biofilms,Weishengwu Xuebao (Acta Microbilogica Sinica),61(09):2726-2748.(王帅涛,牛艳婷,张恒,李盼欣,张宁梅,成娟丽,林金水,2021,靶向破坏铜绿假单胞菌生物被膜的定向蛋白投放技术,微生物学报,61(09):2726-2748.)
[27]	Wang Y.G.,Yang G.R.,Leng F.F.,Yang M.J.,Wang M.G.,and Chen K.,2018,Bioinformatic analysis of three membrane proteins in Escherichia coli MG1655,Jiyinzuxue yu Yingyong Shengwuxue (Genomics and Applied Biology),37(11):4763-4768.(王永刚,杨光瑞,冷非凡,杨明俊,王鸣刚,陈凯,2018,大肠杆菌MG1655三个膜蛋白的生物信息学分析,基因组学与应用生物学,37(11):4763-4768.)
[28]	Whitfield G.B.,Marmont L.S.,Ostaszewski A.,Rich J.D.,Whitney J.C.,Parsek M.R.,Harrison J.J.,and Howell P.L.,2020,Pel polysaccharide biosynthesis requires an inner membrane complex comprised of PelD,PelE,PelF,and PelG,J.Bacteriol.,2202(8):e00684-19.
[29]	Whitney J.C.,Colvin K.M.,Marmont L.S.,Robinson H.,Parsek M.R.,and Howell P.L.,2012,Structure of the cytoplasmic region of PelD,a degenerate diguanylate cyclase receptor that regulates exopolysaccharide production in Pseudomonas aeruginosa,J.Biol.Chem.,287(28):23582-23593.
[30]	Wiens J.R.,Vasil A.I.,Schurr M.J.,and Vasil M.L.,2014,Iron-regulated expression of alginate production,mucoid phenotype,and biofilm formation by Pseudomonas aeruginosa,mBio,5(1):e01010-e01013.
[31]	Xu Y.,Chen W.Y.,You C.P.,and Liu Z.M.,2017,Development of a multiplex PCR assay for detection of Pseudomonas fluorescens with biofilm formation ability,J.Food Sci.,82(10):2337-2342.
[32]	Yu S.S.,Wei L.Y.,Xie H.A.,and Zhang J.F.,2014,Progress on MATE transporters of stress resistance in rice,Fujian Nongye Xuebao (Fujian Journal of Agricultural Sciences),29(4):398-405.(喻丝丝,魏林艳,谢华安,张建福,2014,MATE转运蛋白在水稻抗逆作用中的研究进展,福建农业学报,29(4):398-405.)
[33]	Zheng Y.,Anderson S.,Zhang Y.F.,and Garavito R.M.,2011,The structure of sucrose synthase-1 from Arabidopsis thaliana and its functional implications,J.Biol.Chem.,286(41):36108-36118.

施引文献(4)

期刊类型引用(2)

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