[1]吴岩,邱旭华,刘晓光.普城沙雷氏菌pigX基因的生物信息学分析[J].江苏农业学报,2017,(03):510-516.[doi:doi:10.3969/j.issn.1000-4440.2017.03.005]
 WU Yan,QIU Xu-hua,LIU Xiao-guang.Bioinformatics analysis of pigX gene in Serratia plymuthica[J].,2017,(03):510-516.[doi:doi:10.3969/j.issn.1000-4440.2017.03.005]
点击复制

普城沙雷氏菌pigX基因的生物信息学分析()
分享到:

江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2017年03期
页码:
510-516
栏目:
遗传育种·生理生化
出版日期:
2017-06-30

文章信息/Info

Title:
Bioinformatics analysis of pigX gene in Serratia plymuthica
作者:
吴岩1;2邱旭华2刘晓光1;2
(1.江苏大学食品与生物工程学院,江苏镇江212013;2. 江苏大学生命科学研究院,江苏镇江212013)
Author(s):
WU Yan1;2QIU Xu-hua2LIU Xiao-guang1;2
(1.School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;2.Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China)
关键词:
普城沙雷氏菌GGDEF/EAL结构域pigX基因生物信息学
Keywords:
Serratia plymuthicaGGDEF/EAL domainpigX genebioinformatics
分类号:
S182
DOI:
doi:10.3969/j.issn.1000-4440.2017.03.005
文献标志码:
A
摘要:
通过生物信息学方法对普城沙雷氏菌( Serratia plymuthica) G3菌株中GGDEF/EAL结构域蛋白编码基因pigX启动子区域的调控信息以及编码蛋白质的理化特性和结构特点进行了解析。利用启动子分析软件Softberry和Neural Network Promoter Prediction对pigX基因编码区上游序列进行启动子预测,利用生物信息学方法对PigX蛋白的氨基酸组成和理化特性、磷酸化和糖基化位点、跨膜结构、信号肽二级结构和保守结构域等进行预测分析。结果显示:pigX启动子区有Fur和SoxS结合位点;PigX是微亲水性的脂结合蛋白,具有信号肽和跨膜结构域、糖基化和高水平磷酸化位点,α-螺旋和无规则卷曲是其主要二级结构。生物信息学分析预测结果表明G3菌株PigX具有较高水平磷酸化位点及由α-螺旋和无规则卷曲组成的二级结构,这与预测的PigX 参与铁代谢和氧化应激反应及作为CsrD同源物与CSRB家族sRNAs分子结合的功能相吻合。
Abstract:
To analyze the pigX gene encoding a GGDEF/EAL domain protein in Serratia plymuthica G3 strain, bioinformatics approaches was employed to unravel regulatory information of its promoter region and its nucleotide and amino acid sequences, as well as physicochemical characteristics, phosphrylation and N-glycosylation of PigX in strain G3 and the structure features such as transmembrane domain, signal peptide, secondary structure and conserve domain. Bioinformatics predictions identified that the binding sites of transcriptional regulators Fur and SoxS were located on the promoter of pigX, and PigX is a lipid-binding protein with a N-terminal signal peptide, trans-membrane domain and weak hydrophilicity. Further analysis revealed that PigX contains one N-glycosylation site and 23 phosphrylation sites with α-helix and random coil as its primary secondary structure, which is consistent with the predicted functions of PigX such as modulating iron metabolism and oxidative stress reaction, and binding small non-coding RNAs (sRNAs) belonging to the CsrB family.

参考文献/References:

[1]ROMLING U, GOMELSKY M, GALPERIN M Y. C-di-GMP: the dawning of a novel bacterial signalling system [J]. Mol Microbiol, 2005, 57(3): 629-639.
[2]GALPERIN M Y. Bacterial signal transduction network in a genomic perspective [J]. Environmental Microbiology, 2004, 6(6): 552-567.
[3]PAUL R, ABEL S, WASSMANN P, et al. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization [J]. The Journal of Biological Chemistry, 2007, 282(40): 29170-29177.
[4]LI T N, CHIN K H, SHIH H L, et al. Crystallization and preliminary X-ray diffraction characterization of an essential protein from Xanthomonas campestris that contains a noncanonical PilZ signature motif yet is critical for pathogenicity [J]. Acta Crystallographica Section F, Structural Biology and Crystallization Communications, 2009, 65(10): 1056-1059.
[5]NEWELL P D, MONDS R D, O’TOOLE G A. LapD is a bis-(3′,5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0-1 [J]. Proc Natl Acad Sci USA, 2009, 106(9): 3461-3466.
[6]SUZUKI K, BABITZKE P, KUSHNER S R, et al. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E [J]. Genes Dev, 2006, 20(18): 2605-2617.
[7]ABEL S, CHIEN P, WASSMANN P, et al. Regulatory cohesion of cell cycle and cell differentiation through interlinked phosphorylation and second messenger networks [J]. Molecular Cell, 2011, 43(4): 550-560.
[8]LIU X, JIA J, ATKINSON S, et al. Biocontrol potential of an endophytic Serratia sp. G3 and its mode of action [J]. World Journal of Microbiology and Biotechnology, 2010, 26(8): 1465-1471.
[9]TROXELL B, HASSAN H M. Transcriptional regulation by ferric uptake regulator (Fur) in pathogenic bacteria [J]. Frontiers in Cellular and Infection Microbiology, 2013, 3(59): 1-13.
[10]PLETZER D, SCHWEIZER G, WEINGART H. AraC/XylS family stress response regulators Rob, SoxS, PliA, and OpiA in the fire blight pathogen Erwinia amylovora [J]. J Bacteriol, 2014, 196(17): 3098-3110.
[11]FINERAN P C, WILLIAMSON N R, LILLEY K S, et al. Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX [J]. J Bacteriol, 2007, 189(21): 7653-7662.
[12]WILLIAMSON N R, FINERAN P C, OGAWA W, et al. Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia [J]. Environmental Microbiology, 2008, 10(5): 1202-1217.
[13]黄光,周敏,于晓莉,等. 普城沙雷氏菌rsmB基因删除插入突变体的构建 [J]. 江苏农业学报, 2011, 27(5):969-973.
[14]曾俊,刘晓光,郭忠建,等. 普城沙雷氏菌RsmA蛋白过量表达菌株的构建 [J]. 江苏农业学报, 2010, 26(4): 888-890.
[15]ZHOU M, GAO K, ZENG J, et al. Role of the RNA-binding protein Hfq in Serratia plymuthica [J]. Front Biosci (Elite Ed), 2012, 4:1263-1275.
[16]LIU X, JIA J, POPAT R, et al. Characterisation of two quorum sensing systems in the endophytic Serratia plymuthica strain G3: differential control of motility and biofilm formation according to life-style [J]. BMC Microbiology, 2011, 11(1): 26.
[17]LIU X, WU Y, CHEN Y, et al. RpoS differentially affects the general stress response and biofilm formation in the endophytic Serratia plymuthica G3 [J]. Research in Microbiology, 2015, 167(3):168-177.
[18]WANG Y, XU J, CHEN A, et al. GGDEF and EAL proteins play different roles in the control of Sinorhizobium meliloti growth, motility, exopolysaccharide production, and competitive nodulation on host alfalfa [J]. Acta Biochimica et Biophysica Sinica, 2010, 42(6): 410-417.
[19]ITO M, NOMURA K, SUGIMOTO H, et al. Identification of a Csr system in Serratia marcescens 2170 [J]. The Journal of General and Applied Microbiology, 2014, 60(2): 79-88.

备注/Memo

备注/Memo:
收稿日期:2016-07-21 基金项目:国家自然科学基金项目(31240046);公益性行业(农业)科研专项(201503110-12) 作者简介:吴岩(1981-),女,山东菏泽人,博士研究生,从事植物生防细菌全局调控机制研究,(E-mail)wuyan@mail.ujs.edu.cn 通讯作者:刘晓光,(E-mail)xgliu66@yahoo.com
更新日期/Last Update: 2017-06-29