Strategy for pathogen novel gene function research
DU Xue-qing, HUANG Jin-lin
Jiangsu Key Laboratory of Zoonosis / Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
Abstract：With the development of high-throughput sequencing technology and proteomics technology, more and more pathogen novel genes were discovered. To explore novel genes of pathogen is helpful to prevent and control the diseases caused by these pathogen better. In the perspective of bioinformatics, acquisition and deletion of novel gene, analysing novel gene encoding product, this article reviews strategies that are suitable for the research of pathogenic bacteria novel gene, which provides a reference for genetic and molecular biology. Combined with conventional methods, this article penetrates chip technology, 2D-DIGE technology into the pathogen novel gene research strategy. It enables researchers to find a new breakthrough of gene function research and further formulate feasible research plan of novel gene function.
杜雪晴, 黄金林. 病原菌新基因功能的研究策略[J]. 中国人兽共患病学报, 2016, 32(7): 665-669.
DU Xue-qing, HUANG Jin-lin. Strategy for pathogen novel gene function research. Chinese Journal of Zoonoses, 2016, 32(7): 665-669.
[1] Bu YQ, Yang ZM, Song FZ. Strategies and methods in functional analysis of novel genes[J]. Life Sci Res, 2006, 10(2): 95-98. (in Chinese) 卜友泉, 杨正梅, 宋方洲. 新基因功能研究的策略与方法[J]. 生命科学研究, 2006, 10(2): 95-98. [2] Zhang L, Li QZ. Overall strategy for the study of new gene function[J]. China Anim Husb Vet Med, 2011, 38(5): 109-113. (in Chinese) 张岚, 李庆章. 新基因功能研究的整体策略[J]. 中国畜牧兽医, 2011, 38(5): 109-113. [3] Mount DW. Bioinformatics: Sequence and genome analysis[M]. 2nd ed. New York: Gold Spring Harbor Laboratory Press, 2004. [4] Gao B, Lara-Tejero M, Lefebre M, et al. Novel components of the flagellar system in epsilonproteobacteria [J]. mBio, 2014, 5(3): e01349. doi:10.1128/mBio.01349-14 [5] Marchant J, Wren B, Ketley J. Exploiting genome sequence: predictions for mechanisms of Campylobacter chemotaxis[J]. Trends Microbiol, 2002, 10(4): 155-159. doi:10. 1016/S0966-842X(02)02323-5 [6] Brummelkamp TR, Bernards R. New tools for functional mammalian cancer genetics[J]. Nat Rev Cancer, 2003, 3(10): 781-789. doi:10. 1038/nrc1191 [7] Keestra AM, Winter MG, Klein-Douwel D, et al. A Salmonella virulence factor activates the NOD1/NOD2 signaling pathway[J]. MBio, 2011, 2(6): e00266-11. doi:10.1128/mBio.00266-11 [8] Bu L, Gao X, Jiang X, et al. Targeted conditional gene knockout in human embryonic stem cells[J]. Cell Res, 2010, 20(3): 379-382. doi:10.1038/cr.2010.23 [9] Vonder leyen HE, Dzau VJ. Therapeutic potential of nitric oxide synthase gene manipulation[J]. Cireulation, 2001, 103(22): 12761-12765. doi:10.1161/01.CIR.103.22.2760 [10] Watson RO, Novik V, Hofreuter D, et al. A MyD88-deficient mouse model reveals a role for Nramp1 in Campylobacter jejuni infection[J]. Infect Immun, 2007, 75(4): 1994-2003.doi:10.1128/IAI.01216-06 [11] Han C, Zhang WC, You S. Advances in the red-mediated recombination[J]. China Biotechnol, 2003, 23(12): 17-21. (in Chinese) 韩聪, 张惟材, 游松. Red 同源重组技术研究进展[J]. 中国生物工程杂志, 2003, 23(12): 17-21. [12] Zhu CH, Sun XQ, He SF, et al. Comparison of two methods for constructing Salmonella enteritidis mutants: Red recombination system and suicide vector system[J]. Chin J Pre Vet Med, 2009, 31(2): 81-84. (in Chinese) 朱春红, 孙晓庆, 何素芬, 等. 基于 Red 同源重组和高效自杀性载体系统构建肠炎沙门氏菌突变株方法的比较[J]. 中国预防兽医学报, 2009, 31(2): 81-84. [13] Kao CY, Sheu BS, Wu JJ. CsrA regulates Helicobacter pylori J99 motility and adhesion by controlling flagella formation[J]. Helicobacter, 2014, 19(6): 443-454. doi:10.1111/hel.12148 [14] Tareen AM, Luder CGK, Zautner AE, et al. The Campylobacter jejuni Cj0268c protein is required for adhesion and invasion in vitro [J]. PLoS One, 2013, 8(11): e81069. doi:10.1371/journal.pone.0107076 [15] Hammond SM. An overview of microRNAs[J]. Adv Drug Delivery Rev, 2015, 29(87): 3-14. doi:10.1016/j.addr.2015.05.001 [16] Huntzinger E, Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay[J]. Nat Rev Genet, 2011, 12(2): 99-110. doi:10.1038/nrg2936 [17] Dorsett Y, Tuschi T. siRNAs: application in functional genomics and potential as therapeutics[J]. Nat Rev Drug Discov, 2004, 3(4): 318-329. doi:10.1038/nrd1345 [18] Ozcan G, Ozpolat B, Coleman RL, et al. Preclinical and clinical development of siRNA-based therapeutics[J]. Adv Drug Delivery Rev, 2015, 87(29): 108-119. doi:10.1016/j.addr.2015.01.007 [19] Peer D, Park EJ, Morishita Y, et al. Systemic leukocyte-directed siRNA delivery revealing cyclin D1 as an anti-inflammatory target[J]. Science, 2008, 319(5863): 627-630. doi:10.1126/science.1149859 [20] Ramsay G. DNA chips: state-of-the art[J]. Nat Biotechnol, 1998, 16(1): 40-44. doi:10.1038/nbt0198-40 [21] Marshall A, Hodgson J. DNA chips: an array of possibilities[J]. Nat Biotechnol, 1998, 16(1): 27-32. doi:10.1038/nbt0198-27 [22] Fang AH, Yin YT. Present application situation and prospect of gene chip technology[J]. China Anim Husb Vet Med, 2009, 5: 75-78. (in Chinese) 房爱华, 尹彦涛. 基因芯片技术的应用现状及展望[J]. 中国畜牧兽医, 2009, 5: 75-78. [23] Gong M, Xu S, Jin Y, et al. 5'-UTR of malS increases the invasive capacity of Salmonella enterica serovar Typhi by influencing the expression of bax[J]. Future Microbiol, 2015, 10(6): 941-954. doi:10.2217/fmb.15.12 [24] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genetics, 2009, 10(1): 57-63. doi:10.1038/nrg2484 [25] Butcher J, Handley RA, van Vliet AHM, et al. Refined analysis of the Campylobacter jejuni iron-dependent/independent Fur-and PerR-transcriptomes[J]. BMC genomics, 2015, 16: 498. doi:10.1186/s12864-015-1661-7 [26] Templin MF, Stoll D, Schrenk M, et al. Protein microarray technology[J]. Drug Discov Today, 2002, 7(15): 815-822. doi:10.1016/S1359-6446(00)01910-2 [27] Marouga R, David S, Hawkins E. The development of the DIGE system: 2D fluorescence difference gel analysis technology[J]. Analytical Bioanalytical Chem, 2005, 382(3): 669-678. doi:10.1007/s00216-005-3126-3 [28] Du JB, Wang LH, Duan JY. 2D-DIGE in proteomics applications[J]. J Biol, 2011, 28(3): 84-87. doi:10.3969/j.issn.2095-1736.2011.03.084 (in Chinese) 杜俊变, 王丽惠, 段江燕. 2D-DIGE 技术在蛋白质组学中的应用[J]. 生物学杂志, 2011, 28(3): 84-87. [29] Condell O, Sheridan A, Power KA, et al. Comparative proteomic analysis of Salmonella tolerance to the biocide active agent triclosan[J]. J Proteomics, 2012, 75(14): 4505-4519. doi:10.1016/j. jprot.2012.04.044 [30] Vikis HG, Guan KL. Glutathione-S-transferase-fusion based assays for studying protein-protein interactions[M]. Humana Press: Protein-protein interactions. 2004: 175-186. doi:10.1385/1-59259-762-9:175 [31] Huang Y, Chen SM, Huang QS, et al. Interaction between YggG and Era in Escherichia coli [J]. China Biotechnol, 2009, 29(11): 36-40. doi:10.13523/j.cb.20091107 (in Chinese) 黄勇, 陈苏民, 黄庆生, 等. 大肠杆菌 YggG 与结合蛋白 Era 的相互作用研究[J]. 中国生物工程杂志, 2009, 29(11): 36-40. [32] Kanno E, Ishibashi K, Kobayashi H, et al. Comprehensive screening for novel rab-binding proteins by GST pull-down assay using 60 different mammalian rab s + + [J]. Traffic, 2010, 11(4): 491-507. DOI:10.1111/j.1600-0854.2010.01038.x [33] Minamino T, Kinoshita M, Imada K, et al. Interaction between FliI ATPase and a flagellar chaperone FliT during bacterial flagellar protein export[J]. Mol Microbiol, 2012, 83(1): 168-178. doi:10.1111/j.1365-2958.2011.07924.x [34] Minamino T, Kinoshita M, Hara N, et al. Interaction of a bacterial flagellar chaperone FlgN with FlhA is required for efficient export of its cognate substrates[J]. Mol Microbiol, 2012, 83(4): 775-788. doi:10.1111/j.1365-2958.2011.07964.x [35] Kinoshita M, Hara N, Imada K, et al. Interactions of bacterial flagellar chaperone-substrate complexes with FlhA contribute to co-ordinating assembly of the flagellar filament[J]. Mol Microbiol, 2013, 90(6): 1249-1261. doi:10.1111/mmi.12430 [36] Guo C. Study progress of co-immunoprecipitation technology[J]. Guiding J TCM, 2007, 13(12): 86-88. (in Chinese) 郭纯. 免疫共沉淀技术的研究进展[J]. 中医药导报, 2007, 13(12): 86-88. [37] Lung TWF, Giogha C, Creuzburg K, et al. Mutagenesis and functional analysis of the bacterial arginine glycosyltransferase effector NleB1 from enteropathogenic Escherichia coli [J]. Infect Immun, 2016: IAI. 01523-15. doi:10.1128/IAI.01523-15 [38] Huang Q, Xu WX, Li HB, et al. Protein-protein interaction between Rv3425 and Rv3614c in Mycobacterium tuberculosis [J]. J Microbes Infect, 2015, 10(4): 235-240. (in Chinese) 黄琪, 徐文玺, 粟海波, 等. 结核分枝杆菌 Rv3425 与 Rv3614c 的相互作用[J]. 微生物与感染, 2015, 10(4): 235-240. [39] Monti M, Orru S, Pagnozzi D, et al. Interaction proteomics[J]. Biosci Reports, 2005, 25(1/2): 45-56. doi:10.1007/s10540-005-2847-z [40] Masters SC, Yang H, Datta SR, et al. 14-3-3 inhibits Bad-induced cell death through interaction with serine-136[J]. Mol Pharmacol, 2001, 60(6): 1325-1331. doi:10.1124/mol.60.6.1325
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