RNA-seq Analysis of Drug-resistant Genes Associated with baeSR and acrB Double Gene Deletion Strains of Salmonella typhimurium

doi:10.13560/j.cnki.biotech.bull.1985.2019-0464

Abstract

Abstract: The transcriptome sequencing technology（RNA-seq）was used to screen the target genes related to baeSR and acrB of Salmonella typhimurium,which laid a foundation for further study on the drug resistance mechanism of S. typhimurium. RNA-Seq was applied to screen the related drug-resistant genes with varied expressions after the deletion of baeSR and acrB genes,GO enrichment and KEGG pathways to explore their functions,and qRT-PCR to verify some differential genes. Under the condition of |log₂（Fold Change）| > 1 and q value < 0.005,a total 1 320 differentially expressed genes were screened by CR△acrB/CR as comparison group,of which 894 were down-regulated and 426 were up-regulated. A total 1 377 differentially expressed genes were screened by CR△baeSR△acrB/CR,of which 972 genes were down-regulated and 405 genes were up-regulated. GO enrichment classification results showed that the differential genes were mainly concentrated in transmembrane transport,cell adhesion,cilia or flagellum movement and other functions. KEGG database showed that the differential genes were mainly concentrated in metabolic pathways,ABC transport system,two-component signal transduction system,flagellum assembly,beta-lactam resistance and so on. Among them,ompR,csgD,fliA and fliG regulated their resistances to various antibiotics by regulating the ability of bacterial biofilm formation. emrA,mdtC and yejE belonged to efflux pump-related genes,which mediated the resistance of bacteria to colistin and neomycin. STM3031 endowed Salmonella with ceftriaxone resistance,and pmrF regulated bacterial resistance to polymyxins. In conclusion,the deletion of acrB and baeSR genes in S. typhimurium may affect the expressions of related resistance genes.

Key words: Salmonella typhimurium, baeSR, acrB, RNA-Seq, related drug-resistant genes

XU Jun, WANG Rui, LI Rui, GAO Hai-xia, ZHANG Rui-liang, WANG Wen-jing, ZHAO Xia, LI Lin. RNA-seq Analysis of Drug-resistant Genes Associated with baeSR and acrB Double Gene Deletion Strains of Salmonella typhimurium[J]. Biotechnology Bulletin, 2019, 35(12): 76-84.

References

[1] Cevallos-Almeida M, Martin L, Houdayer C, et al.Experimental infection of pigs by Salmonella Derby, S. Typhimurium and monophasic variant of S. Typhimurium:comparison of colonization and serology[J]. Veterinary Microbiology, 2019, 231:147-153.
[2] Sharma C, Rokana N, Chandra M, et al.Antimicrobial resistance:its surveillance, impact, and alternative management strategies in dairy animals[J]. Frontiers in Veterinary Science, 2018, 4:237.
[3] Neuberger A, Du D, Luisi BF.Structure and mechanism of bacterial tripartite efflux pumps[J]. Research in Microbiology, 2018, 169(7-8):401-413.
[4] Zwama M, Yamaguchi A.Molecular mechanisms of AcrB-mediated multidrug export[J]. Research in Microbiology, 2018, 169(7-8):372-383.
[5] Sandeep T, et al.Two-component signal transduction systems of pathogenic bacteria as targets for antimicrobial therapy:an overview[J]. Frontiers in Microbiology, 2017, 8:1878.
[6] Baranova N, Nikaido H.The baeSR two-component regulatory system activates transcription of the yegMNOB(mdtABCD)transporter gene cluster in Escherichia coli and increases its resistance to novobiocin and deoxycholate[J]. Journal of Bacteriology, 2002, 184(15):4168-4176.
[7] Guerrero P, Collao B, Morales EH, et al.Characterization of the BaeSR two-component system from Salmonella Typhimurium and its role in ciprofloxacin-induced mdtA expression[J]. Archives of Microbiology, 2012, 194(6):453-460.
[8] Lin MF, Lin YY, Yeh HW, et al.Role of the BaeSR two-component system in the regulation of Acinetobacter baumannii adeAB genes and its correlation with tigecycline susceptibility[J]. BMC Microbiology, 2014, 14(1):119.
[9] Lin YH, Yang TC, Hu WS.Characterization of stm3030 and stm3031 genes of Salmonella enterica serovar Typhimurium in relation to cephalosporin resistance[J]. Journal of Microbiology, Immunology and Infection, 2019, 52(2):282-288.
[10] Rosner JL, Martin RG .Reduction of cellular stress by TolC-Dependent efflux pumps in Escherichia coli indicated by BaeSR and CpxARP activation of spy in efflux mutants[J]. Journal of Bacteriology, 2013, 195(5):1042-1050.
[11] 王文静, 徐军, 高海侠, 等. 鼠伤寒沙门菌baeSR基因缺失株的构建及其对抗生素敏感性分析[J]. 微生物学通报, 2019, doi:10. 13344/j. microbiol. china. 181072.
[12] 裘鹏, 郭玉茹, 张泽辉, 等. 基于转录组学技术分析细菌耐药机制的研究进展[J]. 中国家禽, 2019, 41(4):45-49.
[13] Correia S, Michel Hébraud, Patrícia Poeta, et al.How combined multicomparative proteomic approaches can improve the understanding of quinolone resistance in Salmonella Typhimurium[J]. Future Microbiology, 2018, 13(4):403.
[14] Reygaert WC.An overview of the antimicrobial resistance mechanisms of bacteria[J]. AIMS Microbiology, 2018, 4(3):482-501.
[15] Buckner MMC, Blair JMA, et al.Beyond antimicrobial resistance:evidence for a distinct role of the AcrD efflux pump in Salmonella biology[J]. MBio, 2016, 7(6):e01916.
[16] Wood CR, Mack LE, Actis L A.An update on the acinetobacter baumannii regulatory circuitry[J]. Trends in Microbiology, 2018, 26(7):560-562.
[17] Nishino K, Nikaido E, Yamaguchi A .Regulation of multidrug efflux systems involved in multidrug and metal resistance of Salmonella enterica serovar typhimurium[J]. Journal of Bacteriology, 2007, 189(24):9066-9075.
[18] Steinbuch KB, Fridman M.Mechanisms of resistance to membrane-disrupting antibiotics in Gram-positive and Gram-negative bacteria[J]. Med ChemComm, 2016, 7(1):86-102.
[19] Wolska KI, Grudniak AM, Rudnicka Z, et al.Genetic control of bacterial biofilms[J]. J Appl Genet, 2015, 21:1-14.
[20] Seo SW, Gao Y, Kim D, et al.Revealing genome-scale transcrip-tional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655[J]. Scientific Reports, 2017, 7(1):2181.
[21] Newman SL, Will WR, et al.The curli regulator CsgD mediates stationary phase counter-silencing of csgBA in Salmonella Typhim-urium[J]. Molecular Microbiology, 2018, 108(1):101-114.
[22] 朱春红, 董立伟, 张江英, 等. 鞭毛素fliC基因的缺失对肠炎沙门氏菌生物膜形成的影响[J]. 中国预防兽医学报, 2016, 38(4):303-306.
[23] Wang Z, Bie P, Cheng J, et al.The ABC transporter YejABEF is required for resistance to antimicrobial peptides and the virulence of Brucella melitensis[J]. Scientific Reports, 2016, 6:31876.