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:: Volume 11, Number 4 (September - October 2017) ::
Iran J Med Microbiol 2017, 11(4): 21-34 Back to browse issues page
Identification of Genetic and Protein Markers in Salmonella enterica serovar Typhimurium by Bioinformatic Analyses for the Purpose of Diagnosis and Treatment
Mojdeh Amandadi1, Hadi Ravan 2, Mehdi Hassanshahian1
1- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
2- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran , ravan@uk.ac.ir
Abstract:   (89 Views)

Background and Aims: Salmonella enterica serovar Typhimurium is one of the common causes of food poisoning in human. Since the selection of appropriate markers is one of the main challenges for the detection of this pathogen, in the current study, genetic markers of this serovar were screened using bioinformatical tools. In the second phase, structure and function of proteins encoded by these markers, were determined.
Materials and Methods: This study was conducted between 2016 and 2017.  In order to find the genetic markers of Salmonella enterica serovar Typhimurium, 45 complete genomes belonging to Salmonella enterica serovar Typhimurium and the other genera of Enterobacteriacea family were compared using Mauve software. To determine the structure and function of proteins encoded by these sequences, I-TASSER and Phyre2 software beside CDD, Inter Pro Scan, DALI, and Pro Func databases were used for structural and functional modeling, respectively.
Results: Special regions of STM4491-STM4496 genes were determined as specific markers for Salmonella enterica serovar Typhimurium. The function of proteins encoded by these markers  were proposed to be classified in five groups, including Lon protease, nucleotide binding proteins, nucleotide three phosphatases (NTP), proteins involved in the DNA repair , and DNA methylase.
Conclusions: Specific regions of STM4491-STM4496 genes can be used as effective diagnostic targets for the detection of pathogenic Salmonella enterica serovar Typhimurium. Moreover, proteins encoded by these genes can be suggested as suitable targets for the design of new therapeutic agents to prevent  and treat  the infections caused by this pathogen.

Keywords: Salmonella typhimurium, Specific markers, Protein structure modeling
Type of Study: Original | Subject: Molecular Microbiology
1. Fournier P-E, Raoult D. Prospects for the future using genomics and proteomics in clinical microbiology. Annu Rev Microbiol 2011; 65(1):169-188.
2. Xia S, Hendriksen RS, Xie Z, Huang L, Zhang J, Guo W, et al. Molecular characterization and antimicrobial susceptibility of Salmonella isolates from infections in humans in Henan Province, China. J Clin Microbiol 2009; 47(2):401-409.
3. Mousavi SL, Rasooli I, Nazarian S, Amani J. Simultaneous detection of Escherichia coli O157: H7, toxigenic Vibrio cholerae, and Salmonella typhimurium by multiplex PCR. Arch Clin Infect Dis 2009; 4(2):97-103.
4. Soumet C, Ermel G, Rose N, Rose V, Drouin P, Salvat G, et al. Evaluation of a multiplex PCR assay for simultaneous identification of Salmonella sp., Salmonella Enteritidis and Salmonella Typhimurium from environmental swabs of poultry houses. Lett Appl Microbiol 1999; 28(2):113-117.
5. Dilmaghani M, Ahmadi M, Zahraei-Salehi T, Talebi A. Detection of Salmonella enterica serovar Typhimurium from avians using multiplex-PCR. Vet Res Forum 2011; 2(3):157-165.
6. Shanmugasundaram M, Radhika M, Murali H, Batra H. Detection of Salmonella enterica serovar Typhimurium by selective amplification of fliC, fljB, iroB, invA, rfbJ, STM2755, STM4497 genes by polymerase chain reaction in a monoplex and multiplex format. World J Microbiol Biotechnol 2009; 25(8):1385-1394.
7. Lim Y-H, Hirose K, Izumiya H, Arakawa E, Takahashi H, Terajima J, et al. Multiplex polymerase chain reaction assay for selective detection of Salmonella enterica serovar Typhimurium. Jpn J Infect Dis 2003; 56(4):151-155.
8. Zahraei Salehi T, Tadjbakhsh H, Atashparvar N, Nadalian M, Mahzounieh M. Detection and identification of Salmonella Typhimurium in bovine diarrhoeic fecal samples by immunomagnetic separation and multiplex PCR assay. Zoonoses Public Health. 2007; 54(6):231-236.
9. Kim H, Park S, Lee T, Nahm B, Chung Y, Seo K, et al. Identification of Salmonella enterica serovar Typhimurium using specific PCR primers obtained by comparative genomics in Salmonella serovars. J Food Prot 2006; 69(7):1653-1661
10. Akiba M, Kusumoto M, Iwata T. Rapid identification of Salmonella enterica serovars, typhimurium, choleraesuis, infantis, hadar, enteritidis, dublin and gallinarum, by multiplex PCR. J Microbiol Methods 2011; 85(1):9-15.
11. Ravan H, Amandadi M. Analysis of yeh Fimbrial Gene Cluster in Escherichia coli O157: H7 in Order to Find a Genetic Marker for this Serotype. Curr Microbiol 2015; 71(2):274-282.
12. Ravan H, Amandadi M. Molecular detection of pathogenic serovar Salmonella enteritidis by LAMP method using a specific marker screened by comparative genomic methods. Iran J Med Microbiol. 2017; 11(1):18-29. [In Persian]
13. Cash P. Proteomics in medical microbiology. Electrophoresis. 2000; 21(6):1187-1201.
14. Parkhill J, Dougan G, James K, Thomson N, Pickard D, Wain J, et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001; 413(6858):848-852.
15. Liu X, Lu R, Xia Y, Sun J. Global analysis of the eukaryotic pathways and networks regulated by Salmonella typhimurium in mouse intestinal infection in vivo. BMC genomics 2010; 11(1):722.
16. Liu B, Zhou X, Zhang L, Liu W, Dan X, Shi C, et al. Development of a novel multiplex PCR assay for the identification of Salmonella enterica Typhimurium and Enteritidis. Food Control 2012; 27(1):87-93.
17. Wang Y, Huang K-Y, Huo Y. Proteomic comparison between Salmonella Typhimurium and Salmonella Typhi. J Microbiol 2014; 52(1):71.
18. Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009; 19(2):145-155.
19. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 2015; 10(6):845-858.
20. Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010; 5(4):725-738.
21. Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005; 33(2):W89-W93.
22. Holm L, Rosenström P. Dali server: conservation mapping in 3D. Nucleic Acids Res 2010; 38(2):W545-W549.
23. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 2010; 5(6):e11147.
24. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, et al. InterProScan: protein domains identifier. Nucleic Acids Res 2005; 33(2):W116-W120.
25. Hirashima A, Huang H. Homology modeling, agonist binding site identification, and docking in octopamine receptor of Periplaneta americana. Comput Biol Chem 2008; 32(3):185-190.
26. Wallner B, Elofsson A. Can correct protein models be identified? Protein science 2003; 12(5):1073-86.
27. Wiederschain GY. The Proteomics Protocols Handbook. Biochemistry (Moscow) 2006; 71(6):696-700.
28. Rigden DJ. From protein structure to function with bioinformatics. Springer. 2017;91-99.
29. Wang L, Holmes RP, Peng J-B. Molecular modeling of the structural and dynamical changes in calcium channel TRPV5 induced by the African-specific A563T variation. Biochemistry 2016; 55(8):1254-1264.
30. Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 2005; 33(1): 266-8.
31. Lee I, Suzuki CK. Functional mechanics of the ATP-dependent Lon protease-lessons from endogenous protein and synthetic peptide substrates. Biochim Biophys Acta, Proteins Proteomics 2008; 1784(5):727-735.
32. Tamás L, Huttová J, Mistrk I, Kogan G. Effect of carboxymethyl chitin-glucan on the activity of some hydrolytic enzymes in maize plants. Chem Pap 2002; 56(5):326-329.
33. Veiga P, Erkelenz M, Bernard E, Courtin P, Kulakauskas S, Chapot-Chartier M-P. Identification of the asparagine synthase responsible for D-Asp amidation in the Lactococcus lactis peptidoglycan interpeptide crossbridge. J. Bacteriol 2009; 191(11):3752-7.
34. Dy RL, Przybilski R, Semeijn K, Salmond GP, Fineran PC. A widespread bacteriophage abortive infection system functions through a Type IV toxin–antitoxin mechanism. Nucleic Acids Res 2014; 42(7):4590-4605.
35. Williams GJ, Williams RS, Williams JS, Moncalian G, Arvai AS, Limbo O, et al. ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol 2012; 19(3):364.
36. Davidson AL, Dassa E, Orelle C, Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol Biol Rev 2008; 72(2):317-364.
37. Halbach F, Reichelt P, Rode M, Conti E. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell 2013; 154(4):814-826.
38. Haneda T, Ishii Y, Danbara H, Okada N. Genome-wide identification of novel genomic islands that contribute to Salmonella virulence in mouse systemic infection. FEMS Microbiol Lett 2009; 297(2):241-249.
39. Bishop AL, Baker S, Jenks S, Fookes M, Gaora PÓ, Pickard D, et al. Analysis of the hypervariable region of the Salmonella enterica genome associated with tRNAleuX. J Bacteriol 2005; 187(7):2469-2482.
40. Ravan H, Amandadi M, Sanadgol N. A highly specific and sensitive loop-mediated isothermal amplification method for the detection of Escherichia coli O157:H7. Microb Pathog 2016; 91:161-165.
41. Tsilibaris V, Maenhaut-Michel G, Van Melderen L. Biological roles of the Lon ATP-dependent protease. Res Microbiol 2006; 157(8):701-713.
42. Mehta N, Benoit S, Maier RJ. Roles of conserved nucleotide-binding domains in accessory proteins, HypB and UreG, in the maturation of nickel-enzymes required for efficient Helicobacter pylori colonization. Microb Pathog 2003; 35(5):229-234.
43. Garmory HS, Titball RW. ATP-binding cassette transporters are targets for the development of antibacterial vaccines and therapies. Infect Immun 2004; 72(12):6757-6763.
44. Wion D, Casadesús J. N6-methyl-adenine: an epigenetic signal for DNA–protein interactions. Nat Rev Microbiol 2006; 4(3):183-192.
45. Heusipp G, Fälker S, Schmidt MA. DNA adenine methylation and bacterial pathogenesis. Int J Med Microbiol 2007; 297(1):1-7.
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Amandadi M, Ravan H, Hassanshahian M. Identification of Genetic and Protein Markers in Salmonella enterica serovar Typhimurium by Bioinformatic Analyses for the Purpose of Diagnosis and Treatment. Iran J Med Microbiol. 2017; 11 (4) :21-34
URL: http://ijmm.ir/article-1-703-en.html
Volume 11, Number 4 (September - October 2017) Back to browse issues page
مجله میکروب شناسی پزشکی ایران Iranian Journal of Medical Microbiology
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