title: The Bioinformatics Report of Mutation Outcome on NADPH Flavin Oxidoreductase Protein Sequence in Clinical Isolates of H. pylori.
abstract: frxA gene has been implicated in the metronidazole nitro reduction by H. pylori. Alternatively, frxA is expected to contribute to the protection of urease and to the in vivo survival of H. pylori. The aim of present study is to report the mutation effects on the frxA protein sequence in clinical isolates of H. pylori in our community. Metronidazole resistance was proven in 27 of 48 isolates. glmM and frxA genes were used for molecular confirmation of H. pylori isolates. The primer set for detection of whole sequence of frxA gene for the effect of mutation on protein sequence was used. DNA and protein sequence evaluation and analysis were done by blast, Clustal Omega, and T COFFEE programs. Then, FrxA protein sequences from six metronidazole-resistant clinical isolates were analyzed by web-based bioinformatics tools. The result of six metronidazole-resistant clinical isolates in comparison with strain 26695 showed ten missense mutations. The result with the STRING program revealed that no change was seen after alterations in these sequences. According to consensus data involving four methods, residue substitutions at 40, 13, and 141 increase the stability of protein sequence after mutation, while other alterations decrease. Residue substitutions at 40, 43, 141, 138, 169, and 179 are deleterious, while, V7I, Q10R, V34I, and V96I alterations are neutral. As FrxA contribute to survival of bacterium and in regard to the effect of mutations on protein function, it might affect the survival and bacterium phenotype and it need to be studied more. Also, none of the stability prediction tool is perfect; iStable is the best predictor method among all methods.
authors.affiliation: Department of Microbiology, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran.
authors.forename: Nasrin
authors.initials: N
authors.lastname: Mirzaei
authors.affiliation: Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran.
authors.forename: Farkhondeh
authors.initials: F
authors.lastname: Poursina
authors.affiliation: Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran.
authors.forename: Sharareh
authors.initials: S
authors.lastname: Moghim
authors.affiliation: Department of Pathology, Zanjan University of Medical Sciences, Zanjan, Iran.
authors.forename: Abdol Majid
authors.initials: AM
authors.lastname: Ghaempanah
authors.affiliation: Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran. ghasemian@med.mui.ac.ir.
authors.forename: Hajieh Ghasemian
authors.initials: HG
authors.lastname: Safaei
mesh_terms: D020816:Amino Acid Motifs; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D024881:Drug Resistance, Bacterial; D038181:FMN Reductase / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D009154:Mutation; D009249:NADP
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D009249:NADP; D038181:FMN Reductase
references.citation: Mol Syst Biol. 2011 Oct 11;7:539
references.pmid: 21988835
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W239-42
references.pmid: 16845001
references.citation: J Mol Biol. 2000 Sep 8;302(1):205-17
references.pmid: 10964570
references.citation: J Antimicrob Chemother. 1999 Jun;43(6):753-8
references.pmid: 10404313
references.citation: Gene. 2012 Oct 25;508(2):188-96
references.pmid: 22824468
references.citation: Comput Math Methods Med. 2012;2012:805827
references.pmid: 22577471
references.citation: J Med Microbiol. 2004 Nov;53(Pt 11):1123-8
references.pmid: 15496391
references.citation: Hum Mutat. 2006 Dec;27(12):1230-43
references.pmid: 16986121
references.citation: BMC Bioinformatics. 2015 Apr 16;16:116
references.pmid: 25885774
references.citation: Cholesterol. 2014;2014:639751
references.pmid: 25215231
references.citation: Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52
references.pmid: 25352553
references.citation: BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S9
references.pmid: 19758473
references.citation: Genome Announc. 2015 Mar 12;3(2):null
references.pmid: 25767223
references.citation: Antimicrob Agents Chemother. 2001 Sep;45(9):2609-15
references.pmid: 11502537
references.citation: BMC Bioinformatics. 2013;14 Suppl 2:S5
references.pmid: 23369171
references.citation: Hum Mutat. 2010 Sep;31(9):1043-9
references.pmid: 20556796
references.citation: PLoS One. 2012;7(10):e46688
references.pmid: 23056405
references.citation: FEMS Microbiol Lett. 2000 Jul 15;188(2):197-202
references.pmid: 10913705
references.citation: BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S6
references.pmid: 18387208
references.citation: Proteins. 2006 Mar 1;62(4):1125-32
references.pmid: 16372356
references.citation: PLoS Comput Biol. 2012;8(12):e1002819
references.pmid: 23300410
references.citation: Antimicrob Agents Chemother. 2015 Apr;59(4):2343-8
references.pmid: 25645832
references.citation: Appl Transl Genom. 2012 Oct 03;1:37-43
references.pmid: 27896051
references.citation: Antimicrob Agents Chemother. 2000 Aug;44(8):2207-10
references.pmid: 10898705
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W72-6
references.pmid: 15980571
references.citation: PLoS Comput Biol. 2009 Apr;5(4):e1000349
references.pmid: 19381264
references.citation: BMC Genomics. 2010 Nov 02;11 Suppl 2:S5
references.pmid: 21047386
references.citation: Hum Mutat. 2001 Apr;17(4):263-70
references.pmid: 11295823
references.citation: Methods Mol Biol. 2009;541:449-61
references.pmid: 19381537
references.citation: J Antimicrob Chemother. 2003 Apr;51(4):995-9
references.pmid: 12654749
references.citation: J Mol Biol. 2013 Nov 1;425(21):3919-36
references.pmid: 23871686
references.citation: Genome Res. 2001 May;11(5):863-74
references.pmid: 11337480
references.citation: J Bacteriol. 2001 Sep;183(17):5155-62
references.pmid: 11489869
references.citation: Adv Biomed Res. 2014 Mar 14;3:90
references.pmid: 24761398
references.citation: Hum Mutat. 2010 Jun;31(6):675-84
references.pmid: 20232415
references.citation: Res Microbiol. 2003 Mar;154(2):137-44
references.pmid: 12648728
references.citation: Bioinformatics. 2005 Aug 15;21(16):3369-76
references.pmid: 15947016
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3812-4
references.pmid: 12824425
references.citation: Annu Rev Genomics Hum Genet. 2006;7:61-80
references.pmid: 16824020
references.citation: Invest Ophthalmol Vis Sci. 2003 Mar;44(3):1155-9
references.pmid: 12601044
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W306-10
references.pmid: 15980478
references.citation: Helicobacter. 2004 Oct;9(5):400-7
references.pmid: 15361078
references.citation: FEBS J. 2014 Oct;281(19):4495-505
references.pmid: 25132107
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
references.pmid: 21045058