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The Bioinformatics Report of Mutation Outcome on NADPH Flavin Oxidoreductase Protein Sequence in Clinical Isolates of H. pylori

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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.

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Acknowledgment

This study was supported by Grant No: 290054 from Isfahan University of Medical Sciences, Isfahan, Iran.

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Authors and Affiliations

  1. Department of Microbiology, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran

    Nasrin Mirzaei

  2. Department of Microbiology, Isfahan University of Medical Sciences, Isfahan, Iran

    Farkhondeh Poursina, Sharareh Moghim & Hajieh Ghasemian Safaei

  3. Department of Pathology, Zanjan University of Medical Sciences, Zanjan, Iran

    Abdol Majid Ghaempanah

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  1. Nasrin Mirzaei
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  2. Farkhondeh Poursina
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Correspondence to Hajieh Ghasemian Safaei.

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Mirzaei, N., Poursina, F., Moghim, S. et al. The Bioinformatics Report of Mutation Outcome on NADPH Flavin Oxidoreductase Protein Sequence in Clinical Isolates of H. pylori . Curr Microbiol 72, 596–605 (2016). https://doi.org/10.1007/s00284-016-0992-1

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