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Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli

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Abstract

In this study, major factors shaping codon and amino acid usage variation Lactobacillus sakei 23K were investigated. It included 13 other Lactobacillus species for a comparative analysis. The correspondence analysis (COA) showed that in 13 species the major trend of synonymous codon usage was highly correlated with gene expression level as assessed by the “Codon Adaptation Index” (CAI) values. In addition, Nc (effective number of codons) plot, SCUO (synonymous codon usage order) plot and correlation analyses showed that the base composition and mutational bias have dominant role in the codon usage variation. However, the translational selection for genes at higher expression level, where more frequent synonymous codons correspond to more abundant cognate transfer RNAs (tRNAs), was not found to be similar in all species. The study also showed that the amino acid usage in these species was significantly (P < 0.01) influenced by hydrophobicity and aromaticity of proteins. Furthermore, 24 codons that were found to be optimally used by L. sakei and its comparative study with 13 Lactobacillus species might provide some useful information in their further study of molecular evolution and genetic engineering.

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Acknowledgments

I would like to thank the Department of Biotechnology, Ministry of Science and Technology, Govt. of India for financial help and Dr. Subrata K. Das of Institute of Life Sciences for giving suggestions during writing the script. I am thankful to anonymous reviewers for their suggestions for improving the writing of the script.

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  1. Bioinformatics Centre, Institute of Life Sciences, Department of Biotechnology, Govt. India, Nalco Square, Bhubaneswar, 751 023, India

    Kinshuk Chandra Nayak

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Correspondence to Kinshuk Chandra Nayak.

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Nayak, K.C. Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli . Mol Biol Rep 39, 535–545 (2012). https://doi.org/10.1007/s11033-011-0768-4

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  • DOI: https://doi.org/10.1007/s11033-011-0768-4

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