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Codon usage trend in genes associated with obesity

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Abstract

Obesity is not only a social menace but also an economic burden as it reduces productivity and increases health care cost. We used bioinformatic tools to analyze the CUB of obesity associated genes and compared with housekeeping genes (control) to explore the similarities and differences between two data sets as no work was reported yet. The mean effective number of codons (ENC) in genes associated with obesity and housekeeping gene was 50.45 and 52.03 respectively, indicating low CUB. The relative synonymous codon usage (RSCU) suggested that codons namely CTG and GTG were over-represented in both obesity and housekeeping genes while under-represented codons were TCG, TTA, CTA, CCG, CAA, CGT, ATA, ACG, GTA and GCG in obesity genes and TCG, TTA, CCG, ATA, ACG, GTA, and GCG in housekeeping genes. t test analysis suggested that 11 codons namely TTA (Leu), TTG (Leu), CCG (Pro), CAC (His), CAA (Gln), CAG (Gln), CGT (Arg), AGA (Arg), ATA (Ile), ATT (Ile) and GCG (Ala) were significantly differed (p < 0.05 or p < 0.01) between obesity and housekeeping genes. Highly significant correlation was observed between GC12 and GC3 in obesity and housekeeping genes i.e. r = 0.580** and r = 0.498** (p < 0.01) respectively indicating the effect of directional mutation pressure present in all codon positions.

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Acknowledgements

All the authors are thankful to Assam University, Silchar, Assam, India.

Supporting information

S1—List of genes with accession number.

S2—List of Accession number for housekeeping genes.

S3—ENC values of obesity genes.

S4—ENC values of housekeeping genes.

S5—t test of codons between obesity genes and housekeeping genes.

Funding

Unfunded. No fund was received.

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Authors and Affiliations

  1. Department of Biotechnology, Assam University, Silchar, Assam, 788011, India

    Supriyo Chakraborty, Parvin A. Barbhuiya, Sunanda Paul, Arif Uddin & Yashmin Choudhury

  2. Department of Biomedical Science, Hallym University, Hallymdachak-gil, Chuncheon, 24252, Gangwon-do, Korea

    Yeongseon Ahn & Yoon Shin Cho

Authors
  1. Supriyo Chakraborty
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  2. Parvin A. Barbhuiya
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  3. Sunanda Paul
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  4. Arif Uddin
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  5. Yashmin Choudhury
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Correspondence to Supriyo Chakraborty or Yoon Shin Cho.

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Chakraborty, S., Barbhuiya, P.A., Paul, S. et al. Codon usage trend in genes associated with obesity. Biotechnol Lett 42, 1865–1875 (2020). https://doi.org/10.1007/s10529-020-02931-z

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