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Selection on GGU and CGU Codons in the High Expression Genes in Bacteria

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Abstract

The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across the eight family boxes (FBs) defined as Um(g), the unevenness measure of a gene g. The study was made in 545 species of bacteria. In many bacteria, the Um(g) correlated strongly with Nc′—a measure of the CUB. Analysis of the strongly correlated bacteria revealed that the U-ending codons (GGU, CGU) were preferred to the G-ending codons (GGG, CGG) in Gly and Arg FBs even in the genomes with G+C % higher than 65.0. Further evidence suggested that these codons can be used as a good indicator of selection pressure on CUB in genomes with higher G+C %.

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Fig. 1
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Abbreviations

CUB:

Codon usage bias

FB(s):

Family box(es)

FDS:

Fourfold degenerate site

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Acknowledgments

We are extremely thankful to several scientists and colleagues such as EPC Rocha (Institut Pasteur, Farnce), F. Supek (Ruđer Bošković Institute, Zagreb, Croatia), M. dos Reis (University College, London), A. Goel (DuPont, Hyderabad), S. K. Kar (KIIT, Bhubaneswar), and V. J. Baruah (Tezpur University, Tezpur) for their helpful sugegstions on the manuscript. We are extremely grateful to the anonymous reviewers for their critical comments on the work which helped us in improving the quality of the manuscript. SKR is thankful to DBT, Govt. of India for the Bioinformatics Infrastructure Facility at Tezpur University. We also thank Mala Dutta (Gauhati University, Guwahati) for her comment on the English writing of the manuscript.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Tezpur University, Tezpur, 784028, Assam, India

    Siddhartha Sankar Satapathy & Malay Dutta

  2. Department of Statistics, Darrang College, Tezpur, 784001, Assam, India

    Bhesh Raj Powdel

  3. Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India

    Alak Kumar Buragohain & Suvendra Kumar Ray

  4. Dibrugarh University, Dibrugarh, 786004, Assam, India

    Alak Kumar Buragohain

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  1. Siddhartha Sankar Satapathy
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  4. Alak Kumar Buragohain
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  5. Suvendra Kumar Ray
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Correspondence to Suvendra Kumar Ray.

Electronic supplementary material

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239_2013_9596_MOESM1_ESM.tif

Supplementary Fig. 1. A four panel figure presenting in- and off-frame tri-nucleotide frequency analysis in rpoB and rpoC genes. Figure 1 presents comparison of the in- frame and off- frame tri-nucleotides GGU, GGG, CGU and CGG frequencies in rpoB/C genes in five different genome G+C groups (i) very high, 65.0 ≤ G+C %; (ii) high, 55.0 ≤ G+C % < 65.0; (iii) moderate, 45.0 ≤ G+C % < 55.0; (iv) low, 35.0 ≤ G+C % < 45.0; and (v) very low, G+C % < 35.0. Within each group, four bacteria (as analyzed in Fig. 2) that exhibited strong Pearson r(Um(g), Nc′) were considered. It is evident in the Fig. 1 that the abundance values of in-frame GGU/CGU triplets are different from that in off-frame1 and off-frame2. Similarly, the abundance values of in-frame GGG/CGG triplets are different from that in off-frame1 and off-frame2. This study suggests that selection of GGU and CGU codons in the high expression genes is not due to general selection of these triplets in coding regions. (TIFF 110 kb)

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Satapathy, S.S., Powdel, B.R., Dutta, M. et al. Selection on GGU and CGU Codons in the High Expression Genes in Bacteria. J Mol Evol 78, 13–23 (2014). https://doi.org/10.1007/s00239-013-9596-6

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