Characterization of Codon Usage Bias in the RA Ragb/SusD Gene

Abstract:

The analysis on codon usage bias of Riemerella anatipestifer (RA) RagB/SusD gene (GenBank accession No. NC_017045.1) may improve our understanding of the evolution and pathogenesis of RA and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. In this study, the synonymous codon usage in the RagB/SusD gene of RA and 19 reference bacteroidetes have been investigated. The results showed that codon usage bias in the RagB/SusD gene was strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the genetic heterogeneity in RagB/SusD gene of bacteroidetes was constrained by the G + C content. The codon adaptation index (CAI), effective number of codons (ENC), and GC3S values indicated synonymous codon usage bias in the RagB/SusD gene of bacteroidetes, and this synonymous bias was correlated with host evolution. The phylogentic analysis suggested that RagB/SusD was evolutionarily closer to Ornithobacterium rhinotracheale and that there was no significant deviation in codon usage in different bacteroidetes. There are 25 codons showing distinct usage differences between RA RagB/SusD and E. coli, 30 between RA RagB/SusD and Homo sapiens, 26 codons between RA RagB/SusD and yeast. Therefore the yeast and E. coli expression system may be suitable for the expression of RA RagB/SusD gene if some codons could be optimized.

• Periodical: Advanced Materials Research (Volumes 641-642)
• Pages: 654-665
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.641-642.654
• Online since: January 2013
• Authors: Si Si Yang, De Kang Zhu, Xiao Jia Wang, An Chun Cheng, Ming Shu Wang
• Keywords: Codon Usage Bias, RagB/SusD Gene, Riemerella anatipestifer

References

[1] N. Jarrett, S. Payne, P. Turner, R. Hillier. Someone to talk to'and 'pain control,: what people expect from a specialist palliative care team, J. Palliative Medicine. 13（1999）. 139-144.

DOI: 10.1191/026921699669165706

[2] T. Ikemura. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes, J. Journal of molecular biology. 146（1981）. 1-21.

DOI: 10.1016/0022-2836(81)90363-6

[3] T. Ikemura. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system, J. Journal of molecular biology. 151（1981）. 389-409.

DOI: 10.1016/0022-2836(81)90003-6

[4] J. Ellis, D. A. Morrison, B. Kalinna. Comparison of the patterns of codon usage and bias betweenBrugia, Echinococcus, Onchocerca andSchistosoma species, J. Parasitology research. 81（1995）. 388-393.

DOI: 10.1007/bf00931499

[5] J. A. Novembre. Accounting for background nucleotide composition when measuring codon usage bias, J. Molecular Biology and Evolution. 19（2002）. 1390-1394.

DOI: 10.1093/oxfordjournals.molbev.a004201

[6] C. Gustafsson, S. Govindarajan, J. Minshull. Codon bias and heterologous protein expression, J. Trends in biotechnology. 22（2004）. 346-353.

DOI: 10.1016/j.tibtech.2004.04.006

[7] E. N. Moriyama, D. Hartl. Codon usage bias and base composition of nuclear genes in Drosophila, J. Genetics. 134（1993）. 847-858.

DOI: 10.1093/genetics/134.3.847

[8] H. P. Sørensen, K. K. Mortensen. Advanced genetic strategies for recombinant protein expression in Escherichia coli , J. Journal of biotechnology. 115（2005）. 113-128.

DOI: 10.1016/j.jbiotec.2004.08.004

[9] M. Heitzer, A. Eckert, M. Fuhrmann, C. Griesbeck. Influence of codon bias on the expression of foreign genes in microalgae, J. Transgenic Microalgae as Green Cell Factories. 2007. 46-53.

DOI: 10.1007/978-0-387-75532-8_5

[10] G. M. Jenkins, E. C. Holmes. The extent of codon usage bias in human RNA viruses and its evolutionary origin, J. Virus research. 92（2003）. 1-7.

DOI: 10.1016/s0168-1702(02)00309-x

[11] G. M. Jenkins, M. Pagel, E. A. Gould, P. M. A. Zanotto, E. C. Holmes. Evolution of base composition and codon usage bias in the genus Flavivirus, J. Journal of molecular evolution. 52（2001）. 383-390.

DOI: 10.1007/s002390010168

[12] D. B. Levin, B. Whittome. Codon usage in nucleopolyhedroviruses, J. Journal of General Virology. 81（2000）. 2313-2325.

DOI: 10.1099/0022-1317-81-9-2313

[13] T. Ghosh, S. Gupta, S. Majumdar. Studies on codon usage in Entamoeba histolytica, J. International journal for parasitology. 30（2000）. 715-722.

DOI: 10.1016/s0020-7519(00)00042-4

[14] T. Ikemura. Codon usage and tRNA content in unicellular and multicellular organisms, J. Molecular Biology and Evolution. 2（1985）. 13-34.

DOI: 10.1093/oxfordjournals.molbev.a040335

[15] R. Grantham, C. Gautier, M. Gouy, M. Jacobzone, R. Mercier. Codon catalog usage is a genome strategy modulated for gene expressivity, J. Nucleic Acids Research. 9（1981）. 213-213.

DOI: 10.1093/nar/9.1.213-b

[16] P. M. Sharp, E. Cowe. Synonymous codon usage in Saccharomyces cerevisiae, J. Yeast. 7（1991）. 657-678.

DOI: 10.1002/yea.320070702

[17] M. Oresic, D. Shalloway. Specific correlations between relative synonymous codon usage and protein secondary structure1, J. Journal of molecular biology. 281（1998）. 31-48.

DOI: 10.1006/jmbi.1998.1921

[18] S. Gupta, S. Majumdar, T. Bhattacharya, T. Ghosh. Studies on the relationships between the synonymous codon usage and protein secondary structural units, J. Biochemical and biophysical research communications. 269（2000）. 692-696.

DOI: 10.1006/bbrc.2000.2351

[19] S. Das, S. Paul, C. Dutta. Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy, J. Virus research. 117（2006）. 227-236.

DOI: 10.1016/j.virusres.2005.10.007

[20] W. Gu, T. Zhou, J. Ma, X. Sun, Z. Lu. The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens , J. Biosystems. 73（2004）. 89-97.

DOI: 10.1016/j.biosystems.2003.10.001

[21] T. Banerjee, S. Basak, S. Gupta, T. Ghosh. Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus, J. Journal of biomolecular structure & dynamics. 22（2004）. 13-23.

DOI: 10.1080/07391102.2004.10506976

[22] B. Garat, H. Musto. Trends of Amino Acid Usage in the Proteins from the Unicellular Parasite Giardia lamblia , J. Biochemical and biophysical research communications. 279（2000）. 996-1000.

DOI: 10.1006/bbrc.2000.4051

[23] S. Basak, T. Banerjee, S. Gupta, T. Ghosh. Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis, J. Journal of biomolecular structure & dynamics. 22（2004）. 205.

DOI: 10.1080/07391102.2004.10506996

[24] H. Grosjean, W. Fiers. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes, J. Gene. 18（1982）. 199.

DOI: 10.1016/0378-1119(82)90157-3

[25] M. Gouy, C. Gautier. Codon usage in bacteria: correlation with gene expressivity, J. Nucleic Acids Research. 10（1982）. 7055-7074.

DOI: 10.1093/nar/10.22.7055

[26] L. E. Post, M. Nomura. DNA sequences from the str operon of Escherichia coli, J. Journal of Biological Chemistry. 255（1980）. 4660-4666.

DOI: 10.1016/s0021-9258(19)85545-x

[27] P. M. Sharp, W. H. Li. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias, J. Molecular Biology and Evolution. 4（1987）. 222-230.

DOI: 10.1093/oxfordjournals.molbev.a040443

[28] S. D. Hooper, O. G. Berg. Gradients in nucleotide and codon usage along Escherichia coli genes, J. Nucleic Acids Research. 28（2000）. 3517-3523.

DOI: 10.1093/nar/28.18.3517

[29] X. Wang, D. K. Zhu, M. S. Wang, A. C. Cheng, R. Y. Jia, Y. Zhou, Z. Chen, Q. H. Luo, F. Liu, Y. Wang. Complete Genome Sequence of Riemerella anatipestifer Reference Strain, J. Journal of bacteriology. 194（2012）. 3270-3271.

DOI: 10.1128/jb.00366-12

[30] N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices, J. Structure. 16（2008）. 1105-1115.

DOI: 10.1016/j.str.2008.03.017

[31] M. Curtis, J. Slaney, R. Carman, N. Johnson. Identification of the major surface protein antigens of Porphyromonas gingivalis using IgG antibody reactivity of periodontal case‐control serum, J. Oral microbiology and immunology. 6（1991）. 321-326.

DOI: 10.1111/j.1399-302x.1991.tb00502.x

[32] S. A. Hanley, J. Aduse-Opoku, M. A. Curtis. A 55-Kilodalton Immunodominant Antigen ofPorphyromonas gingivalis W50 Has Arisen via Horizontal Gene Transfer, J. Infection and immunity. 67（1999）. 1157-1171.

DOI: 10.1128/iai.67.3.1157-1171.1999

[33] P. M. Sharp, W. H. Li. An evolutionary perspective on synonymous codon usage in unicellular organisms, J. Journal of molecular evolution. 24（1986）. 28-38.

DOI: 10.1007/bf02099948

[34] F. Wright. The effective number of codons, used in a gene, J. Gene. 87（1990）. 23-29.

DOI: 10.1016/0378-1119(90)90491-9

[35] J. M. Comeron, M. Aguadé. An evaluation of measures of synonymous codon usage bias, J. Journal of molecular evolution. 47（1998）. 268-274.

DOI: 10.1007/pl00006384

[36] H. Sakai, T. Washio, R. Saito, A. Shinagawa, M. Itoh, K. Shibata, P. Carninci, H. Konno, J. Kawai, Y. Hayashizaki. Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes, J. Gene. 276（2001）. 101-105.

DOI: 10.1016/s0378-1119(01)00671-0

[37] H. Lü, W. M. ZHAO, Y. Zheng, H. Wang, M. Qi, X. P. YU. Analysis of synonymous codon usage bias in Chlamydia, J. Acta biochimica et biophysica Sinica. 37（2005）. 1-10.

DOI: 10.1093/abbs/37.1.1

[38] W. Gu, T. Zhou, J. Ma, X. Sun, Z. Lu. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales, J. Virus research. 101（2004）. 155-161.

DOI: 10.1016/j.virusres.2004.01.006

[39] P. Jiang, X. Sun, Z. Lu. Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms, J. Journal of Genetics and Genomics. 34（2007）. 275-284.

DOI: 10.1016/s1673-8527(07)60029-0

[40] P. M. Sharp, W. H. Li. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, J. Nucleic Acids Research. 15（1987）. 1281-1295.

DOI: 10.1093/nar/15.3.1281

[41] S. Karlin, I. Ladunga, B. Blaisdell. Heterogeneity of genomes: measures and values, J. Proceedings of the National Academy of Sciences. 91（1994）. 12837-12841.

DOI: 10.1073/pnas.91.26.12837

[42] N. Sueoka. Directional mutation pressure, selective constraints, and genetic equilibria, J. Journal of molecular evolution. 34（1992）. 95-114.

DOI: 10.1007/bf00182387

[43] X. F. Wan, D. Xu, A. Kleinhofs, J. Zhou. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes, J. BMC Evolutionary Biology. 4（2004）. 19.

[44] W. J. Blake, M. Kærn, C. R. Cantor, J. J. Collins. Noise in eukaryotic gene expression, J. Nature. 422（2003）. 633-637.

DOI: 10.1038/nature01546

[45] H. S. Najafabadi, J. Lehmann, M. Omidi. Error minimization explains the codon usage of highly expressed genes in Escherichia coli, J. Gene. 387（2007）. 150-155.

DOI: 10.1016/j.gene.2006.09.004