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Identification of Translationally Optimal Codons and Suitable Expression Host of DPV gB Gene
Abstract:
In this report, we conduct study on codon composition and codon usage of DPV glycoprotein B (gB) gene, its homologs constitute the most highly conserved family of herpesvirus glycoproteins and are present in members of each herpesvirus subfamily. Our results show that sixty-one codons (excluding the termination codons) in the polypeptide, a high level of diversity in codon usage bias existed for coding the Ala, Gly, Leu, Pro, Arg, Ser, Thr and Val amino acids. Sixteen codons (each for a amino acid), including GCA (Ala), GAT (Asp), GAA (Glu), GGA (Gly), CAT (His), ATA (Ile), AAA (Lys), CTA (Leu), AAT (Asn), CCA (Pro), CAA (Gln), AGA (Arg), TCT (Ser), ACT (Thr), GTA (Val) and TAT (Tyr) were determined as the translationally optimal codons. The codon preferences of DPV gB gene were compared with those of E. coli, yeast, and H. sapiens, we can speculate that the DPV gB gene may be more efficiently expressed in the E. coli system. In summary, knowledge of codon usage of herpesvirus gB genes provides insights into molecular and species evolution, and also plays important role in furthering some biotechnological applications. These would be fruitful areas for further study.
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729-736
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Online since:
September 2011
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© 2012 Trans Tech Publications Ltd. All Rights Reserved
Citation:
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[20] 6.
[16] 1.
[16] 1.
[29] 970.
[1] 45.
[1] 86.
[1] 86 GCC.
[25] 5.
[12] 5.
[28] 4.
[13] 986.
55.
[1] 12.
49 GCG.
[31] 7.
[6] 1.
[7] 5.
[10] 989.
35.
[1] 80.
[1] 47 GCT.
[15] 6.
[21] 1.
[18] 6.
[17] 982.
[1] 15.
85.
97 C(Cys) TGC.
[6] 9.
[4] 7.
[12] 2.
[6] 993.
[1] 01.
[1] 49.
57 TGT.
[5] 5 8 10.
[6] 993.
[1] 27.
87.
70 D(Asp) GAC.
[18] 6.
[20] 2.
[25] 6.
[24] 975.
[1] 34.
[1] 24.
98 GAT.
[32] 1.
[37] 8.
[21] 9.
[33] 966.
[1] 06.
90.
[1] 55 E(Glu) GAA.
[38] 2.
[48] 5 29.
[44] 955.
[1] 18.
93.
[1] 55 GAG.
[17] 7.
[19] 1.
[39] 9.
[18] 981.
[1] 07.
99.
48 F(Phe) TTC.
[16] 9.
[18] 2.
[20] 6.
[16] 983.
[1] 00.
93.
82 TTT.
[23] 2.
[26] 1.
[17] 1.
[16] 983.
73.
65.
99 G(Gly) GGA 9.
[10] 9.
[16] 4.
[16] 983.
[1] 89.
[1] 56.
[1] 04 GGC.
[27] 9.
[9] 7.
[22] 5.
[13] 986.
50.
[1] 44.
62 GGG.
[11] 3 6.
[16] 3.
[11] 988.
[1] 06.
[2] 00.
74 GGT.
[24] 4 24.
[10] 8.
[15] 984.
66.
67.
[1] 48 H(His) CAC.
[9] 8.
[7] 7 15.
[4] 995.
51.
65.
33 CAT.
[13] 6.
[13] 7.
[10] 5.
[8] 991.
66.
66.
86 I(Ile) ATA.
[5] 4.
[17] 8.
[7] 7.
[23] 976.
[4] 44.
[1] 35.
[3] 11 ATC.
[24] 2 17.
[21] 6.
[8] 991.
37.
53.
42 ATT.
[29] 8.
[30] 4.
[16] 1.
[7] 992.
27.
26.
50 K(Lys) AAA.
[33] 2.
[42] 2.
[24] 1.
[25] 974.
78.
62.
[1] 08 AAG.
[10] 7.
[30] 7.
[32] 2.
[21] 978.
[2] 05.
72.
68 L(Leu) CTA 4.
[13] 3.
[7] 8.
[20] 979.
[5] 24.
[1] 58.
[2] 69 CTC 11.
[5] 4.
[19] 8.
[3] 996.
36.
74.
20 CTG.
[50] 9.
[10] 4.
[39] 8.
[13] 986.
27.
[1] 34.
35 CTT.
[11] 7.
[12] 1 13.
[14] 985.
[1] 28.
[1] 24.
[1] 15 TTA.
[13] 9.
[26] 7.
[7] 5.
[12] 987.
93.
49.
[1] 73 TTG 14 27.
[12] 6.
[12] 987.
93.
48.
[1] 03 N(Asn) AAC.
[21] 4.
[24] 9.
[19] 5.
[21] 978.
[1] 03.
88.
[1] 13 AAT.
[18] 6.
[36] 3.
[16] 7.
[27] 972.
[1] 50.
77.
[1] 67 P(Pro) CCA.
[8] 5.
[18] 2.
[16] 7.
[19] 98.
[2] 35.
[1] 10.
[1] 20 CCC.
[5] 8.
[6] 8.
[20] 1.
[4] 995.
86.
73.
25 CCG.
[21] 8.
[5] 3.
[6] 9.
[5] 994.
27.
[1] 13.
87 CCT.
[7] 3.
[13] 6.
[17] 3.
[7] 992.
[1] 09.
59.
46 Q(Gln) CAA 15.
[27] 5 12.
[18] 981.
[1] 27.
69.
[1] 58 CAG.
[29] 5.
[12] 1.
[34] 1.
[7] 992.
27.
66.
23 R(Arg) AGA.
[2] 9.
[21] 3.
[11] 5.
[24] 975.
[8] 61.
[1] 17.
[2] 17 AGG.
[1] 9.
[9] 2.
[11] 4.
[9] 99.
[5] 26.
[1] 09.
88 CGA.
[3] 9 3.
[6] 3.
[14] 985.
[3] 84.
[5] 00.
[2] 38 CGC 21.
[2] 6.
[10] 7.
[14] 985.
71.
[5] 76.
[1] 40 CGG.
[6] 3.
[1] 7.
[11] 6.
[7] 992.
[1] 27.
[4] 70.
69 CGT.
[20] 3.
[6] 5.
[4] 6.
[15] 984.
79.
[2] 46.
[3] 47 S(Ser) AGC 16.
[9] 7.
[19] 3.
[9] 99.
62.
[1] 03.
52 AGT.
[9] 5.
[14] 2.
[11] 9.
[7] 992.
84.
56.
67 TCA.
[7] 8.
[18] 8 12.
[15] 984.
[2] 05.
85.
[1] 33 TCC.
[8] 9.
[14] 2.
[11] 9.
[5] 994.
67.
42.
50 TCG.
[8] 7.
[8] 5.
[4] 4.
[14] 985.
[1] 72.
[1] 76.
[3] 41 TCT.
[8] 7.
[23] 5.
[14] 7.
[20] 979.
[2] 41.
89.
[1] 43 T(Thr) ACA.
[8] 2.
[17] 8.
[15] 1.
[17] 982.
[2] 19.
[1] 01.
[1] 19 ACC.
[22] 8.
[12] 6.
[19] 4.
[7] 992.
35.
63.
41 ACG.
[14] 8.
[7] 9.
[6] 1.
[16] 983.
[1] 15.
[2] 15.
[2] 78 ACT.
[9] 1.
[20] 3 13.
[19] 98.
[2] 20.
98.
[1] 54 V(Val) GTA.
[11] 1.
[11] 8.
[7] 2.
[25] 974.
[2] 34.
[2] 20.
[3] 61 GTC.
[15] 1.
[11] 6.
[14] 6.
[10] 989.
73.
95.
75 GTG.
[25] 5.
[10] 6.
[28] 4.
[12] 987.
51.
[1] 23.
46 GTT.
[18] 5 22 11.
[23] 976.
[1] 30.
[1] 09.
[2] 18 Y(Tyr) TAC.
[12] 1.
[14] 6.
[15] 5.
[21] 978.
[1] 82.
[1] 51.
[1] 42 TAT.
[16] 5.
[18] 9.
[12] 1.
[30] 969.
[1] 88.
[1] 64.
[2] 56 Notes: DPV/E. coli, DPV/yeast and DPV/H. sapiens indicate the ratio of codon usage frequency in DPV gB gene to that in E. coli, yeast and H. sapiens, respectively. A ratio higher than 2 or lower than 0. 5 (indicated in bold) indicates that the codon preference differs greatly, and vice versa. Fig. 1. Graphs showing the relationships between codon usage in DPV gB gene against E. coli, yeast and H. sapiens. Values plotted are the proportions of each of the 59 codons within its synonymous family (ignoring the single codons for Trp and Met and the 3 termination codons). The ratio higher than 2 or lower 0. 5 indicates that the codon usage preference differs, and vice versa. The lines indicate ratio values of 0. 5 and 2.