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1、Characterization of Codon Usage Bias in the Us4 Gene of Duck Plague Virus Xiaoyuan Yang, Anchun Cheng, Mingshu Wang, Dekang Zhu, Xiaoyue Chen Avian Diseases Research Center College of Veterinary Medicine of Sichuan Agricultural University Yaan, Sichuan, 625014, China Anchun Cheng, Mingshu Wang, Deka
2、ng Zhu, Renyong Jia, Qihui Luo, Hengmin Cui, Yi Zhou, Yin Wang, Zhiwen Xu, Zhengli Chen, Xiaoyue Chen, Xiaoyu Wang Key laboratory of Animal Disease and Human Health of Sichuan Province Yaan, Sichuan, 625014, China Anchun Cheng, Xiaoyue Chen Epizootic Diseases Institute of Sichuan Agricultural Univer
3、sity Yaan, Sichuan, 625014, China E-mail: AbstractThe analysis on codon usage bias of Us4 gene of Duck Plague Virus (DPV) may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target genes in vi
4、vo and in vitro. In this study, the synonymous codon usage in the Us4 gene of DPV and 17 reference herpesviruses have been investigated . The results reveals that the synonymous codons with A and T at the third codon positon have widely usage in the codon of Us4 gene of DPV. The phylogentic analysis
5、 suggested that DPV was evolutionarily closer to fowl herpesviruses which further clustered into Alphaherpesvirinae. In addition, rare condons analysis showed that there are 36 rare condons in the ORF of the DPV Us4 on line (http:/nihserver.mbi.ucla.edu/RACC/), and the codon usage bias of DPV Us4 ge
6、ne was compared with those of E. coli, yeast and Humans. There are 25 codons showing distinct usage differences between DPV and E. coli, 25 codons between DPV and yeast, 27 between DPV and Homo sapiens. Therefore the E. coli and yeast expression system may be suitable for the expression of DPV Us4 g
7、ene if some codons could be optimized. Keywords-Duck Plague Virus (DPV); Us4 gene; codon usage bias I. INTRODUCTION The alternative synonymous codons for any amino acid are not randomly used and the occurrence of certain synonymous codons more frequently than others in coding sequences is known as c
8、odon usage bias. Codon usage bias is widely studied in particular organisms to achieve high expression of heterologous proteins and to improve the design of oligonucleotide probes and primers in order to provide a general understanding of the molecular evolution of species 14. Previous codon usage a
9、nalyses showed that codon usage bias is very complicated and is associated with various biological factors, such as gene expression level 5 gene length 6, gene translation initiation signal 7, protein amino acid composition 8, protein structure 9, tRNA abundance 10,11, mutation frequency and pattern
10、s 8,12, and GC composition 13,14. Codon usage information in different viruses has also been analyzed. In Mimivirus genes, mutational pressure and translational selection leaded to codon usage bias 15. Mutational pressure, G + C content, the segmented nature of the genome and the route of transmissi
11、on were the reasons of codon usage bias in human RNA viruses 16. For some vertebrate DNA viruses, genome-wide mutational pressure is the main determinant of codon usage 17. Due to uneven base composition and strong preference for the A nucleotide, human immunodeficiency virus (HIV) and Nucleopolyhed
12、roviruses have a marked codon usage bias 18,19. Codon usage of the bovine papillomavirus type 1 (BPV-1) late genes are related to tRNA availability 20. Codon usage may play a key role in regulating latent versus productive infection in Epstein-Barr virus 21. Studies of the synonymous codon usage in
13、viruses can reveal information about the molecular evolution of individual genes and such information would be relevant to understanding the regulation of viral gene expression and also to vaccine design where the efficient expression of viral proteins may be required to generate immunity 22,23. Duc
14、k virus enteritis, known as duck plague, which is caused by the duck plague virus (DPV), a member of the Herpesviridae family, is an acute and contagious herpesvirus infection of waterfowls such as ducks, geese, and swans with high morbidity and mortality 24. DPV genomic library was constructed succ
15、essfully in our laboratory, and we have reported the complete sequence of the newly isolated Us4 gene of DPV25. Us4 gene encodes a non-structural envelope glycoprotein G (gG) 26. It is a kind of chemokine binding proteins (vCKPBs) which could help virus counteract host immune defenses 27,28. Althoug
16、h gG in Herpesviridae is not essential for virus replication in cultured cells 29,30,31,32, it facilitates viral cell-to-cell spread by maintaining the cell-to-cell junctions among the infected cells 29. Moreover, gG has the function to opsonize cells of host. BHV-1 gG is involved in stabilizing the
17、978-1-4244-4713-8/10/$25.00 2010 IEEETABLE I. SUMMARY ANALYSIS OF DPV AND 17 REFERENCE HERPERVIRUS US4 GENE Species GenBank accession no. Virus name SeqLen (bp) CAI Nc GC % GC3S(%) Alpha herpesvirus EU071043 Duck enteritis virus 1380 0.651 56.855 44.49 39.57 NC_006623 Gallid herpesvirus 1 879 0.711
18、52.027 56.20 65.87 NC_005264 Psittacid herpesvirus 1 843 0.754 47.435 59.43 70.46 AY881693 Baboon herpesvirus 2 1974 0.693 33.152 80.50 92.55 NC_007653 Papiine herpesvirus 2 1974 0.693 33.114 80.50 92.55 NC_006560 Cercopithecine herpesvirus 2 1815 0.714 33.390 80.66 93.39 NC_004812 Macacine herpesvi
19、rus 1 2022 0.743 35.325 78.19 89.47 NC_001806 Human herpesvirus 1 717 0.717 47.354 63.74 71.97 NC_001798 Human herpesvirus 2 2100 0.704 46.560 71.33 76.29 AY048540 Macropodid herpesvirus type 2 1752 0.680 55.965 53.48 53.25 NC_001847 Bovine herpesvirus 1 1335 0.772 36.761 69.74 84.49 NC_005261 Bovin
20、e herpesvirus 5 1323 0.769 36.708 68.63 86.62 AY464052 Equine herpesvirus 1 1236 0.698 57.419 49.92 52.67 AF030027 Equine herpesvirus 4 1308 0.669 56.129 45.34 45.87 AP010838 Equid herpesvirus 9 1236 0.699 59.280 50.24 52.67 AY740677 Felid herpesvirus 1 1305 0.635 52.516 41.99 32.64 AJ290955 Phocid
21、herpesvirus 1 1239 0.619 40.889 30.10 15.50 NC_006151 Suid herpesvirus 1 1497 0.824 29.900 71.21 93.79 cell structure, postponing apoptotic process, and efficient BHV-1 replication in infected rabbit kidney (RK13) cells 30. In this study, the synonymous codon usage data of DPV Us4 gene was analyzed,
22、 and compared with the 17 other herpervirus Us4 gene codon usage. Moreover, we analysied the rare codons of the Us4 ORF, and compared with those of E. coli, yeast, and human. It provided a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropri
23、ate host expression system to improve the expression of target genes in vitro. II. MATERIAL AND METHOD A. Virus and gene sequences The DPV CHv strain, a highly virulent field strain that was identified by Cheng, A.C 25, was used, and the DPV Us4 gene (GenBank accession no. EU071043) was reported, an
24、d the other 17 reference herperviruses Us4 gene nucleotide sequences were employed from the NCBI GenBank nucleotide database (see Table 1). B. Codon usage bias analysis of the DPV Us4 gene and the other 17 reference herperviruses We computed codon-usage bias ENC (effective number of codons used in a
25、 gene) value15, RSCU (relative synonymous codon usage)16, CAI (codon adaptation index)17, and GC3s (G+C content at the third positions of codons)18 of the DPV Us4 gene and 17 reference herperviruses with the programs of the EMBOSS(European Molecular Biology Open Software Suite) online19,20, respecti
26、vely(see Table 1 and Table 2). And the three parameters (ENc, CAI, GC3s) was analyzed using SPSS 14.0. C. Phylogenetic Analysis of the DPV Us4 Gene SHOWORF, an EMBOSS nucleotide translation program, was used to read and transfer the nucleotide sequence data to a computer file. Phylogenetic analysis
27、were performed for the Us4 gene of 18 herpesviruses with CLUSTAL-X and MEGA software. D. Rare condons analysis of the DPV Us4 gene and the comparison of DPV Us4 gene codon usage bias with E.coli, yeast and human We analysied the rare condons in the ORF of the DPV Us4 with using codon usage database
28、on line (http:/nihserver.mbi.ucla.edu/RACC/), and compared the codon usage bias among DPV Us4 gene with those of E. coli, yeast, and human. The codons usage database of E. coli, yeast, human refer to online service: http:www.kazusa.or.jp/condon. III. RESULTS A. Variation in DPV Us4 gene codon usage
29、composition While CAI, Nc and the related measures indicate the DPV Us4 gene codon bias, it is also important to closely investigate the pattern of codon bias. Table 2 shows the codon preferences of the DPV Us4 gene. 59 codons (excluding Met, Trp, and the termination codons) in the polypeptide, with
30、 7 synonymous codons strong bias towards A-ended and 9 towards T-ended at the third codon position, were used. A high level of diversity in codon usage bias is existed for coding the Glu, Phe, His, Gln, Ser, Val and Tyr amino acids. B. Codon usage analysis of Us4 gene between DPV and 17 reference he
31、rperviruses The CAI, ENC and coding GC and GC3S content analysis of DPV and 17 herpesviruses Us4 genes are shown in Table 1 TABLE II. CONDON PREFERENCES OF US4 GENE ANALYZED BY CUSPS PROGRAM Condon AA Fracta Frequency (1/1000)b Num ber RSCU Condon AA Fracta Frequency (1/1000)b Num ber RSCU GCA A(Ala
32、) 0.227 10.870 5 0.909 CCA P(Pro) 0.423 23.913 11 1.692 GCC A 0.273 13.043 6 1.091 CCC P 0.154 8.696 4 0.615 GCG A 0.182 8.696 4 0.727 CCG P 0.192 10.870 5 0.769 GCT A 0.318 15.217 7 1.273 CCT P 0.231 13.043 6 0.923 TGC C(Cys) 0.462 13.043 6 0.923 CAA Q(Gln) 0.800 17.391 8 1.600 TGT C 0.538 15.217 7
33、 1.077 CAG Q 0.200 4.348 2 0.400 GAC D(Asp) 0.562 39.130 18 1.125 AGA R(Arg) 0.190 8.696 4 1.143 GAT D 0.438 30.435 14 0.875 AGG R 0.190 8.696 4 1.143 GAA E(Glu) 0.643 19.565 9 1.286 CGA R 0.190 8.696 4 1.143 GAG E 0.357 10.870 5 0.714 CGC R 0.238 10.870 5 1.429 TTC F(Phe) 0.385 10.870 5 0.769 CGG R
34、 0.143 6.522 3 0.857 TTT F 0.615 17.391 8 1.231 CGT R 0.048 2.174 1 0.286 GGA G(Gly) 0.326 30.435 14 1.302 AGC S(Ser) 0.091 6.522 3 0.545 GGC G 0.233 21.739 10 0.930 AGT S 0.303 21.739 10 1.818 GGG G 0.186 17.391 8 0.744 TCA S 0.061 4.348 2 0.364 GGT G 0.256 23.913 11 1.023 TCC S 0.091 6.522 3 0.545
35、 CAC H(His) 0.267 8.696 4 0.533 TCG S 0.121 8.696 4 0.727 CAT H 0.733 23.913 11 1.467 TCT S 0.333 23.913 11 2.000 ATA I(Ile) 0.324 23.913 11 0.971 ACA T(Thr) 0.357 32.609 15 1.429 ATC I 0.206 15.217 7 0.618 ACC T 0.190 17.391 8 0.762 ATT I 0.471 34.783 16 1.412 ACG T 0.262 23.913 11 1.048 AAA K(Lys)
36、 0.545 13.043 6 1.091 ACT T 0.190 17.391 8 0.762 AAG K 0.455 10.870 5 0.909 GTA V(Val) 0.250 15.217 7 1.000 CTA L(Leu) 0.257 19.565 9 1.543 GTC V 0.036 2.174 1 0.143 CTC L 0.114 8.696 4 0.686 GTG V 0.214 13.043 6 0.857 CTG L 0.057 4.348 2 0.343 GTT V 0.500 30.435 14 2.000 CTT L 0.200 15.217 7 1.200
37、TGG W(Trp) 1.000 15.217 7 1.000 TTA L 0.143 10.870 5 0.857 TAC Y(Tyr) 0.217 10.870 5 0.435 TTG L 0.229 17.391 8 1.371 TAT Y 0.783 39.130 18 1.565 ATG M(Met) 1.000 34.783 16 1.000 TAA * 1.000 2.174 1 3.000 AAC N(Asn) 0.143 6.522 3 0.286 TAG * 0.000 0.000 0 0 AAT N 0.857 39.130 18 1.714 TGA * 0.000 0.
38、000 0 0 a. The “Fract” column gives that proportion of usage of a given codon among its redundant set (i.e. the set of codons which code for this codons amino acid); b. The “1/1000” column represents the number of codons, given the input sequence(s), there are per 1000 bases. by EMBOSS. Codon usage
39、in the Us4 gene is highly nonrandom in all the herpesviruses, and the overall base composition of the Us4 genes in these species also differs dramatically. The CAI values of different Us4 genes vary from 0.619 to 0.824, with a mean value of 0.708 and standard deviation (S.D.) of 0.051. The ENC value
40、s of different Us4 genes vary from 29.000 to 59.280, with a mean value of 45.043 and a standard deviation (SD) of 10.239. In general, if the ENC value of a gene is 35 or less, that gene is thought to possess strong codon bias39. Analyzing the ENC values of all the Us4 genes, the results showed the m
41、ajority of them do not have a strong codon bias excepting BaHV-2, PaHV-2, CeHV-2 and SuHV-1 which had high condon bias for the ENC value being 33.152, 33.114, 33.390 and 29.900, respectively. GC3S content of 18 herpesviruses species vary from 15.50 to 93.79% with a mean of 67.20% and SD of 0.239. It
42、 is noticeably that GC content of BaHV-2, PaHV-2, CeHV-2 and SuHV-1 are 80.50%, 80.50%, 80.66% and 71.21%, even the GC3S content reach to 93%. C. Characterization of the DPV Us4 Gene A phylogenetic tree was established from the deduced amino acids encoded by the 1380 bp ORF of the Us4 gene of DPV an
43、d the 17 reference herpesviruses (Fig. 1). It shows that there are mainly two branches for the 17 herpesvirus family. They all belong to Alphaherpesvirinae. DPV has been clustered in one branch. The DPV, GaHV-1, and PsHV-1 are clustered in a distinct subbranch. The identified high amino acid sequenc
44、e similarity suggests that the Us4 protein of DPV is evolutionary closer related to GaHV-1 and PsHV-1. D. Rare condons analysis of the DPV Us4 gene and the comparison codon usage analysis of DPV Us4 gene codon usage bias with E. coli, yeast and human Rare condons analysis showed that there are 36 ra
45、re condons in the ORF of the DPV Us4 by using codon usage database on line (http:/nihserver.mbi.ucla.edu/RACC/). It contained AGG(4), AGA(4), CGA(4), CCC(4), CTA(9), ATA(11), and contained 4 consecutive rare codons (AGGATA, ATACGA, CTACTA, CTAAGA). Data of comparison analysis revealed that there are
46、 25 codons showing distinct usage differences between DPV Us4 and E. coli (a DPV-to-E. coli ratio higher than 2 or lower than 0.50), 25 between DPV Us4 and yeast (a DPV -to-yeast ratio higher than 2 or lower than 0.50), 27 between DPV Us4 and humans(a DPV -to- humans ratio higher than 2 or lower tha
47、n 0.50). Codons usage analysis datas (Fig. 2) shows variation between DPV Us4, E. coli, yeast and humans. Figure 1. Phylogenetic tree based on the Us4 amino acid sequences in 18 herpesviruses (Table 1), and constructed with CLUSTAL-X and MEGA software Figure 2. Comparison of codon usage between DPV
48、and Escherichia coli, yeast and Humans Figure 3. The plot of effective number of codons (ENC) and guanine(G) + cytosine (C) frequency at the synonymous third position of codons(GC3S) of the Us4 gene in the DPV and reference herpesviruses. IV. DISCUSSION It has been well established that synonymous c
49、odon usage in various organisms. Mutational biases and natural selection acting at the level of translation are the most commonly accepted hypothesis for the unequal usage of synonymous codons. With codon usage bias of some viruses, mutational biases may be a more important factor than translational
50、 selection 16,17,40,41. Compared with those of the 17 regerence herpesvirus species, a comprehensive analysis of codon usage including ENC, GC content and the RSCU values of DPV Us4 gene was performed. The data of synonymous codon usage bias showed that A-ended or T-ended codon at the third codon po
51、sition were widely used and the biased trend towards A and T coincides with high A+T content in DPV Us4 gene. So the content of A and/or T ending codons is a important factor. And we also compare Us4 genes in DPV and the reference herpesviruses, the analysis indicated that synonymous codon usage in
52、these genes are phylogenetically conserved. Data in Table 1 show that the Us4 genes in DPV, GaHV-1 and PsHV-1 have similar sequence length and GC content, whose natural host is avian. Simultaneously, form Fig. 1 we can see that DPV was more closely related to Iltovirus in light of the phylogenetic t
53、rees analysis. Therefore we can conclude that species has a centain influence to the preference of codon usage. Codon Adaptation Index (CAI), is a species-dependent codon bias measure, and used as a measure for gene expressivity in studies investigating mutational and selectional 42. The CAI value i
54、s much closer to 1, the codon usage is much stronger, and generally speaking, highly expressed genes are characterized with respect to their strength of codon usage. The mean CAI value for Us4 genes is a slight variation among different species, ranging from 0.619 to 0.824 with a mean value of 0.708
55、 and standard deviation (S.D.) of 0.051. The mean CAI value for Us4 is a little slight lower, we can infer Us4 gene is lowly expressed gene in DPV genome. ENc is the effective number of codons used in a gene which is used to quantify how far the codon usage of a gene departs from equal usage of syno
56、nymous codons and without dependence on sequence length or specific knowledge of preferred codons, although it is affected by base composition 38. Values of ENc can range between 20 (when only one codon is used per amino acid) and 61 (when all synonyms are used with equal frequency). The ENC values
57、of herpesvirus Us4 genes are much lower (61ENC 20), the codon usage bias is more stronger. The ENC value of DPV Us4 is a little slight higher (ENC 40), the codon usage bias is weaker, and there is the great variation in codon usage pattern among different herpesvirus Us4 genes (S.D. = 10.239). GC3s
58、is a good indicator of the extent of base composition bias, which represents the frequency of the nucleotide G+C at the synonymous third position of codons, excluding Met, Trp and the stop codons. The GC3S contents of each Us4 gene also confirm the homogeneity of synonymous codon usage among differe
59、nt Us4 genes of herpesvirus, which range from 15.50 to 93.79% with a mean of 67.20% and S.D. of 0.239. The most commonly accepted hypothesis for the unequal usage of synonymous codons states that it is the result of mutational biases and natural selection acting at the level of translation43. Recent
60、ly, several measures of the degree of codon usage bias in a certain gene have been developed. The ENC value and GC3S content, two important codon usage indices, have been widely used to explore the codon usage variation among different genes 35,44,45. ENC values of each virus gene were plotted again
61、st its corresponding GC3S. It has been reported that a plot of ENC against GC3S can be effectively used to explore the heterogeneity of codon usage among genes33. If G+C compositional constraint influences the codon usage, then the GC3S and ENC correlated spots would lie on46 or just below the expec
62、ted curve. If a gene is subject to selection for translationally optimal codons, it will lie considerably below the expected curve47. In Fig. 3, a large number of points do not follow the theoretical curve, which lie near the solid curve of this distribution, it indicates that codon usage bias has s
63、trong species-specificity between DPV and 17 reference herpesviruses, and suggests that other factors other than gene composition contribute to the codon usage pattern in most of the reference herpesviruses, which maybe mutational bias and natural selection, such as translational selection, lead to
64、the codon usage variation among genes in different organisms. A noticeably higher codon bias was found in BaHV-2, PaHV-2, CeHV-2 and SuHV-1 because of the higher GC% and GC3S% and the lower ENC values. This suggested that nucleotide composition (high GC% and GC3S%) is likely to be the primary factor
65、 behind the significantly high codon bias of the four genes. Analysis of codon usage data has both theoretical and practical importance in understanding the basics of molecular biology. Highly expressed genes displayed much more significant variation in codon usage than genes expressed at lower leve
66、ls, suggesting that codon usage patterns had a functional significance43. From the CAI and ENC value of the DPV Us4, we can infer Us4 gene is lowly expressed gene in DPV genome, the codon usage bias is weaker. And we analyzed the rare condons of the DPV Us4 and the codon usage bias of DPV Us4 with t
67、hose of E. coli, yeast and Humans. There was 36 rare codons and 4 consecutive rare codons in Us4 ORF, which may influence the expression of the Us4 in vitro. In addition, there are 25 codons showing distinct usage differences between DPV Us4 and E. coli, 25 between DPV Us4 and yeast, 27 between DPV
68、Us4 and humans. The codon usage bias pattern in the DPV Us4 gene is distinct with the Escherichia coli, yeast, and Humans. But the E. coli and yeast expression system may be more suitable for the expression of DPV Us4 gene if some codons could be optimized. It can serve as a guide for the expression
69、 of the DPV Us4 gene in a given host. The codons optimized of DPV Us4 gene based on host-preferred codons bias is likely to improve the expression level. All of these may be of great importance for gene characterization and for assessing the possible role of Us4 protein in viral pathogenesis. In sum
70、mary, our work has provided a basic understanding of the evolution and pathogenesis of DPV Us4 gene and offered a useful tool for gene classification, what is more important is some new insights into the mechanisms for codon usage bias and vaccine development to prevent DPV. ACKNOWLEDGMENT The resea
71、rch were supported by grants from, Changjiang Scholars and Innovative Research Team in University(PCSIRT0848), the earmarked fund for Modern Agro-industry Technology Research System (nycytx-45-12), the Cultivation Fund of the Key Scientific and Technical Innovation Project, the Ministry of Education
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