Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus

The analysis on codon usage bias of UL24 gene of duck enteritis virus (DEV) may improve our understanding of the evolution and pathogenesis of DEV 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. The codon usage bias of UL24 genes of DEV and 27 reference herpesviruses were analyzed. The results showed that codon of UL24 gene of DEV was strong bias toward 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 UL24 gene of herpesviruses was constrained by the G + C content. The phylogentic analysis suggested that DEV was evolutionarily closer to Alphaherpesvirinae and that there was no significant deviation in codon usage in different virus strains. There were 20 codons showing distinct usage differences between DEV and Escherichia coli, 23 between DEV and Homo sapiens, but only 16 codons between DEV and yeast. Therefore the yeast expression system may be more suitable for the expression of DEV genes. Renyong Jia, Anchun Cheng, Mingshu Wang, and Hongyi Xin contributed equally to this work and should be considered as first author.     

Lost in translation: implications of HIV-1 codon usage for immune escape and drug resistance

Synonymous nucleotide substitutions in protein-coding sequences are often regarded as evolutionarily neutral and not subject to selective pressure. However, synonymous codons can sometimes lead to different patterns of amino acid substitution by single nucleotide changes. Based on the deconstruction of the standard genetic code, we propose the term 'quasi-synonymous' to describe codons that specify the same amino acid, but lie on different mutational pathways, and we show that in at least one rapidly evolving organism, HIV-1, quasi-synonymy plays a role in its evolution. We present concrete examples that demonstrate the relevance of codon usage in the development of antiretroviral-drug resistance. In the case of the host immune response, the data indicates that viral evasion is achieved through use of codons that lie on the direct path to escape mutants, and equally, permit rapid reversion to wild-type in the absence of these selective pressures. Quasi-synonymy conditions HIV-1 and, potentially, other rapidly evolving organisms in their exploration of the mutational space.     

The extent of codon usage bias in human RNA viruses and its evolutionary origin

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there is little variation in bias between genes. Furthermore, the strong correlation between base and dinucleotide composition and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. However, we also detected correlations between codon usage bias and some characteristics of viral genome structure and ecology, with increased bias in segmented and aerosol-transmitted viruses and decreased bias in vector-borne viruses. This suggests that translational selection may also have some influence in shaping codon usage bias.     

Detection,genetic, and codon usage bias analyses of the VP2 gene of mink bocavirus

Virus Genes - Mink bocavirus 1 (MiBoV1), a novel virus detected from the feces of domestic minks in China in 2016, may be related to gastrointestinal diseases. However, its prevalence and genetic...     

An extensive analysis on the global codon usage pattern of baculoviruses

Baculovirus-insect cell systems have been widely used over the past decades. However, few studies to date have addressed baculovirus codon usage. In this study, we calculated the effective number of codons (ENC) for all 5,842 ORFs from 42 completely sequenced baculoviruses. The results revealed that most of the baculoviruses lacked strong codon bias (ENC > 35). Exceptions were Lymantria dispar nucleopolyhedrovirus (LdMNPV) and Orgyia pseudotsugata nucleopolyhedrovirus (OpMNPV), which were found to have a strong codon bias (ENC < 35) in 20.9 and 11.8%, respectively, of their total genes. Comparisons of preferred codons based on taxonomic clades showed that the preferred codons were different in different clades, but nine codons (UUU, UAC, UUG, CAC, CAA, AAA, GUG, GAA, and AUU) were preferably adopted by most baculovirus genes. Correspondence analysis showed that the major trend in codon usage variation among all genes significantly correlated with the GC content of sequences. Analyses also suggested that the high condon bias of LdMNPV and OpMNPV were correlated with their high GC%.     

优化密码促进HPV 6b E7蛋白表达及DNA疫苗诱导的细胞免疫反应

目的：探讨优化密码对人乳头瘤病毒6b型（HPV 6b）基因表达及免疫原性的影响，为治疗性DNA疫苗的研究奠定基础。方法：设计合成含优化密码及pRB结合位点突变的HPV 6bE7(humE7）全长基因。测序验证无误后，定向克隆于pcDNA3的Kpn I和EcoR I位点，成功构建真核表达质粒pcDNA3-hu-mE7。体外转染COS－1细胞，免疫荧光检测其E7蛋白表达。C57BL／6小鼠胫前肌内接种裸DNA，观察其诱导的细胞免疫反应。结果：pcDNA3-hu-mE7在COS－1细胞获得明显表达，表达产物主要位于细胞核中。DNA免疫结果显示，与含有野生型E7基因的表达质粒pcDNA3-wtE7比较，pcDNA3-hu-mE7免疫小鼠脾细胞培养上清中IFN-γ产生明显升高，CD8^ 和CD4^ 淋巴细胞活性增强。结论：优化密码能促进HPV 6b E7蛋白表达及DNA疫苗诱导的细胞免疫反应。     

Codon usage bias of the phosphoprotein gene of spring viraemia of carp virus and high codon adaptation to the host

In this study, we calculated the relative synonymous codon usage (RSCU) value and the effective number of codons (ENC) value to carry out principal component analysis (PCA) and correlation analysis of the codon usage pattern of the phosphoprotein gene (P gene) of spring viraemia of carp virus (SVCV). The synonymous codon usage pattern in P genes is geography-specific, based on PCA analysis. The high correlation between (G + C)_1,2 % and (G + C)₃ % suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base components in P genes. At least 40 out of 59 synonymous codons are similarly selected in all functional genes within five complete SVCV genomes, and the hosts based on the RSCU data. These results not only provide insight into variations in the codon usage pattern of SVCV but also may help in understanding the processes governing the evolution of SVCV.     

Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales

In this study, we calculated the codon usage bias in severe acute respiratory syndrome Coronavirus (SARSCoV) and performed a comparative analysis of synonymous codon usage patterns in SARSCoV and 10 other evolutionary related viruses in the Nidovirales. Although there is a significant variation in codon usage bias among different SARSCoV genes, codon usage bias in SARSCoV is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that synonymous codon usage pattern in these virus genes was virus specific and phylogenetically conserved, but it was not host specific. Phylogenetic analysis based on codon usage pattern suggested that SARSCoV was diverged far from all three known groups of Coronavirus. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.     

A detailed comparative analysis on the overall codon usage patterns in hepatitis A virus

Hepatitis A virus (HAV) is a hepatotropic member of the family Picornaviridae. HAV has several unique biological characteristics that distinguish it from other members of this family. Recent and previous studies revealed that codon usage plays a key role in HAV replication and evolution. In this study, the patterns of synonymous codon usage in HAV have been studied through multivariate statistical methods on 30 complete open reading frames (ORFs) from the available 30 full-length HAV sequences. Effective number of codons (ENC) indicates that the overall extent of codon usage bias in HAV genomes is significant. The relative dinucleotide abundances suggest that codon usage in HAV can also be strongly influenced by underlying biases in dinucleotide frequencies. These factors strongly correlated with the first major axis of correspondence analysis (COA) on relative synonymous codon usage (RSCU). The distribution of the HAV ORFs along the plane defined by the first two major axes in COA showed that different genotypes are located at different places in the plane, suggesting that HAV codon usage is also reflecting an evolutionary process. It has been very recently described that fine-tuning translation kinetics selection also contributes to codon usage bias of HAV. The results of these studies suggest that HAV genomic biases are the result of the co-evolution of genome composition, controlled translation kinetics and probably the ability to escape the antiviral cell responses.     

Analysis of codon usage bias and base compositional constraints in iridovirus genomes

The codon usage bias and the base composition variations in the available 12 complete iridovirus genome sequences have been investigated. We re-evaluated the number of open reading frames (ORFs) in each published iridovirus genome and analyzed its correlation against the genome size. The result shows that there is a direct relationship between the number of ORFs and the genome size. The codon usage patterns of these iridoviruses are found to be phylogenetically conserved. A significant variation in the base content among the 12 iridovirus genomes has been observed, with G+C content ranges widely from 27 to 55%. Moreover, the preferential use of bases in codons is different among higher and lower G+C content genomes. A preferential codon usage among viral genomes is also noticed. Effective number of codon (Enc) plot reveals that the G+C compositional constraint is the main factor that determines the codon usage bias. Relative synonymous codon usage analysis of methyltransferase containing as well as lacking viruses suggests that the codon usage is not influenced by the methylation-mediated mutation. In addition, the comparison of the codon usage of iridovirus hosts and the iridovirus genomes reveals that the host tRNA pool may be responsible for the base compositional constraint. This study represents the most comprehensive analysis to date for iridovirus codon usage patterns.     

Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus

Foot-and-mouth disease (FMD) is economically the most important viral-induced livestock disease worldwide. In this study, we report the results of a survey of codon usage bias of FMD virus (FMDV) representing all seven serotypes (A, O, C, Asia 1, SAT 1, SAT 2, and SAT 3). Correspondence analysis, a commonly used multivariate statistical approach, was carried out to analyze synonymous codon usage bias. The analysis showed that the overall extent of codon usage bias in FMDV is low. Furthermore, the good correlation between the frequency of G + C at the synonymous third position of sense codons (GC_3S) content at silent sites of each sequence and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. In addition, other factors, such as the lengths of open reading frame (ORF) and the hydrophobicity of genes also influence the codon usage variation among the genomes of FMDV in a minor way. The result of phylogenetic analyses based on the relative synonymous codon usage (RSCU) values indicated a few obvious phylogenetic incongruities, which suggest that more FMDV genome diversity may exist in nature than is currently indicated. Our work might give some clues to the features of FMDV genome and some evolutionary information of this virus.     

Consistency of the lateral canthus as an anatomic landmark and its clinical implications

Successful oculofacial procedures require the availability of a reliable surgical and anatomic landmark. This study aimed to determine the usefulness of the lateral canthus as a surface landmark. Seventy‐seven from 42 Korean cadavers were dissected. The horizontal distance from the lateral canthus to the lateral orbital margin and the vertical distances from the zygomaticofrontal suture and the inferior orbital margin to the lateral canthus were measured. The mean horizontal distance from the lateral canthus to the lateral orbital margin was 7.8 mm. Although the horizontal position of the lateral canthus appears to alter with age, the variation was only 2–3 mm. The mean vertical distances from the zygomaticofrontal suture and inferior orbital margin to the lateral canthus were 8.1 and 17.2 mm. The vertical position of the lateral canthus did not vary with age, being located inferiorly within a fingernail width from the zygomaticofrontal suture. The lateral canthus, which is easily accessible and supported by muscular and fibrous lateral orbital attachments, exhibits small anatomic variations. Thus, the lateral canthus could act as a reliable surface landmark for identifying the location of underlying structures and describing a lesion on the face. Clin. Anat. 32:630–634, 2019. © 2019 Wiley Periodicals, Inc.     

Host-related nucleotide composition and codon usage as driving forces in the recent evolution of the Astroviridae

The evolutionary history of the Astroviridae comprises the ancient separation between avian and mammalian astrovirus lineages followed by diversification among mammalian astroviruses. The latter process included several cross-species transmissions. We found that the recent, but not the ancient, evolution of astroviruses was associated with a switch in nucleotide composition and codon usage among non-human mammalian versus human/avian astroviruses. Virus and hosts phylogenies based on codon usage agreed with each other and matched the hosts' evolutionary emergence order. This recent switch in driving forces acting at the synonymous level points to the adaptation of codon usage by viruses to that of their hosts after cross-species transmissions. This is the first demonstration of nucleotide composition and codon usage being active driving forces during the recent evolutionary history of a virus group in the host-parasite system.     

Influence of codon usage and translation initiation codon context in theAcNPV-based expression system: Computer analysis using homologous and heterologous genes

Codon usage by all the known gene sequences fromAutographa californica nuclear polyhedrosis virus (AcNPV) was compared with that of firefly luciferase (luc) and the beta subunit of human chorionic gonadotropin (hCG) expressed to contrasting levels in the baculovirus system. The highly expressedluc gene showed a codon usage similar toAcNPV genes, as reflected by a very low D-squared statistic value (0.78) and a similar G/C usage (45%) at wobble positions. However, the underexpressed hCG gene displayed a high D-squared value (7.3) and G/C usage (82.5%) at the wobble base positions. Alignment of the 20 nucleotides around the initiation codon of 23AcNPV genes identified a novel consensus translation initiation sequence aag/ta/tat/aa/cAAaATGaa/ct/ag/aAan, which was quite different from the Kozak consensus sequence (GCC)GCCA/GCCATGG. An extension of these analyses to a sample of other heterologous genes overexpressed and underexpressed in BEVS suggested similar trends. These theoretical analyses have important implications for heterologous gene expression in this system.     

Studies on gene transfer and reversion to UV resistance in xeroderma pigmentosum cells

We have examined several parameters which address the feasibility of complementing the UV-sensitive phenotype of xeroderma pigmentosum (XP) fibroblasts by gene transfer. We present a comparative study which demonstrates that, relative to immortalized cells, human diploid cells are poor recipients for gene transfer. As measured by both transient and stable expression assays, diploid fibroblasts were completely refractory to DNA transfer by calcium phosphate coprecipitation and exhibited substantially reduced levels of expression following gene transfer by fusion with E. coli protoplasts. We also examined the significance of reversion of the phenotype of UV sensitivity in SV40-immortalized XP-A cell lines. In addition to confirming a previous report of reversion to wild-type levels of UV resistance at a frequency of 10^–7, we have attempted to facilitate the identification of XP-A cells complemented with genomic DNA by employing less stringent selection schemes and cotransfection of a selectable marker. Under these conditions, we observed an increased frequency of reversion and were unable to identify true transfectants.     

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids

We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the genomic changes following symbiosis. We identified clear strand asymmetries, distribution biases (putative high-expression genes were found more often on the leading strand), and a residual slight codon bias within each strand. Amino acid usage was strongly biased in putative high-expression genes, characterized by avoidance of aromatic amino acids, but above all by greater conservation and resistance to AT enrichment. Despite the almost complete loss of codon bias and heavy mutational pressure, selective forces are still strong at nonsynonymous sites of a fraction of the genome. However, Buchnera from Baizongia pistaciae appears to have suffered a stronger symbiotic syndrome than the two other species.     

Detection and widespread distribution of Chlamydia pneumoniae in the vascular system and its possible implications.

AIMS: To attempt to detect Chlamydia pneumoniae DNA in atheromatous vascular tissue. METHODS: A modification of an existing polymerase chain reaction (PCR) assay and immunofluorescence staining with a monoclonal antibody directed against C pneumoniae were used to detect C pneumoniae. Specimens from 32 patients undergoing abdominal aortic aneurysm repair were examined. Vascular tissue, ostensibly normal, from six liver transplant donors was also examined for comparison. Altogether, 43 vessels from these 38 subjects (age range 36-85 years) were examined. RESULTS: C pneumoniae was detected in 11 (44%) of 25 aortas, five (55%) of nine iliac arteries, two (40%) of five femoral arteries, and one of two iliac veins. Immunofluorescence staining supported positive PCR results in three of 12 cases in which it was used. Overall, C pneumoniae was detected in the arteries of 14 (44%) of the patients undergoing vascular surgery and three (50%) of the donors. CONCLUSIONS: This study is the first in the UK in which C pneumoniae organisms have been found in atherosclerotic vessels and the tendency for the organisms to be present most often in such vessels exhibiting chronic inflammatory changes suggests that a search for them in various forms of arteritis may also be rewarding.