密码子偏性对痘苗病毒载体表达效率影响的研究

为了研究密码子偏性对痘苗病毒载体表达效率的影响,分别采用痘苗病毒及其宿主细胞的优势密码子对绿色荧光蛋白基因进行改造,利用荧光、Western blot和FCM等方法分析其在痘苗病毒载体系统的表达水平。结果显示,全部采用痘苗病毒优势密码子(富含A T)和全部采用宿主细胞优势密码子(富含G C),以及部分使用宿主细胞优势密码子的三种绿色荧光蛋白基因都能够有效表达,表达水平相近,表明痘苗病毒载体对目的基因密码子的使用具有很好宽容性。为了探讨这种宽容性的机理,分别利用在胞核内和在胞浆内转录的质粒载体对不同密码子偏性的绿色荧光蛋白基因进行表达分析。结果显示,胞核内转录目的基因的pcDNA3质粒载体能有效表达富含G C的绿色荧光蛋白基因,不能有效表达富含A T的绿色荧光蛋白基因,而胞浆内转录目的基因的pSCA质粒载体能同样有效表达上述不同密码子偏性的目的基因。这些结果表明,位于胞浆内的富含A U的转录产物能够有效表达,细胞核内生成的富含A U的转录产物可能受核膜屏障或其它核内因素影响而不能有效表达。因此,胞浆内繁殖的特性是痘苗病毒载体具有密码子宽容性的主要原因。此研究为痘苗病毒载体和常用真核表达载体的选择使用提供了重要实验依据。     

按痘苗病毒优势密码子改造HIV-1 gag基因提高表达水平的研究

为确定痘苗病毒密码子偏向性与基因表达的关系及其在痘苗病毒与宿主细胞相互作用过程中的作用,按痘苗病毒的优势密码子对HIV-1 gag基因进行改造,并对合成基因与野生型HIV-1 gag基因在痘苗病毒载体系统的表达水平进行了研究。结果显示：①各目的基因分别正向插入了痘苗病毒TK区7．5k启动子下游;②免疫荧光检测显示,改造前后的gag基因均能够很好地在痘苗病毒中表达;③Western blot检测显示,在相同感染量时,改造后的gag基因具有更高的表达水平;④流式细胞术检测显示,密码子改造后的gag基因较野生型gag基因表达水平提高约17％。上述结果表明：按照痘苗病毒优势密码子进行外源基因改造,可作为提高外源基因在痘苗病毒中表达的策略,同时提示,密码子偏向性是痘苗病毒与宿主细胞相互作用的重要调控因素。     

病毒密码子使用频率研究进展

密码子使用频率的研究多集中在自养生物中,对于寄生生物如病毒的研究相对较少,近些年的研究表明某些病毒基因的密码子使用频率和宿主细胞不完全匹配,密码子使用在病毒和宿主的相互作用中起了重要的作用。本对病毒密码子使用频率的特点,影响病毒密码子使用频率的因素,几种典型病毒的密码子使用特点和密码子使用频率研究的方法做了论述。     

寨卡病毒基因组密码子偏爱性分析

寨卡病毒是一类对人类危害极重的RNA病毒,为了解其密码子使用特点和主要影响因素,本研究采用CHIPS、CUSP、Codon W和SPSS软件对寨卡病毒所有基因序列进行了偏爱性分析和多元统计分析,获得了每个基因密码子3个位置的GC含量和ENC值以及所有基因序列的RSCU值,并与大肠杆菌、酵母、人的密码子使用频率进行了对比分析。结果显示,寨卡病毒GC3含量相对较高,为54.14%,ENC值为52.54,表明该病毒密码子偏爱性偏低且偏爱以G、C、A碱基结尾的密码子,这和一般病毒的偏爱性有所不同。中性绘图和ENC绘图分析表明密码子的偏爱性主要受到选择作用的影响。通过和其它3种生物密码子使用频率进行比较,发现其与人的密码子使用频率相差最小。在此基础上确定了寨卡的18个最优密码子。研究结果对寨卡病毒寻找最佳宿主进行体外表达,从而研发基因工程疫苗及治疗性抗体具有一定的意义。     

中东呼吸综合征冠状病毒结构蛋白与附属蛋白编码基因密码子偏爱性分析

中东呼吸综合征冠状病毒是一类对人类危害极重的RNA病毒,为了解其密码子使用特点和主要影响因素,该文采用CHIPS、CUSP、CodonW和SPSS软件对MERS-CoV 9条基因序列进行了偏爱性分析和多元统计分析,获得了每个基因密码子3个位置的GC含量和ENC值以及所有基因序列的RSCU值,并与大肠杆菌、酵母、人的密码子使用频率进行了对比分析。结果显示GC3明显低于GC2、GC1且小于50%,ENC值为50.59,表明该病毒密码子偏爱性偏低且偏爱以A、T碱基结尾的密码子。中性绘图和ENC绘图分析表明密码子的偏爱性主要受到选择作用的影响。通过和其它三种生物密码子使用频率进行比较,发现其与酵母密码子使用频率相差最小。在此基础上确定了MERS-CoV的19个最优密码子。研究结果对MERS-CoV寻找最佳宿主进行体外表达,从而研发基因工程疫苗及治疗性抗体具有一定的意义。     

杨树派间不同种的遗传密码子使用频率分析

遗传密码子的简并性特征造成了不同物种使用的密码子存在偏爱性。了解不同物种的密码子使用特点,可以为外源基因导入过程中的基因改造提供依据,从而实现外源基因的高效表达。杨树是世界上广泛栽培的重要造林树种之一,已经成为林木基因工程研究的模式植物。本研究采用高频密码子分析法,对美洲山杨P.tremuloides,毛白杨P.tomentosa,美洲黑杨P.deltoids和毛果杨P.trichocarpa 4种杨树的蛋白质编码基因序列(CDS)进行了分析,计算出了杨树同义密码子相对使用频率(RFSC),确定了4种杨树的高频率密码子,发现虽然不同种类的杨树密码子使用上有一些差别,但是偏爱密码子的差别却很小,共性的密码子占绝大多数。仅有Pro,Thr和Cys等少数几个氨基酸的偏爱密码子有差别。这种“共性”提示我们,用不同种的杨树中任何一种杨树的偏爱密码子所设计的外源基因在其他杨树中也可以使用。     

人埃博拉病毒密码子偏爱性与聚类分析

埃博拉病毒(Ebola virus,EBOV)宿主广泛,其遗传进化关系复杂,影响埃博拉病毒密码子偏爱性的因素众多。为了明确人埃博拉病毒密码子使用的偏爱性,揭示影响其偏爱性的影响因素和不同宿主来源的埃博拉病毒间的遗传进化关系。本研究通过计算有效密码子数(Effective number of codons,ENC),同义密码子相对使用频率(Relative synonymous codon usage,RSCU)和其他指标,对人埃博拉病毒的密码子使用模式进行综合分析。结果显示,人埃博拉病毒各蛋白的ENC均值分布于55.66～55.77,RSCU1的密码子中77%以上都是以A/U结尾。中性绘图分析和PR2绘图分析等相关分析表明,自然选择是影响密码子使用模式的主要因素,突变压力的影响相对较小。聚类分析结果表明,猪和人来源的埃博拉病毒亲缘关系最近,提示猪来源的埃博拉病毒感染人的风险最大。新发现的bombali型埃博拉病毒与人的亲缘关系距离较远,在大多数蛋白中均单独聚类。本研究结果对深入了解人埃博拉病毒的遗传进化关系,进而研究埃博拉疫苗和制备抗体具有重大意义。     

溶瘤痘苗病毒对肿瘤细胞作用机制的研究进展

溶瘤病毒治疗,是指利用具有复制能力的病毒选择性地感染和摧毁癌细胞,而对正常细胞或组织影响很少甚至没有影响的一种癌症治疗方法.痘苗病毒在肿瘤的基因治疗应用研究中以其独特的优势而备受关注.痘苗病毒感染细胞后具有产生病毒颗粒快、宿主范围广、基因组容量大、安全性高、传播高效等优点.尤为重要的是,基于溶瘤痘苗病毒的天然特性或遗传工程的改造,溶瘤痘苗病毒可以选择性地在肿瘤细胞中复制并对其产生杀伤效果.痘苗溶瘤病毒引起肿瘤细胞裂解和死亡是由多种不同的机制引起的.本文就近年来溶瘤痘苗病毒对细胞作用机制和相关信号通路的影响作一简要综述.     

病毒-宿主密码子使用的若干统计特征及其协同进化

基于归1000密码子使用频次,从垂直和水平两个方向研究了不同进化阶层宿主-病毒密码子使用的若干统计特征及其协同进化规律。结果表明,病毒密码子和氨基酸多样性总体上高于相应宿主;细菌-噬菌体、真菌-真菌病毒、无脊椎动物-无脊椎动物病毒的密码子使用频次匹配较好,细菌-噬菌体、无脊椎动物-无脊椎动物病毒的氨基酸丰度匹配较好;病毒基因AU含量、AU3s含量总体上高于相应宿主;病毒和宿主密码子第一位碱基含量均GA>CU;密码子第二位碱基含量均A>U>C>G;病毒与宿主编码区碱基的相对分子量和相对π电子共振能总体上存在较明显的跟随现象。病毒和宿主基因在密码子使用频次等多个统计特征方面既呈现协同进化趋势,又有较明显的分化。     

H1N1流感病毒聚合酶片段的CpG抑制及其对密码子偏爱性的影响

H1N1流感病毒的聚合酶具有RNA复制、转录等功能,并且对流感病毒片段包装、子代繁殖及宿主适应性等有着重要作用。通过分析人、猪及禽类H1N1流感病毒聚合酶片段的二核苷酸频率及同义密码子的偏爱性,发现不同宿主中,流感病毒聚合酶片段的CpG频率最低,且均被强烈抑制;通过三类宿主间的比较发现,人流感病毒抑制最为强烈,且其CpG频率随年份呈下降趋势,但2009年毒株的CpG频率突然上升。比较同义密码子使用频率发现,含有CpG的同义密码子相对使用频率均小于1,证明CpG抑制作用是影响同义密码子偏爱性的一个重要因素。以上结果暗示,CpG抑制对H1N1流感病毒的进化及跨宿主传播可能有重要影响。     

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.Key words: correspondence analysis, synonymous codon usage, horizontal gene transfer, strand-specific mutational bias, translational selection     

Analysis of synonymous codon usage in 11 human bocavirus isolates

Human Bocavirus (HBoV) is a novel virus which can cause respiratory tract disease in infants or children. In this study, the codon usage bias and the base composition variations in the available 11 complete HBoV genome sequences have been investigated. Although, there is a significant variation in codon usage bias among different HBoV genes, codon usage bias in HBoV is a little slight, which is mainly determined by the base compositions on the third codon position and the effective number of codons (ENC) value. The results of correspondence analysis (COA) and Spearman's rank correlation analysis reveals that the G + C compositional constraint is the main factor that determines the codon usage bias in HBoV and the gene's function also contributes to the codon usage in this virus. Moreover, it was found that the hydrophobicity of each protein and the gene length are also critical in affecting these viruses’ codon usage, although they were less important than that of the mutational bias and the genes’ function. At last, the relative synonymous codon usage (RSCU) of 44 genes from these 11 HBoV isolates is analyzed using a hierarchical cluster method. The result suggests that genes with same function yet from different isolates are classified into the same lineage and it does not depend on geographical location. These conclusions not only can offer an insight into the codon usage patterns and gene classification of HBoV, but also may help in increasing the efficiency of gene delivery/expression systems.     

Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity.

The genetic code is degenerate, but alternative synonymous codons are generally not used with equal frequency. Since the pioneering work of Grantham's group it has been apparent that genes from one species often share similarities in codon frequency; under the "genome hypothesis" there is a species-specific pattern to codon usage. However, it has become clear that in most species there are also considerable differences among genes. Multivariate analyses have revealed that in each species so far examined there is a single major trend in codon usage among genes, usually from highly biased to more nearly even usage of synonymous codons. Thus, to represent the codon usage pattern of an organism it is not sufficient to sum over all genes as this conceals the underlying heterogeneity. Rather, it is necessary to describe the trend among genes seen in that species. We illustrate these trends for six species where codon usage has been examined in detail, by presenting the pooled codon usage for the 10% of genes at either end of the major trend. Closely-related organisms have similar patterns of codon usage, and so the six species in Table 1 are representative of wider groups. For example, with respect to codon usage, Salmonella typhimurium closely resembles E. coli, while all mammalian species so far examined (principally mouse, rat and cow) largely resemble humans.     

Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern

Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irrespective of their near universality. A clear distinction in the codon usage pattern of gram positive and gram negative bacteria, which is a major classification criterion for bacteria, in terms of pentose phosphate pathway was an important observation of this study. The codon utilization scheme in all the organisms indicates the presence of translation selection as a major force in shaping codon usage. Another key observation was the segregation of the H. sapiens genes as a separate cluster by correspondence analysis, which is primarily attributed to the different codon usage pattern in this genus along with its longer gene lengths. We have also analyzed the amino acid distribution comparison of transketolase protein primary structures among all the organisms and found that there is a certain degree of predictability in the composition profile except in A. fumigatus and H. sapiens, where few exceptions are prominent. In A. fumigatus, a human pathogen responsible for invasive aspergillosis, a significantly different codon usage pattern, which finally translated into its amino acid composition model portraying a unique profile in a key pentose phosphate pathway enzyme transketolase was observed.     

Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes

To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.     

Codon usage bias: causative factors,quantification methods and genome‐wide patterns: with emphasis on insect genomes

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole‐genome sequencing of numerous species, both prokaryotes and eukaryotes, genome‐wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole‐genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome‐sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome‐sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.     

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens

The role of silent position in the codon on the protein structure is an interesting and yet unclear problem. In this paper, 563 Homo sapiens genes and 417 Escherichia coli genes coding for proteins with four different folding types have been analyzed using variance analysis, a multivariate analysis method newly used in codon usage analysis, to find the correlation between amino acid composition, synonymous codon, and protein structure in different organisms. It has been found that in E. coli, both amino acid compositions in differently folded proteins and synonymous codon usage in different gene classes coding for differently folded proteins are significantly different. It was also found that only amino acid composition is different in different protein classes in H. sapiens. There is no universal correlation between synonymous codon usage and protein structure in these two different organisms. Further analysis has shown that GC content on the second codon position can distinguish coding genes for different folded proteins in both organisms.     

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome 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 the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. 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.