用图论方法研究核酸序列的密码子使用与基因表达水平的关系

研究了Escherichiacoli（115个基因）和SacharomycesYeast（97个基因）核酸序列的密码子使用频率与基因表达水平的关系．将同义密码子按使用频率统计值分成三种特性的密码子：最适密码子（H）、非最适密码子（L）和稀有密码子（R）,对每一基因序列的编码区,算出它们各自出现的概率P（H）,P（L）和P（R）．以P（H）和P（R）为指标,用图论法聚类,发现每种生物的高低表达基因明显分开,基因表达水平被分为四级：甚高表达基因（VH）、高表达基因（H）、较低表达基因（LM）和低表达基因（LL）．每类基因的表达水平与实验结果保持了很好的相关性,与E．coli和Yeast的现有资料相比,符合很好．     

转座因子对水稻同义密码子使用偏性的影响

利用635个包含完整转座因子插入的粳稻CDS序列,对转座因子如何影响基因编码区的碱基组成及基因的表达水平,进而对基因同义密码子的使用偏性产生影响进行了详细分析。结果表明:转座因子插入极显著地影响到基因编码区的同义密码子使用但并非唯一因素;转座因子对不同基因的表达水平具有多重影响,有的基因表达被抑制,有的反而增强,但总的来说它减少了基因表达水平对同义密码子使用的影响程度。     

同义密码子通过精微翻译选择机制实现对基因的表达调控

自然界中,同义密码子的存在使得众多氨基酸能够同时被多种密码子编码合成。随着研究的深入,同义密码子使用偏嗜性发挥出的生物学功能已经渗透到了基因复制、转录、翻译以及化学修饰等生命活动过程中。基于同义密码子使用偏嗜性的生物学特性,陆续发现密码子对(codon pair)和密码子共现(codon co-occurrence)同样在使用模式上存在明显的偏嗜性。在基因表达的过程中,针对编码序列的密码子优化能够显著提升基因的表达水平,这在生物工程领域对于蛋白表达有着重要的生物学意义。此外,同义密码子使用模式在调控基因转录、化学修饰以及翻译过程中间接控制着细胞内生命活动的有序性。而这些与同义密码子使用模式有着千丝万缕联系的生命过程主要是受精微翻译选择压力来调控运行的。本文中,我们结合当前同义密码子使用模式介导的精微翻译选择压力,简述密码子使用模式如何从转录、化学修饰以及翻译等方面来影响基因表达及蛋白产物生物学功能。这将为今后生物工程学领域如何优化蛋白高效表达以及深入研究重要生物学活动中基因表达调控提供可参考的思路与理念。     

影响链球菌属肺炎球菌基因组密码子使用的因素分析

链球菌属肺炎球菌（Steptococcus pneumoniae)的完整基因组序列已经测定完毕并于近期发表,对肺炎球菌基因组序列进行了详细分析,研究了基因组密码子的使用模式和影响密码子使用的因素,高水平高达基因的密码子第三位碱基使用胞嘧啶（C）的频率比表达水平低的基因使用C有显著的提高,表达水平较低的基因在密码子的第三位碱基更趋向使用嘌呤）,基因的表达水平与对应分析的第一条向量轴呈显著相关（R＝0．86）,比较表达水平高,低的两组基因的密码子使用模式发现,基因的表达水平对于密码子使用有显著的影响,基因碱基G＋C的组成与基因的表达水平（R＝0．44）,对应分析的第一条向量轴（R＝0．5）有显著的相关,对基因的表达水平,密码子的使用有显著的影响,通过GC－skew,蛋白质的疏水性,基因的长度分析,发现不同长度的基因表达水平,GC含量,GC3s有差异,结果表明,在表达水平上的自然选择以及基因的碱基组成是影响肺炎球菌基因密码子使用的主要因素,基因的长度对密码子的使用有一定影响。     

影响鼻疽伯克霍尔德氏菌基因组密码子用法的因素分析

鼻疽伯克霍尔德氏菌(Burkholderia mallei ATCC 23344)的基因组密码子使用受多种因素的影响,本研究根据该菌的完整基因组序列,运用多元统计分析和对应分析的方法,探讨了鼻疽伯克霍尔德氏菌全基因组序列密码子的使用模式和影响密码子使用的因素。结果表明基因表达水平的高低是影响密码子使用的主要因素;基因组中编码区的碱基组成、蛋白质的疏水性和基因的长度对密码子的使用也有一定的影响,但影响力不及基因的表达水平。同时,通过比较高表达的基因、低表达的基因密码子使用情况,GCG 和 CUC 等 21 个密码子被确定为鼻疽伯克霍尔德氏菌的主要偏爱密码子。以上结果对鼻疽伯克霍尔德氏菌的密码子用法研究、在分子水平上研究物种进化、基因组中未知基因的预测、开放阅读框的判断、功能基因的表达以及鼻疽病疫苗的研发等工作都提供了理论基础,具有较强的指导作用。     

籼稻品种93-11同义密码子的使用偏性

利用籼稻品种93－11的全基因组序列及相应的EST数据,对影响同义密码子用法的若干因子进行了详细分析。指出93－11基因的表达水平（mRNA丰度）与3个同义密码子偏性指标CAI、CPP和ENC相关极显著（r=0.227^**,0.145^**和-0.147^**),表明高表达的基因其同义密码子非随机使用的程度越大;基因长度与CAI和CPP极显著负相关（r=-0.413^**和-0.480^**),与ENC极显著正相关（r=0.210^**),暗示较短的基因具有更高的转录活性;编码区G＋C含量对其同义密码子偏性的贡献率远高于mRNA丰度和基因长度,G＋C含量与CAI、CPP和ENC相关系数分别高达0.877^**,0.832^**和-0.740^**;起始编码区内A、T、C、G4种碱基呈明显的3周期振荡,尤以ATG下游第一个密码子所在的3个位点（＋4、＋5和＋6）偏置最强烈,由此认为在这3个特殊位点有较高的自然选择压存在;93－11中25个最优密码子的首次确定将对水稻转基因具有指导意义。     

鸡基因组差异表达基因翻译起始密码子上下游序列的比较研究

翻译起始调控是基因表达调控的一个关键步骤之一。本文以鸡为研究材料,比较研究了鸡基因组高表达基因和低表达基因翻译起始密码子上下游的碱基序列差异,旨在寻找影响鸡基因表达水平的特异性调控位点。全部3 020个单剪接基因完整的mRNA序列及有详细注释的5＇UTRs序列从Ensembl下载。编写计算机程序,读取每个基因mRNA起始密码子上下游各位点的碱基。研究发现,起始密码子上游-3、-2位点可能是鸡基因组基因表达起始密码子正确识别的关键位点。起始密码子上下游的碱基组成分析发现,高表达基因和低表达基因起始密码子的上游均倾向使用（G＋C）,高表达基因的使用偏倚尤为强烈。序列差异比较发现,高表达基因在-9、-6、-3、＋4位点显著偏向G,在-1、-2、-4、-5位点显著偏向C。低表达基因起始密码子上游使用A、U的频率显著高于低表达基因。在-19位点强烈偏向A,在＋1、＋11、＋14位点强烈偏向U。     

双孢蘑菇基因组密码子的偏好性分析

双孢蘑菇Agaricus bisporus是世界上最广泛栽培的食用菌之一。本研究通过分析双孢蘑菇基因组密码子使用偏性,探讨密码子偏性的影响因素及其对基因表达的影响。以双孢蘑菇基因组和转录组数据为依据,分析了双孢蘑菇基因组基因、高表达基因（high expression gene,HEG）和低表达基因（low expression gene,LEG）的密码子使用性。发现双孢蘑菇基因组编码基因平均GC含量为49.08%,T3s值（35.59%）最高,平均ENC值偏高,多数基因表达潜力较低。共鉴定出14个最优密码子,均以C或T结尾,并且遵循密码子中嘌呤和嘧啶使用的均衡性原则。高表达基因具有更强的密码子偏性,进化过程中受到基因突变和自然选择等多种因素影响。基因表达与G/C碱基含量和CAI值呈极显著正相关。高表达基因编码了多种与真菌生长发育相关的蛋白和酶类。研究结果明确了双孢蘑菇基因密码子的使用偏性,为双孢蘑菇转基因育种和品质改良提供了参考。     

同义密码子使用偏嗜性对mRNA半衰期及翻译调控的影响北大核心CSCD

随着基因组学和转录组学在不同生物体遗传和细胞生物学领域的广泛应用,同义密码子使用的偏嗜性逐渐被接受,并且在研究生物进化与生物表型之间的深层联系时,同义密码子使用模式受到相关领域研究人员的重视。信使RNA(messenger RNA,mRNA)最终表达出具有正常生物活性的蛋白产物是生命活动的重要环节。被称为“第二遗传密码”的同义密码子使用模式,可以通过精微调控翻译选择压力等分子机制,从转录调控、翻译调控及代谢活动等水平表达其承载的遗传信息。研究表明,mRNA半衰期的长短对mRNA活性以及转录和翻译过程有显著的影响。因此,系统地归纳同义密码子使用模式在基因转录、翻译调控及翻译后修饰等生命活动中所扮演的角色,将有助于全方位审视生物体如何巧妙利用密码子使用模式所产生的遗传效应来精准合成不同种类蛋白质,并以此保障生长或分化的特定基因表达程序顺利执行、维持正常的生命周期。     

影响耶尔森氏鼠疫杆菌基因组密码子使用的因素分析

基因组密码子使用的影响因素分析有助于发现影响密码子使用的进化动力学 ,对发现和预测进化的方向和模式有重要的作用。同时 ,分析完整的基因组可以发现特定基因组中密码子的使用模式 ,从而重新设计高效的PCR引物和外源导入基因 ,促进外源基因在特定生物体中的高效率表达。导致瘟疫等外源性感染疾病的耶尔森氏鼠疫杆菌完整基因组序列已经测序公布。为了对鼠疫杆菌的同义密码子使用的进化模式有更加深入的了解 ,详细的研究分析鼠疫杆菌的基因组密码子的使用模式和影响密码子使用的因素。结果发现 ,尽管鼠疫杆菌基因组序列中“G” “C”含量相对较低 (4 7.6 4 % ) ,高水平表达基因的密码子第三位碱基使用胞嘧啶 (C)的频率比表达水平低的基因使用胞嘧啶 (C)有显著的提高 ,表达水平较低的基因在密码子的第三位碱基更趋向使用鸟嘌呤 (G)。在表达水平高低的两组基因中 ,对密码子的第三位碱基使用腺嘌呤 (A)和胸腺嘧啶 (T)总体上趋于随机使用。基因的表达水平与对应分析的第一条向量轴呈高度相关 (R =0 .6 3,P <0 .0 0 0 1)。通过分析比较表达水平高低两组基因的密码子使用模式发现 ,基因的表达水平对于密码子使用有显著的影响。GC skew分析结果显示 ,复制转录阶段的选择对密码子使用有一定的影响。在不同长度     

The Effect of Multiple Evolutionary Selections on Synonymous Codon Usage of Genes in the Mycoplasma bovis Genome

Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains’ genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins.     

Trends in the codon usage patterns of Chromohalobacter salexigens genes

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.     

The Selective Advantage of Synonymous Codon Usage Bias in Salmonella

The genetic code in mRNA is redundant, with 61 sense codons translated into 20 different amino acids. Individual amino acids are encoded by up to six different codons but within codon families some are used more frequently than others. This phenomenon is referred to as synonymous codon usage bias. The genomes of free-living unicellular organisms such as bacteria have an extreme codon usage bias and the degree of bias differs between genes within the same genome. The strong positive correlation between codon usage bias and gene expression levels in many microorganisms is attributed to selection for translational efficiency. However, this putative selective advantage has never been measured in bacteria and theoretical estimates vary widely. By systematically exchanging optimal codons for synonymous codons in the tuf genes we quantified the selective advantage of biased codon usage in highly expressed genes to be in the range 0.2–4.2 x 10⁻⁴ per codon per generation. These data quantify for the first time the potential for selection on synonymous codon choice to drive genome-wide sequence evolution in bacteria, and in particular to optimize the sequences of highly expressed genes. This quantification may have predictive applications in the design of synthetic genes and for heterologous gene expression in biotechnology.     

Codon usage and amino acid usage influence genes expression level

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.     

Gene expression,nucleotide composition and codon usage bias of genes associated with human Y chromosome

Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome.     

Codon replacement in the PGK1 gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression.

The coding sequences of genes in the yeast Saccharomyces cerevisiae show a preference for 25 of the 61 possible coding triplets. The degree of this biased codon usage in each gene is positively correlated to its expression level. Highly expressed genes use these 25 major codons almost exclusively. As an experimental approach to studying biased codon usage and its possible role in modulating gene expression, systematic codon replacements were carried out in the highly expressed PGK1 gene. The expression of phosphoglycerate kinase (PGK) was studied both on a high-copy-number plasmid and as a single copy gene integrated into the chromosome. Replacing an increasing number (up to 39% of all codons) of major codons with synonymous minor ones at the 5' end of the coding sequence caused a dramatic decline of the expression level. The PGK protein levels dropped 10-fold. The steady-state mRNA levels also declined, but to a lesser extent (threefold). Our data indicate that this reduction in mRNA levels was due to destabilization caused by impaired translation elongation at the minor codons. By preventing translation of the PGK mRNAs by the introduction of a stop codon 3' and adjacent to the start codon, the steady-state mRNA levels decreased dramatically. We conclude that efficient mRNA translation is required for maintaining mRNA stability in S. cerevisiae. These findings have important implications for the study of the expression of heterologous genes in yeast cells.     

Two types of linkage between codon usage and gene-expression levels

The relation between codon usage and gene-expression levels is an intensively investigated and discussed topic in the field of molecular evolution. We statistically analyzed 25 Escherichia coli gene sequences by a new classification of synonymous codons and found that (i) there are two distinct types of linkage between codon usage and gene-expression levels in E. coli, and (ii) one of the two kinds of codon preferences (the codon preference concerned with interaction of GC/AT choice at three codon positions) is observed significantly in weakly expressed genes.     

Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.     

Analysis of synonymous codon usage in <Emphasis Type="Italic">Zea mays</Emphasis>

It is important and meaningful to understand the codon usage pattern and the factors that shape codon usage of maize. In this study, trends in synonymous codon usage in maize have been firstly examined through the multivariate statistical analysis on 7402 cDNA sequences. The results showed that the genes positions on the primary axis were strongly negatively correlated with GC3s, GC content of individual gene and gene expression level assessed by the codon adaptation index (CAI) values, which indicated that nucleotide composition and gene expression level were the main factors in shaping the codon usage of maize, and the variation in codon usage among genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. At the same time, CDS length and the hydrophobicity of each protein were, respectively, significantly correlated with the genes locations on the primary axis, GC3s and CAI values. We infer that genes length and the hydrophobicity of the encoded protein may play minor role in shaping codon usage bias. Additional 28 codons ending with a G or C base have been defined as “optimal codons”, which may provide useful information for maize gene-transformation and gene prediction.