杨树同义密码子用法的初步分析

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。用杨树的314个蛋白编码基因,通过对应分析和ENC-plot分析探讨了若干重要因子对杨树密码子用法的效应。从分析结果中可以看出,在影响最大的第一条向量轴上,基因的坐标位置与该基因的表达水平(CAI)极显著负相关(r=-0.94**),其次是与GC3S和基因长度极显著相关(r=0.86**和r=-0.57**),说明基因表达水平高低是影响密码子发挥作用的主要因素,基因编码区碱基组成和基因长度次之。ENC-plot分析结果也证明了这一点。相对密码子使用值(RSCU)的计算结果表明,高表达基因强烈偏好以A或T结尾的密码子,并确定了TTA和ATA等10个密码子为杨树的主要偏爱密码子。将杨树的密码子使用频率与拟南芥、水稻、大肠杆菌和人等不同模式生物种比较后发现,杨树密码子的偏爱性与同为双子叶植物的拟南芥最为相似,与人和大肠杆菌之间的差异较大。     

痘苗病毒基因组密码子使用频率分析

密码子使用的差别是普遍存在的现象,每一个密码子被某些生物偏爱,而在另一些生物中则很少使用.以往这方面的研究多集中在自养生物中,而对纯寄生的病毒本身及其与宿主细胞基因密码子使用频率关系的研究则很少.分析痘苗病毒哥本哈根株189个基因的密码子使用频率发现:总体上痘苗病毒偏爱使用以A/U为结尾的密码子;基因的异质性不强,没有影响密码子使用的主要趋势;在不同转录方向上和表达时相上,基因密码子使用略有不同;不同功能的基因其密码子使用上差别较大;晚期基因比早期基因与宿主密码子使用频率的差别大.上述结果表明:密码子是影响病毒和细胞相互作用、保证其自身生存的重要机制.     

草菇密码子偏好性分析

以草菇全基因组编码序列为研究对象,利用软件CodonW1.4.2分析草菇基因组密码子使用模式,确定了草菇的24个最优密码子。利用Create a condon usage table(CUSP)程序分析计算草菇密码子使用频率,并将它与人、酵母、拟南芥、小鼠、斑马鱼、果蝇6个代表性物种及灰盖鬼伞、双孢蘑菇、香菇、平菇4个食用菌进行比较。结果显示草菇密码子偏好性与人、酵母、拟南芥、小鼠、斑马鱼、果蝇和平菇都有较大的差异,与灰盖鬼伞、双孢蘑菇、香菇的密码子偏好性差异较小。利用软件SPSS16.0聚类分析表明密码子偏好性差异大小在一定程度上反映物种间的进化关系,可作为研究物种进化关系的参考。首次以食用菌全基因组为分析对象,解析草菇的密码子偏好性,并将其与其他生物进行比较,这些将为不同来源的外源基因在草菇中的异源表达提供重要参考。     

SARS冠状病毒的密码子偏爱性分析

为了分析SARS(Severe Acute Respiratory Syndrome)冠状病毒的密码子偏爱性(codon preference),为SARS冠状病毒基因表达中宿主系统的选择提供参考。运用EMBOSS(The European Molecular Biology Open Software Suite)的CHIPS(Codon Hetemzygosity in a Protein-codingSequence)和CUSP(Create a eodon usege table)程序对SARS冠状病毒的6个编码蛋白的基因进行分析,并将这6个编码序列拼接在一起进行全基因组的密码子偏爱性分析。分析结果与大肠杆菌、酵母及人的密码子偏爱性进行比较。结果显示SARS冠状病毒的CHIPS分析Nc(effective number of codons)值为53．338,S、E、M、N蛋白、3CL水解酶、RNA聚合酶的Nc值分别为45．733,61．000,59．040,46．618,46．924,51．902。编码SARS冠状病毒A,P,R,S,T,L等氨基酸的不同密码子使用频率有较大差异。大肠杆菌有25个、酵母有12个、人有20个密码子与SARS冠状病毒密码子使用偏爱性差异较大．因此可以得出结论：编码SARS冠状病毒氨基酸的密码子出现的频率较均一。SARS冠状病毒的密码子偏爱性与真核生物较接近,与原核生物相差较远,其基因表达选择在酵母等真核系统可能更为合适。     

嗜热泉生古细菌及其他泉古菌同义密码子使用偏向性分析

比较分析了嗜热泉生古细菌(Aeropyrum pernix K1)和其他两种系统发育相关的泉古菌[嗜气菌(Pyrobaculum aerophi-lumstr.IM2)和嗜硫菌(Sulfolobus acidocaldarius DSM 639)]的同义密码子使用偏向性。结果表明嗜热泉生古细菌(Aeropyrum pernix K1)的密码子偏向性很小,并且与GC3S成高度的相关性。这3种泉古菌的密码子使用模式在进化上很保守。与基因的功能对密码子使用的影响相比,这些泉古菌密码子的使用偏向性更是由其物种所决定的。嗜热泉生古细菌(A.pernix K1),嗜气菌(P.aerophilum str.IM2)和嗜硫菌(S.acidocaldarius DSM 639)生存在不同的极限环境中。推测正是这些极限环境决定了这些泉古菌的密码子使用偏向性模式。此外在这些泉古菌的基因组中并没有发现其正义链和反义链的密码子使用偏向性差别。嗜热泉生古细菌(A.pernix K1)和嗜硫菌(S.acidocaldarius DSM 639)的密码子偏向性程度与基因表达水平有高度的相关性,而嗜气菌(P.aerophilum str.IM2)的基因组并没有发现这种规律。     

西藏高原人群铁调素基因hamp密码子偏好性分析

目的:通过对西藏高原人群及平原人群、恒河猴等其他5种物种的密码子使用进行分析,从而得出西藏高原人群铁调素基因(hamp)的密码子偏好性。方法:采用PCR技术获得西藏高原人群铁调素全基因序列,利用在线软件CodonW进行密码子偏好性分析,通过在线软件PredictProtein以及Signal P等软件进行西藏高原人群铁调素基因的结构分析,比较与GenBank数据库中选取的平原人群、恒河猴等其他5种物种的密码子偏好性的差异。结果:西藏高原人群的铁调素基因全长为2681 bp,由3个外显子和2个内含子组成,编码84个氨基酸的铁调素前体肽,包含信号肽、中间肽与成熟肽,其密码子偏好性与平原人群、恒河猴等其他5个物种的密码子偏好性均有不同程度的差异。结论:西藏高原人群铁调素基因hamp密码子偏好性与其他物种的密码子偏好性均有不同程度的差异。     

拟南芥基因密码子偏爱性分析

密码子偏爱性对外源基因的表达强度有一定影响,特别是编码蛋白质N端7～8个氨基酸残基的密码子.通过对拟南芥染色体中26 827个蛋白质对应的基因密码子进行分析,得到了编码氨基酸的61种密码子在拟南芥中的使用频率,并与大肠杆菌和哺乳动物进行了比较,结果表明三者间的密码子偏爱性有较大差异.这一分析结果对于动物基因在植物中的表达,及植物基因在微生物中的表达具有一定指导意义.同时提供了一种直接以XML文档为数据源解析巨型XML格式染色体数据的方法.     

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。     

使用偏爱密码子大幅度提高苯丙氨酸脱氨酶在食品级乳酸乳球菌中的表达

为获得苯丙氨酸脱氨酶(PAL)在食品级乳酸乳球菌中的高效表达,将欧芹palcDNA(palnat)及根据乳酸乳球菌偏爱密码子设计人工合成的pal基因(palart)重组并转化到两种乳酸乳球菌NICE诱导表达系统中,测定基因工程菌表达PAL酶的量及活性,对比分析密码子偏爱性对乳酸乳球菌表达外源蛋白的影响。结果表明在两种乳酸乳球菌NICE表达系统中,使用偏爱密码子均可显著提高PAL酶的表达效率,使NZ9000/pNZ8048表达系统表达量提高22.23倍,NZ3900/pNZ8149系统提高35.90倍。此研究获得了安全高效表达PAL,可用于治疗苯丙酮尿症的基因工程菌。     

真核基因起始与终止密码子旁侧序列特征分析

真核基因起始与终止密码子旁侧序列的特征对于确定cDNA开放阅读框架 (ORF)和预测基因组序列中的编码区 (CDS)非常重要。基于高质量RefSeq数据库 ,在较大数据规模下统计分析了起始密码子旁侧序列所具有的“Kozak规则” ,发现不同物种之间存在差别。同时分析了不同终止密码子旁侧序列的统计学特征 ,给出了相应的正则表达式。由于发现多种基因中存在同相位起始、终止密码子串联使用的情况 ,亦对此进行了讨论。     

Analysis of mitochondrial protein‐coding genes of Antheraea assamensis: Muga silkworm of Assam

To understand the synonymous codon usage pattern in mitochondrial genome of Antheraea assamensis, we analyzed the 13 mitochondrial protein‐coding genes of this species using a bioinformatic approach as no work was reported yet. The nucleotide composition analysis suggested that the percentages of A, T, G,and C were 33.73, 46.39, 9.7 and 10.17, respectively and the overall GC content was 19.86, that is, lower than 50% and the genes were AT rich. The mean effective number of codons of mitochondrial protein‐coding genes was 36.30 and it indicated low codon usage bias (CUB). Relative synonymous codon usage analysis suggested overrepresented and underrepresented codons in each gene and the pattern of codon usage was different among genes. Neutrality plot analysis revealed a narrow range of distribution for GC content at the third codon position and some points were diagonally distributed, suggesting both mutation pressure and natural selection influenced the CUB.     

Comparison of codon usage and tRNAs in mitochondrial genomes of Candida species

To gain insight into the nature of the mitochondrial genomes (mtDNA) of different Candida species, the synonymous codon usage bias of mitochondrial protein coding genes and the tRNAs in C. albicans, C. parapsilosis, C. stellata, C. glabrata and the closely related yeast Saccharomyces cerevisiae were analyzed. Common features of the mtDNA in Candida species are a strong A+T pressure on protein coding genes, and insufficient mitochondrial tRNA species are encoded to perform protein synthesis. The wobble site of the anticodon is always U for the NNR (NNA and NNG) codon families, which are dominated by A-ending codons, and always G for the NNY (NNC and NNU) codon families, which is dominated by U-ending codons, and always U for the NNN (NNA, NNU, NNC and NNG) codon families, which are dominated by A-ending codons and U-ending codons. Patterns of synonymous codon usage of Candida species can be classified into three groups: (1) optimal codon-anticodon usage, Glu, Lys, Leu (translated by anti-codon UAA), Gln, Arg (translated by anti-codon UCU) and Trp are containing NNR codons. NNA, whose corresponding tRNA is encoded in the mtDNA, is used preferentially. (2) Non-optimal codon-anticodon usage, Cys, Asp, Phe, His, Asn, Ser (translated by anti-codon GCU) and Tyr are containing NNY codons. The NNU codon, whose corresponding tRNA is not encoded in the mtDNA, is used preferentially. (3) Combined codon-anticodon usage, Ala, Gly, Leu (translated by anti-codon UAG), Pro, Ser (translated by anti-codon UGA), Thr and Val are containing NNN codons. NNA (tRNA encoded in the mtDNA) and NNU (tRNA not encoded in the mtDNA) are used preferentially. In conclusion, we propose that in Candida species, codons containing A or U at third position are used preferentially, regardless of whether corresponding tRNAs are encoded in the mtDNA. These results might be useful in understanding the common features of the mtDNA in Candida species and patterns of synonymous codon usage.     

毕赤酵母的密码子用法分析

通过分析Pichia pastoris的28个蛋白编码基因的同义密码子使用情况并计算该酵母的密码子用法,首次确定出P.pastoris的19个高表达优越密码子。这些结果经与已知的Saccharomyces cerevisiae及Kluyveromyces lactis的密码子用法基本相似,但在氨基酸谷氨酸的密码子选择上截然相反,提示这可能属于P.pastoris所偏爱的密码子用法。     

Codon usage in the siliceous sponge Geodia cydonium: highly expressed genes in the simplest multicellular animals prefer C- and G-ending codons

Among a sample of 39 Geodia cydonium (Demospongiae, Porifera) genes, with an average G + C content of 51.2%, extensive structural heterogeneity and considerable variations in synonymous codon usage were found. The G + C content of coding sequences and G + C content at silent codon positions (GC3S) varied from 42.4 to 59.2% and from 35.6 to 76.5%, respectively. Correspondence analysis of 39 genes revealed that putative highly expressed genes preferentially use a limited subset of codons, which were therefore defined as preferred codons in G. cydonium . A total of 22 preferred codons for 18 amino acids with synonyms in codons were identified and they all (with one exception) end with C or G. Among these codons there are also C- and G-ending codons which were previously identified as codons optimal for translation in a variety of eukaryotes, including metazoans and plants. The bias in synonymous codon usage in putative highly expressed G. cydonium genes is moderate, indicating that these genes are not shaped under strong natural selection. We postulate that the preference for C- and G-ending codons was already established in the ancestor of all Metazoa, including also sponges. This ancestor most probably also had a G + C rich genome. The selection toward C- and G-ending codons has been largely conserved throughout eukaryote evolution; exceptions are, for example, mammals for which strong mutational biases caused switches from that rule.     

Regularities of the nucleotide sequence at the 5'-end of the codon in Escherichia coli genes

The frequencies of occurrence of nucleotides at the 5' side of codons have been determined in highly and weakly expressed genes from E. coli. Significant constraints on the nucleotide 5' to some codons were found in highly expressed genes. Certain rules of synonymous codon usage depending on the amino acid 3' of the codon were established. E. g., codon possessing quanosine in the third position (NNG) are preferred over NNA if the next amino acid is lysine (P less than 10(-5)). On the other hand, rules of synonymous codon usage in relation to 5' flanking nucleotide were found. For example, when coding for aspartic acid, GAC codon is preferred over GAU (P less than 0.001) if uridine is 5' to codon and on the contrary GAU is favoured (P less than 0.0001) if quanosine is at the 5' side of aspartic acid codon. These rules can be used in the chemical synthesis of genes designed for expression in E. coli.     

The Nonrandom Location of Synonymous Codons Suggests That Reading Frame-Independent Forces Have Patterned Codon Preferences

Biased codon usage is common in eukaryotic and prokaryotic genes. Evidence from Escherichia, Saccharomyces, and Drosophila indicates that it favors translational efficiency and accuracy. However, to date no functional advantages have been identified in the codon–anticodon interactions involving the most frequently used (preferred) codons. Here we present evidence that forces not related to the individual codon–anticodon interaction may be involved in determining which synonymous codons are preferred or avoided. We show that the ``off-frame' trinucleotide motif preferences inferrable from Drosophila coding regions are often in the same direction as Drosophila's ``in-frame' codon preferences, i.e., its codon usage. The off-frame preferences were inferred from the nonrandomness of the location of confamilial synonymous codons along coding regions—a pattern often described as a context dependence of nucleotide choice at synonymous positions or as codon-pair bias. We relied on randomizations of the location of confamilial codons that do not alter, and cannot be influenced by, the encoded amino acid sequences, codon usage, or base composition of the genes examined. The statistically significant congruency of in-frame and off-frame trinucleotide preferences suggests that the same kind of reading-frame-independent force(s) may also influence synonymous codon choice. These forces may have produced biases in codon usage that then led to the evolution of the translational advantages of these motifs as preferred codons. Under this scenario, tRNA pool size differences between preferred and nonpreferred codons initially were evolved to track the default overrepresentation of codons with preferred motifs. The motif preference hypothesis can explain the structuring of codon preferences and the similarities in the codon usages of distantly related organisms. Received: 10 November 1998 / Accepted: 23 February 1999     

栽培大豆和野生大豆线粒体基因组密码子使用偏性的比较分析

为分析栽培大豆和野生大豆线粒体基因组的密码子使用特征差异,该文以其线粒体基因组编码序列为研究对象,比较其密码子偏性形成的影响因素和演化过程。结果表明:(1)栽培大豆和野生大豆线粒体基因组编码区的GC含量分别为44.56%和44.58%,说明栽培大豆和野生大豆线粒体编码基因均富含A/T碱基。(2)栽培大豆和野生大豆线粒体基因组密码子第1位、第2位GC含量平均值与第3位GC含量的相关性均呈极显著水平,说明突变在其密码子偏性形成中的作用不可忽略; PR2-plot分析显示,在同义密码子第3位碱基的使用频率上,嘌呤低于嘧啶; Nc-plot分析中Nc比值位于-0.1～0.2区间的基因数占总基因数的95%以上;突变和选择等多重因素共同作用影响了大豆线粒体基因组编码序列密码子使用偏性的形成。(3)有20、21个密码子分别被确定为栽培大豆和野生大豆线粒体基因组编码序列的最优密码子,其中除丝氨酸TCC密码子外均以A或T结尾。综上结果认为,栽培大豆线粒体密码子偏性的形成受选择的影响要高于野生大豆,这可能是栽培大豆由野生大豆经长期人工栽培驯化的结果。     

Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants

Synonymous codons are widely selected for various biological mechanisms in both prokaryotes and eukaryotes. Recent evidence suggests that microRNA (miRNA) function may affect synonymous codon choices near miRNA target sites. To better understand this, we perform genome-wide analysis on synonymous codon usage around miRNA target sites in four plant genomes. We observed a general trend of increased site accessibility around miRNA target sites in plants. Guanine-cytosine (GC)-poor codons are preferred in the flank region of miRNA target sites. Within-genome analyses show significant variation among miRNA targets in species. GC content of the target gene can partly explain the variation of site accessibility among miRNA targets. miRNA targets in GC-rich genes show stronger selection signals than those in GC-poor genes. Gene's codon usage bias and the conservation level of miRNA and its target also have some effects on site accessibility, but the expression level of miRNA or its target and the mechanism of miRNA activity do not contribute to site accessibility differences among miRNA targets. We suggest that synonymous codons near miRNA targets are selected for efficient miRNA binding and proper miRNA function. Our results present a new dimension of natural selection on synonymous codons near miRNA target sites in plants, which will have important implications of coding sequence evolution.     

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.