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 expre...     

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

Background  

It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codons. This phenomenon, termed codon usage bias, is common to many organisms and has been recognized as influencing cellular fitness. This suggests that the global extent of codon usage bias of an organism might be associated with its phenotypic traits.     

Codon usage is associated with the evolutionary age of genes in metazoan genomes

Background  

Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes.     

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。     

Codon usage bias analysis of genes linked with esophagus cancer

Esophageal cancer involves multiple genetic alternations. A systematic codon usage bias analysis was completed to investigate the bias among the esophageal cancer responsive genes. GC-rich genes were low (average effective number of codon value was 49.28). CAG and GTA are over-represented and under-represented codons, respectively. Correspondence analysis, neutrality plot, and parity rule 2 plot analysis confirmed the dominance over mutation pressure in modulating the codon usage pattern of genes linked with esophageal cancer.     

Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes

Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood fluke Schistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally.     

Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons

In the work presented, the changes in codon and amino acid contents have been studied as a function of environmental conditions by comparing pairs of homologs in a group of extremophilic/non-extremophilic genomes. Our results obtained based on such analysis highlights a number of notable observations: (i) the overall preference of amino acid usages in the proteins of a given organism is significantly affected by major environmental factors. The changes in amino acid preferences (amino acid usage profiles) in an extremophile compared to its non-extremophile relative recurs in the organisms of similar extreme habitats. (ii) On the other hand, changes in codon usage preferences in these extremophilic/non-extremophilic pairs, lack such persistency not only in different genome-pairs but also in the individual genes of a specific pair. (iii) We have noted a correlation between cellular function and codon usage profiles of the genes in the studied pairs. (iv) Based on this correlation, we could obtain a decent prediction of cellular functions solely based on codon usage profile data. (v) Comparisons made between two sets of randomly generated genomes suggest that different patterns of codon usage changes in genes of different functional categories result in a partial resistance towards the changes in the concentration of a given amino acid. This buffering capacity might explain the observed differences in codon usage trends in genes of different functions. In the end, we suggest codon usage and amino acid profiles as powerful tools that can be utilized to improve function predictions and genome-environment mappings.     

Codon usage bias in human cytomegalovirus and its biological implication

Human cytomegalovirus (HCMV) infection, a worldwide contagion, causes a serious disorder in infected individuals. Analysis of codon usage can reveal much molecular information about this virus. The effective number of codon (ENC) values, relative synonymous codon usage (RSCU) values, codon adaptation index (CAI), and nucleotide contents was investigated in approximately 160 coding sequences (CDS) among 17 human cytomegalovirus genomes using the software CodonW. Linear regression analysis and logistic regression were performed to explore the preliminary data. The results showed that, overall, HCMV genomes had low codon usage bias (mean ENC = 47.619). However, the ENC of individual CDS varied widely and was distributed unevenly between host-related genes and viral-self-function genes (P = 0.002, odds ratio (OR) = 3.194), as did the GC content (P = 0.016, OR = 2.178). The ENC values correlated with CAI, GC content, and the nucleotide composing at the 3rd codon position (GC3s) (P < 0.001). There was a significant variation in the codon preference that depended on the RSCU data. The predicted ENC curve suggested that mutational pressure, rather than natural selection, was one of the main factors that determined the codon usage bias in HCMV. Among 123 genes with known function, the genes related to viral self-replication and viral–host interaction showed different ENC and CAI values, and GC and GC3s contents. In conclusion, the detailed codon usage bias theoretically revealed information concerning HCMV evolution and could be a valuable additional parameter for HCMV gene function research.     

紫九牛叶绿体基因组密码子偏好性分析

为确定瑶药紫九牛叶绿体基因组密码子的使用模式及其成因,该研究以紫九牛叶绿体基因组50条蛋白质编码序列为研究对象,利用Codon W 1.4.2和在线软件CUSP和Chips分析其密码子偏好性。结果表明：(1)RSCU>1的密码子有29个,其中有28个以A/U结尾,说明叶绿体基因组的同义密码子中偏好以A/U结尾。(2)紫九牛叶绿体基因组密码子的GC含量GC₁(47.38%)>GC₂(39.81%)>GC₃(29.60%),ENC值大于45的有40个,说明紫九牛叶绿体基因组存在较弱的偏性。(3)中性绘图分析和ENC-plot分析说明了紫九牛叶绿体基因组密码子的偏好性既受到选择的作用,又受到突变因素的影响。(4)通过构建的高低基因表达库最终确定了15个最优密码子,分别为UUG、AUU、GUU、GUA、UCU、 CCU、ACU、ACA、GCU、CAA、AAC、GAA、UGU、CGU和GGU。该研究为紫九牛叶绿体基因组的确定以及遗传多样性分析提供了依据。     

落叶松-杨栅锈菌基因组密码子使用偏好分析

为了解落叶松‐杨栅锈菌密码子使用模式,并探究影响其密码子偏好形成的因素,本研究利用CondonW对落叶松‐杨栅锈菌标准菌株98AG31基因组中14 650个基因进行分析,计算基因的有效密码子数,及64个密码子的相对使用度等偏好性参数。结果表明,落叶松‐杨栅锈菌全基因组水平的密码子偏好程度较低,只有少数基因呈现出高偏好性。落叶松‐杨栅锈菌的高频密码子多以A或T结尾,而最优密码子则倾向以G或C结尾。PR2-plot分析及ENC-plot曲线与中性绘图分析显示,落叶松‐杨栅锈菌基因密码子使用模式受到选择压力和突变压力等多重因素的影响,相较于选择压力,落叶松‐杨栅锈菌基因密码子的偏好更多地受到突变压力的影响。相关性分析表明,密码子碱基组成会对密码子偏好性产生影响,其他因素如序列长度等均不会影响密码子偏好性。     

Codon usage bias and evolutionary analyses of Zika virus genomes

Zika virus (ZIKV) is a member of the family Flaviviridae and contains a single-stranded RNA genome with positive-polarity. Like Dengue, Zika virus uses Aedes aegypti mosquito as a vector to infect human with a wide range of clinical signs, from asymptomatic to influenza-like syndrome. Despite significant progress in genomic analyses, how a viral relationship with two different hosts affect the overall fitness, constancy, and dodging of hosts immune system are elusive. Here we analyzed Zika virus codon-based evolution using eleven strains from different geographical locations. The overall codon usage was similar and slightly bias among all strains. An occurrence of A-ending in highly-preferred codons and analysis by various approaches strongly suggests that mutational bias is the main force shaping codon usage in this virus. However, natural selection and geographical realities cannot be ignored in marginal influence on codon usage. The viral genomes naturally favor Aedes aegypti over human host for tRNA pool in translation. Such findings will assist researchers in understanding elements contribute to viral adaptation and evolutionary setup with hosts.     

Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabditis remanei

Adaptive codon usage provides evidence of natural selection in one of its most subtle forms: a fitness benefit of one synonymous codon relative to another. Codon usage bias is evident in the coding sequences of a broad array of taxa, reflecting selection for translational efficiency and/or accuracy as well as mutational biases. Here, we quantify the magnitude of selection acting on alternative codons in genes of the nematode Caenorhabditis remanei, an outcrossing relative of the model organism C. elegans, by fitting the expected mutation-selection-drift equilibrium frequency distribution of preferred and unpreferred codon variants to the empirical distribution. This method estimates the intensity of selection on synonymous codons in genes with high codon bias as N(e)s = 0.17, a value significantly greater than zero. In addition, we demonstrate for the first time that estimates of ongoing selection on codon usage among genes, inferred from nucleotide polymorphism data, correlate strongly with long-term patterns of codon usage bias, as measured by the frequency of optimal codons in a gene. From the pattern of polymorphisms in introns, we also infer that these findings do not result from the operation of biased gene conversion toward G or C nucleotides. We therefore conclude that coincident patterns of current and ancient selection are responsible for shaping biased codon usage in the C. remanei genome.     

Codon usage bias and determining forces in green plant mitochondrial genomes

The phenomenon of codon usage bias has been observed in a wide range of organisms. As organisms evolve, how their codon usage pattern change is still an intriguing question. In this article, we focused on the green plant mitochondrial genomes to analyze the codon usage patterns in different lineages, and more importantly, to investigate the possible change of determining forces during the plant evolution. Two patterns were observed between the separate lineages of green plants: Chlorophyta and Streptophyta. In Chlorophyta lineages, their codon usages showed substantial variation (from strongly A, T-biased to strongly G, C-biased); while in Streptophyta lineages, especially in the land plants, the overall codon usages are interestingly stable. Further, based on the Nc-GC3s plots and Akashi's scaled χ(2) -tests, we found that lineages within Chlorophyta exhibit much stronger evidence of deviating from neutrality; while lineages within Streptophyta rarely do so. Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force.     

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

Background  

The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20^th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease.     

Codon usage in regulatory genes in Escherichia coli does not reflect selection for ''rare'' codons.

It has often been suggested that differential usage of codons recognized by rare tRNA species, i.e. "rare codons", represents an evolutionary strategy to modulate gene expression. In particular, regulatory genes are reported to have an extraordinarily high frequency of rare codons. From E. coli we have compiled codon usage data for highly expressed genes, moderately/lowly expressed genes, and regulatory genes. We have identified a clear and general trend in codon usage bias, from the very high bias seen in very highly expressed genes and attributed to selection, to a rather low bias in other genes which seems to be more influenced by mutation than by selection. There is no clear tendency for an increased frequency of rare codons in the regulatory genes, compared to a large group of other moderately/lowly expressed genes with low codon bias. From this, as well as a consideration of evolutionary rates of regulatory genes, and of experimental data on translation rates, we conclude that the pattern of synonymous codon usage in regulatory genes reflects primarily the relaxation of natural selection.     

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Background  

Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms.     

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.