Comparative genome analysis of six malarial parasites using codon usage bias based tools

Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in nearly all organisms. Previous studies of codon bias in Plasmodium species were based on a limited dataset. This study uses whole genome datasets for comparative genome analysis of six Plasmodium species using CUB and other related methods for the first time. Codon usage bias, compositional variation in translated amino acid frequency, effective number of codons and optimal codons are analyzed for P.falciparum, P.vivax, P.knowlesi, P.berghei, P.chabaudii and P.yoelli. A plot of effective number of codons versus GC3 shows their differential codon usage pattern arises due to a combination of mutational and translational selection pressure. The increased relative usage of adenine and thymine ending optimal codons in highly expressed genes of P.falciparum is the result of higher composition biased pressure, and usage of guanine and cytosine bases at third codon position can be explained by translational selection pressure acting on them. While higher usage of adenine and thymine bases at third codon position in optimal codons of P.vivax highlights the role of translational selection pressure apart from composition biased mutation pressure in shaping their codon usage pattern. The frequency of those amino acids that are encoded by AT ending codons are significantly high in P.falciparum due to action of high composition biased mutational pressure compared with other Plasmodium species. The CUB variation in the three rodent parasites, P.berghei, P.chabaudii and P.yoelli is strikingly similar to that of P.falciparum. The simian and human malarial parasite, P.knowlesi shows a variation in codon usage bias similar to P.vivax but on closer study there are differences confirmed by the method of Principal Component Analysis (PCA).

Abbreviations

CDS - Coding sequences, GC1 - GC composition at first site of codon, GC2 - GC composition at second site of codon, GC3 - GC composition at third site of codon, Ala - Alanine, Arg - Arginine, Asn - Asparagine, Asp - Aspartic acid, Cys - Cysteine, Gln - Glutamine Glu - Glutamic acid Gly - Glycine His - Histidine Ile - Isoleucine Leu - Leucine Lys - Lysine Met - Methionine Phe - Phenylalanine Pro - Proline Ser - Serine Thr - Threonine Trp - Tryptophan Tyr - Tyrosine Val - Valine.     

圆红冬孢酵母的密码子用法分析

运用CodonW等软件,分析了圆红冬孢酵母Rhodosporidium toruloides基因组中191个蛋白质编码基因的密码子使用模式,包括密码子3个位置上的GC含量、有效密码子数和密码子使用频率。圆红冬孢酵母有效密码子数ENc值为38.9,密码子GC含量为63%,密码子第三位GC含量为78.3%,且偏好使用G或C结尾的密码子,确定了圆红冬孢酵母R. toruloides的21个高表达优越密码子。研究发现,圆红冬孢酵母与毕赤酵母、酿酒酵母、大肠杆菌和拟南芥在密码子使用频率上有较大差异,而与解脂耶氏酵母和果蝇差异相对较小。研究结果对提高外源基因在圆红冬孢酵母中表达效率及相关代谢工程和合成生物学研究有一定意义。     

Analysis of synonymous codon usage bias in Chlamydia

Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexuallytransmitted diseases,and are associated with cardiovascular diseases.The analysis of codon usage mayimprove our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of targetgenes to improve their expression for gene therapy.Here,we analyzed the codon usage of C.muridarum,C.trachomatis(here indicating biovar trachoma and LGV),C.pneumoniae,and C.psittaci using the codonusage database and the CUSP(Create a codon usage table)program of EMBOSS(The European MolecularBiology Open Software Suite).The results show that the four genomes have similar codon usage patterns,with a strong bias towards the codons with A and T at the third codon position.Compared with Homosapiens,the four chlamydial species show discordant seven or eight preferred codons.The ENC(effectivenumber of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained bythe G+C content,while translational selection and gene length exert relatively weaker influences.Moreover,mutational pressure appears to be the major determinant of the codon usage variation among the chlamydialgenes.In addition,we compared the codon preferences of C.trachomatis with those of E.coli,yeast,adenovirus and Homo sapiens.There are 23 codons showing distinct usage differences between C.trachomatisand E.coli,24 between C.trachomatis and adenovirus,21 between C.trachomatis and Homo sapiens,butonly six codons between C.trachomatis and yeast.Therefore,the yeast system may be more suitable for theexpression of chlamydial genes.Finally,we compared the codon preferences of C.trachomatis with those ofsix eukaryotes,eight prokaryotes and 23 viruses.There is a strong positive correlation between the differ-ences in coding GC content and the variations in codon bias(r=0.905,P<0,001).We conclude that thevariation of codon bias between C.trachomatis and other organisms is much less influenced by phylogeneticlineage and primarily determined by the extent of disparities in GC content.     

几种模式生物基因组中最适密码对和稀有密码对使用的规律性

以6种模式生物基因组为样本,从密码对的碱基组成及密码子的使用两方面,分析了最适密码对与稀有密码对的使用。结果显示:6种生物的最适密码对rP双碱基TA出现的频数都是最低的,而出现频率最大的双碱墓对于古菌、细菌、真核是不同的;稀有密码对中双碱基TA出现的频数却是最高的,而出现频率最低的双碱基刘·于古菌、细菌、真核是不同的。这说明双碱基的分布与密码对的偏好性有很强的相关性,同时也与基因组进化存在关联。另外,我们也分析了本文的6种生物编码序列叶,最适密码对与稀有密码对的出现频数与密码了的相对使用频率的关系,发现密码对的出现频数与其密码子的使用存在相关性。     

Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ

To reveal how the AT-rich genome of bacteriophage PhiKZ has been shaped in order to carryout its growth in the GC-rich host Pseudomonas aeruginosa,synonymous codon and amino acid usage bias ofPhiKZ was investigated and the data were compared with that of P.aeruginosa.It was found that synonymouscodon and amino acid usage of PhiKZ was distinct from that of P.aeruginosa.In contrast to P.aeruginosa,the third codon position of the synonymous codons of PhiKZ carries mostly A or T base;codon usage biasin PhiKZ is dictated mainly by mutational bias and,to a lesser extent,by translational selection.A clusteranalysis of the relative synonymous codon usage values of 16 myoviruses including PhiKZ shows that PhiKZis evolutionary much closer to Escherickia coli phage T4.Further analysis reveals that the three factors ofmean molecular weight,aromaticity and cysteine content are mostly responsible for the variation of aminoacid usage in PhiKZ proteins,whereas amino acid usage of P.aeruginosa proteins is mainly governed bygrand average of hydropathicity,aromaticity and cysteine content.Based on these observations,we suggestthat codons of the phage-like PhiKZ have evolved to preferentially incorporate the smaller amino acid residuesinto their proteins during translation,thereby economizing the cost of its development in GC-rich P.aeruginosa.     

Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern

Amino acids are essential measurements for the potential growth stage because of connecting to protein structures and functions. The objective of this paper was to analyze chromosomes feature at plastid region of rice represented by nucleotide, synonymous codon, and amino acid usage to predict gene expression through codon usage pattern. The results showed that the values of the codon adaption index ranged from 0.733 in chromosome 9 to 0.631 in chromosome 8 with full length of these two chromosomes were 3738 and 1635 respectively. The higher value of guanine and cytosine content was 60% in chromosomes 9 while the lower values was 37% in chromosomes 11. Eight chromosomes (ch1, ch2, ch3, ch5, ch7, ch8, ch10, and ch12) were greater value of modified relative codon bias than threshold (threshold: 0.66) especially in cysteine for ch1, ch2, ch5, ch10, and ch12. While other remaining chromosomes were less than the threshold. Relative synonymous codon usage found that the over-represented of amino acids were asparagine, aspartate, cysteine, glutamate, and phenylalanine across all 12 chromosomes. These results would establish a platform for more and further projects concerning rice breeding and genetics and codon optimization in the amino acids for developing varieties. These results also will help breeders to select desirable genes through the genome for improve target traits.     

敏捷气热菌起始密码子侧翼序列与密码子偏好及基因长度相关性研究

好氧超嗜热古菌敏捷气热菌 (Aeropyrumpernix)mRNA中起始密码子AUG侧翼序列的保守性以及它与密码子使用偏好及基因长度之间具有相关性。AUG侧翼序列的保守性由M1(1)值表示 ,AUG侧翼序列对翻译起始的有效性由AUGCAI值表示。研究表明 :高表达和低表达基因的 - 2 0位到 13位中某些位点的保守性存在差异 ,其中高表达基因的 - 4位和 - 3位可能与其高表达的特性有关 ;在A .pernix中一个普遍的趋势是 :较短的基因有较高的表达效率 ,较长的基因的表达效率较低。与仅使用密码子偏好相比 ,将AUGCAI值引入到研究古菌在翻译水平上的自然选择更准确、更具有广泛适应性     

Prediction of gene expression under drought stress in spring wheat using codon usage pattern

Spring wheat (Triticum aestivum) is a staple food providing sources of essential proteins for human. In fact, gene expressions of wheat play an important role in growth and productivity that are affected by drought stress. The objective of this work focused on analysis gene feature on spring wheat represented by nucleotide and gene expressions under drought stress. It was found that the higher codon adaptation index was in both wheat root and L-galactono-1, 4-lactone dehydrogenase. It was also found that guanine and cytosine content were high (55.56%) in wheat root. Whereas, guanine and cytosine content were low (41.28%) in L-galactono-1, 4-lactone dehydrogenase. Moreover, the higher relative synonymous codon usage value was observed in codon CAA (1.20), GAA (1.33), GAT (1.00), and ATG (1.00) in wheat root and thus about 62.95% of the total variation in relative synonymous codon was explained by principal component analysis. Additionally, high averages frequency number of codon were (above 15.76) in Met, Lys, Ala, Gly, Phe, Asp, Glu, His, and Tyr; whereas, low averages were in remaining amino acids and majority (90%) of modified relative codon bias values was between 0.40 and 0.90. Shortly, calculations and analysis of codon usage pattern under drought stress would help for genetic engineering, molecular evolution, and gene prediction in wheat studies for developing varieties that associate with drought tolerance.     

Understanding molecular biology of codon usage in mitochondrial complex IV genes of electron transport system: Relevance to mitochondrial diseases

The mitochondrial cytochrome oxidase (CO) genes are involved in complex IV of the electron transport system, and dysfunction of CO genes leads to several diseases. However, no work has been reported on the codon usage pattern of these genes. We used bioinformatic methods to analyze the compositional properties and the codon usage pattern of the COI, COII, and COIII genes in fishes, birds, and mammals to understand the similarities and dissimilarities of codon usage in these genes, which gave an insight into the molecular biology of these genes. The effective number of codons (ENC) value of genes was high in different species of fishes, birds and mammals, which indicates that the codon bias of CO genes was low and the ENC values were significantly different among fishes, birds, and mammals, as revealed from the t test. The overall guanine and cytosine (GC) content in fishes, birds, and mammals was lower than 50% in all genes, indicating that the genes were AT-rich and significantly different among fishes, birds, and mammals. The TCA codon was overrepresented in fishes, birds, and mammals for the COI gene, in birds and mammals for the COII gene, but it was not overrepresented in others. Only three codons, namely CTA, CGA, and AAA, were overrepresented in all three groups for the COI, COII, and COIII genes, repectively. From the neutrality plot in fishes, birds, and mammals, it was observed that the slopes of the regression lines (regression coefficients) in the COI, COII, and COIII genes were <0.5, suggesting that natural selection played a major role, whereas mutation pressure played a minor role.     

Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives

Protein translation has been elucidated to be dictated by evolutionary constraints, namely, variations in tRNA availabilities and/or variations in codon-anticodon binding that is manifested in biased codon usage. Taking advantage of publicly available mRNA expression and protein abundance data for Saccharomyces cerevisiae, we have performed a comprehensive analysis of the diverse factors guiding translation leading to desired protein levels irrespective of the corresponding high or low mRNA levels. It has been elucidated in this study that different combinations of most abundant/non abundant tRNA isoacceptors are selected for in S. cerevisiae that helps in achieving the optimum speed and accuracy in the protein translation process. This is also accompanied by the strategic location of codon pairs in coherence to mRNA secondary structure folding stability for the above mentioned combinations of tRNA isoacceptors. We thus find that codon pair contextual effects; in addition to tRNA abundance and mRNA folding stability during translation elongation process play plausible roles in maintaining translation accuracy and speed that can achieve desired protein levels.     

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。     

Insights into the riddles of codon usage patterns and codon context signatures in fungal genus Puccinia,a persistent threat to global agriculture

The fungal genus Puccinia, comprising of several menacing pathogens, has been a persistent peril to global agriculture. Genome sequencing of various members of Puccinia offers a scope to excavate their genomic riddles. The present study has been addressed at exploring the complex niceties of codon and amino acid usage patterns and subsequent elucidation of the determinants that drive such behavior. Multivariate statistical analysis revealed a complex interplay of natural selection for translation and compositional bias to be operational on the codon usage patterns. Gene expression level was observed to be the most competent factor governing codon usage behavior of the genus. In spite of subtle AT richness of the genus, potential highly expressed gene sets were found to preferentially employ GC rich optimal codons. Estimation of relative dinucleotide abundance revealed preference toward the employment of GpA, CpA, TpC, and TpG dinucleotides and restraint from using TpA dinucleotide among the members of the genus. Extensive codon context analysis revealed that codon pairs with GpA, CpA, TpC, and TpG dinucleotides were over-represented and codon pairs with TpA dinucleotide were extensively avoided at the codon–codon (cP3–cA1) junctions. Amino acid usage signatures of the genus were found to be influenced considerably by several imperative factors like aromatic and hydrophobic character of the encoded gene products, genomic compositional constraint, and gene expressivity. Detailed know-how of the potential highly expressed gene sets and associated optimal codons in the genus promise to be informative for the scientific community engaged in combating Puccinia pathogenesis.     

Characteristics of codon usage bias in two regions downstream of the initiation codons of foot-and-mouth disease virus

The mechanism of utilization of alternative two AUGs in foot-and-mouth disease virus (FMDV) is still unknown to date. In this study, the characteristics of codon usage bias (CUB) of the region between the two AUGs (the region-La) and of the same-sized region behind the second AUG (the region-Lb) in 94 different FMDV RNA sequences were analyzed using relative synonymous codon usage (RSCU) values. The results indicated that many codons with negative CUB were preferentially used in the region-La. There were two conserved residues (Thr and Cys) on the 4th and 6th residue positions of the region-La. The conserved residues had a general tendency to choose synonymous codons with negative CUB. Although most positions in the region-La did not contain conserved residues, many positions tended to use codons with negative CUB in this region. Among these codons, the majority belonged to the amino acids containing synonymous codons with clearly positive and negative CUB, including Asp, Val, Ile, Leu, Thr, Ala, Ser, Asn and Arg. The presence of many codons with negative CUB in the region-La might impair the efficiency of the first AUG selection. The phylogenetic incongruence of the region-La and the region-Lb implied that intertypic recombination played an important role in the evolution of FMDV. Furthermore, due to the existence of more positions with positive CUB and more widespread phylogenetic incongruence in the region-Lb than the region-La, a probable relationship between the degree of CUB and the evolution of the two target regions was revealed.     

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。     

紫花苜蓿叶绿体基因组密码子偏好性分析

为分析紫花苜蓿叶绿体基因组密码子偏好性的使用模式,该文以紫花苜蓿叶绿体基因组中筛选到的49条蛋白质编码序列为研究对象,利用CodonW、CUSP、CHIPS、SPSS等软件对其密码子的使用模式和偏好性进行研究。结果表明:(1)紫花苜蓿叶绿体基因的第3位密码子的平均GC含量为26.44%,有效密码子数(ENC)在40.6～51.41之间,多数密码子的偏好性较弱。(2)相对同义密码子使用度(RSCU)分析发现,RSCU>1 的密码子数目有30个,以A、U结尾的有29个,说明了紫花苜蓿叶绿体基因组A或U出现的频率较高。(3)中性分析发现,GC3与 GC12的相关性不显著,表明密码子偏性主要受自然选择的影响; ENC-plot 分析发现一部分基因落在曲线的下方及周围,表明突变也影响了部分密码子偏性的形成。此外,有17个密码子被鉴定为紫花苜蓿叶绿体基因组的最优密码子。紫花苜蓿叶绿体基因组的密码子偏好性可能受自然选择和突变的共同作用。该研究将为紫花苜蓿叶绿体基因工程的开展和目标性状的遗传改良奠定基础。     

Mutation bias is the driving force of codon usage in the Gallus gallus genome

Synonymous codons are used with different frequencies both among species and among genes within the same genome and are controlled by neutral processes (such as mutation and drift) as well as by selection. Up to now, a systematic examination of the codon usage for the chicken genome has not been performed. Here, we carried out a whole genome analysis of the chicken genome by the use of the relative synonymous codon usage (RSCU) method and identified 11 putative optimal codons, all of them ending with uracil (U), which is significantly departing from the pattern observed in other eukaryotes. Optimal codons in the chicken genome are most likely the ones corresponding to highly expressed transfer RNA (tRNAs) or tRNA gene copy numbers in the cell. Codon bias, measured as the frequency of optimal codons (Fop), is negatively correlated with the G + C content, recombination rate, but positively correlated with gene expression, protein length, gene length and intron length. The positive correlation between codon bias and protein, gene and intron length is quite different from other multi-cellular organism, as this trend has been only found in unicellular organisms. Our data displayed that regional G + C content explains a large proportion of the variance of codon bias in chicken. Stepwise selection model analyses indicate that G + C content of coding sequence is the most important factor for codon bias. It appears that variation in the G + C content of CDSs accounts for over 60% of the variation of codon bias. This study suggests that both mutation bias and selection contribute to codon bias. However, mutation bias is the driving force of the codon usage in the Gallus gallus genome. Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns.     

Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.     

Chronic obstructive pulmonary disease: A crosstalk on nucleotide compositional dynamics and codon usage patterns of the genes involved in disease

Chronic obstructive pulmonary disease (COPD), a lung disease, affects a large number of people worldwide, leading to death. Here, we analyzed the compositional features and trends of codon usage of the genes influencing COPD to understand molecular biology, genetics, and evolutionary relationships of these genes as no work was reported yet. Coding sequences of COPD genes were found to be rich in guanine-cytosine (GC) content. A high value (34-60) of the effective number of codons of the genes indicated low codon usage bias (CUB). Correspondence analysis suggested that the COPD genes were distinct in their codon usage patterns. Relative synonymous codon usage values of codons differed between the more preferred codons and the less-preferred ones. Correlation analysis between overall nucleotides and those at third codon position revealed that mutation pressure might influence the CUB of the genes. The high correlation between GC12 and GC3 signified that directional mutation pressure might have operated at all the three codon positions in COPD genes.     

Decoding mechanisms by which silent codon changes influence protein biogenesis and function

ScopeSynonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health.PurposeThis synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics.Physiological and medical relevanceUnderstanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.     

Factors influencing synonymous codon and amino acid usage biases in Mimivirus

Synonymous codon and amino acid usage biases have been investigated in 903 Mimivirus protein-coding genes in order to understand the architecture and evolution of Mimivirus genome. As expected for an AT-rich genome, third codon positions of the synonymous codons of Mimivirus carry mostly A or T bases. It was found that codon usage bias in Mimivirus genes is dictated both by mutational pressure and translational selection. Evidences show that four factors such as mean molecular weight (MMW), hydropathy, aromaticity and cysteine content are mostly responsible for the variation of amino acid usage in Mimivirus proteins. Based on our observation, we suggest that genes involved in translation, DNA repair, protein folding, etc., have been laterally transferred to Mimivirus a long ago from living organism and with time these genes acquire the codon usage pattern of other Mimivirus genes under selection pressure.