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Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria  [cached]
Suzuki Haruo,Saito Rintaro,Tomita Masaru
EURASIP Journal on Bioinformatics and Systems Biology , 2007,
Abstract: G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.
Synonymous codon usage and selection on proteins  [PDF]
Joshua B. Plotkin,Jonathan Dushoff,Michael M. Desai,Hunter B. Fraser
Quantitative Biology , 2004,
Abstract: Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein sequences from their synonymous codon usage (Plotkin and Dushoff 2003, Plotkin et al 2004a). Here we provide a theoretical foundation for this approach. We derive the expected frequencies of synonymous codons as a function of the strength of selection, the mutation rate, and the effective population size. We analyze the conditions under which we can expect to draw inferences from biased codon usage, and we estimate the time scales required to establish and maintain such a signal. Our results indicate that, over a broad range of parameters, synonymous codon usage can reliably distinguish between negative selection, positive selection, and neutrality. While the power of volatility to detect negative selection depends on the population size, there is no such dependence for the detection of positive selection. Furthermore, we show that phenomena such as transient hyper-mutators in microbes can improve the power of volatility to detect negative selection, even when the typical observed neutral site heterozygosity is low.
Molecular evolution of synonymous codon usage in Populus
P?r K Ingvarsson
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-307
Abstract: I examined the evolution of synonymous codons using EST data from five species of Populus. Data on relative synonymous codon usage in genes with high and low gene expression were used to identify 25 codons from 18 different amino acids that were deemed to be preferred codons across all five species. All five species show significant correlations between codon bias and gene expression, independent of base composition, thus indicating that translational selection has shaped synonymous codon usage. Using a set of 158 orthologous genes I detected an excess of unpreferred to preferred (U → P) mutations in two lineages, P. tremula and P. deltoides. Maximum likelihood estimates of the strength of selection acting on synonymous codons was also significantly greater than zero in P. tremula, with the ML estimate of 4Nes = 0.720.The data is consistent with weak selection on preferred codons in all five species. There is also evidence suggesting that selection on synonymous codons has increased in P. tremula. Although the reasons for the increase in selection on codon usage in the P. tremula lineage are not clear, one possible explanation is an increase in the effective population size in P. tremula.Codon bias, the preferential use of subset of synonymous codons, has been documented in a wide variety of organisms, from prokaryotes, to unicellular and multicellular eukaryotes [1-3]. While codon bias appears to be almost universal, the magnitude of codon bias largely depends on the effective population size, with codon bias being higher in species with larger effective population sizes [4]. Evolution of synonymous codon usage is a process where natural selection is sufficiently weak (Ns ~ 1) that the outcome is influenced by both selection, mutation and genetic drift [1,2]. At the same time, synonymous changes within and between species are sufficiently common that abundant data is available for testing evolutionary hypotheses of synonymous codon usage, explaining why much attent
Analysis of synonymous codon usage in Hepatitis A virus
Yiqiang Zhang, Yongsheng Liu, Wenqian Liu, Jianhua Zhou, Haotai Chen, Yin Wang, Lina Ma, Yaozhong Ding, Jie Zhang
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-174
Abstract: The overall extent of codon usage bias in HAV is high in Picornaviridae. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.HAV presents a higher codon usage bias than other members of Picornaviridae. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.Hepatitis A virus (HAV), the causative agent of type A viral hepatitis, is an ancient human virus that was first identified in the stools of infected people in 1973 [1]. HAV is a non-enveloped, single-stranded positive-sence RNA virus which belongs to order Picornavirales, family Picornaviridae, the genus Hepatovirus in virus taxonomy [2-4]. The genome of HAV is approximately 7500 nucleotide in length and contains a large open-reading frame (ORF) encoding a polyprotein in which the major capsid proteins represent the amino-terminal third, with the remainder of the polyprotein comprising a series of nonstructural proteins required for HAV RNA replication: 2B, 2C, 3A, 3B, 3Cpro and 3Dpol. Based on the studies of genetics, HAV was proposed to divide into six different genotypes [5]. However, there is only one known serological group of human HAV [6,7]. Although HAV causes occasional, dramatic disease outbreaks of acute hepatitis with fatal outcomes in otherwise healthy adults as well as isolated severe cases of hepatitis, it has never been associated with chronic liver disease [8].As we all know, the genetic code chooses 64 codons to represent 20 standard amino acids and stop signals. These alternative codons for the same amino acid are termed as synonymous codons. Synonymous mutations t
Patterns and influencing factor of synonymous codon usage in porcine circovirus
Xin-sheng LIU, Yong-guang Zhang, Yu-zhen Fang, Yong-lu Wang
Virology Journal , 2012, DOI: 10.1186/1743-422x-9-68
Abstract: We carried out comprehensive analysis on codon usage pattern in the PCV genome, by calculating relative synonymous codon usage (RSCU), effective number of codons (ENC), dinucleotides and nucleic acid content of the PCV genome.PCV genomes have relatively much lower content of GC and codon preference, this result shows that nucleotide constraints have a major impact on its synonymous codon usage. The results of the correspondence analysis indicate codon usage patterns of PCV of various genotypes, various subgenotypes changed greatly, and significant differences in codon usage patterns of Each virus of Circoviridae.There is much comparability between PCV and its host in their synonymous codon usage, suggesting that the natural selection pressure from the host factor also affect the codon usage patterns of PCV. In particular, PCV genotype II is in synonymous codon usage more similar to pig than to PCV genotype I, which may be one of the most important molecular mechanisms of PCV genotype II to cause disease. The calculations results of the relative abundance of dinucleotides indicate that the composition of dinucleotides also plays a key role in the variation found in synonymous codon usage in PCV. Furthermore, geographic factors, the general average hydrophobicity and the aromaticity may be related to the formation of codon usage patterns of PCV.The results of these studies suggest that synonymous codon usage pattern of PCV genome are the result of interaction between mutation pressure and natural selection from its host. The information from this study may not only have theoretical value in understanding the characteristics of synonymous codon usage in PCV genomes, but also have significant value for the molecular evolution of PCV.Genetic information is transmitted from mRNA to protein in a mode of triplet codon. Each amino acid matches with at least one codon, at most six codons. The codons encoding the same amino acid is called synonymous codon. During biosynthesis
Patterns of Synonymous Codon Usage on Human Metapneumovirus and Its Influencing Factors
Qiao Zhong,Weidong Xu,Yuanjian Wu,Hongxing Xu
Journal of Biomedicine and Biotechnology , 2012, DOI: 10.1155/2012/460837
Abstract: Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity.
Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes
Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, Jizhong Zhou
BMC Evolutionary Biology , 2004, DOI: 10.1186/1471-2148-4-19
Abstract: Based on an informatics method (SCUO) we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC3)2 + 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC3)2 + 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation.The synonymous codon usage bias could be simply expressed as 1+ (p/2)log2(p/2) + ((1-p)/2)log2((l-p)/2), where p = GC3. The software we developed for measuring SCUO (codonO) is available at http://digbio.missouri.edu/~wanx/cu/codonO webcite.All amino acids except Met and Trp are encoded by more than one codon. DNA sequence data from diverse organisms have shown that synonymous codons for any amino acid are not used with equal frequency, even though choices among codons should be equivalent in terms of protein sequences [1-6]. Previous codon usage analyses showed that codon usage bias is very complicated and is associated with various biological factors, such as gene expression level [7-10], gene length [11-13], gene translation initiation signal [14], protein amino acid composition [6,15], protein structure [16,17], tRNA abundance [18-21], mutation frequency and patterns [22,23], and GC composition [24-27]. In this paper, we further explore the relationship between codon usage and GC composition.GC composition may be described at three levels: 1) Overall GC content. The overall genome GC content in living organisms varies from 25–75% [28]. However, within a single ge
Compare the differences of synonymous codon usage between the two species within cardiovirus
Wen-qian Liu, Jie Zhang, Yi-qiang Zhang, Jian-hua Zhou, Hao-tai Chen, Li-na Ma, Yao-zhong Ding, Yongsheng Liu
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-325
Abstract: The mean ENC values of EMCV and ThV are 54.86 and 51.08 respectively, higher than 40.And there are correlations between (C+G)12% and (C+G)3% for both EMCV and ThV (r = -0.736;r = 0.986, P < 0.01, repectively). For ThV the (C+G)12%, (C+G)3%, axis f'1 and axis f'2 had a significant correlations respectively but not for EMCV. According to the RSCU values, the EMCV species seemed to prefer U, G and C ending codon, while the ThV spice seemed to like using U and A ending codon. However, in both genus AGA for Arg, AUU for Ile, UCU for Ser, and GGA for Gly were chosen preferentially. Correspondence analysis detected one major trend in the first axis (f'1) which accounted for 22.89% of the total variation, and another major trend in the second axis (f'2) which accounted for 17.64% of the total variation. And the plots of the same serotype seemed at the same region at the coordinate.The overall extents of codon usage bias in both EMCV and ThV are low. The mutational pressure is the main factor that determines the codon usage bias, but the (C+G) content plays a more important role in codon usage bias for ThV than for EMCV. The synonymous codon usage pattern in both EMCV and ThV genes is gene function and geography specific, but not host specific. Maybe the serotype is one factor effected the codon bias for ThV, and location has no significant effect on the variations of synonymous codon usage in these virus genes.Synonymous codon usage is biased and the bias seems to be different in different organisms[1,2]. Many factors are concerned to be the reasons for this bias, such as degree and timing of gene expression, codon-anticodon interactions, transcription and translation rate and fidelity, codon context, and global and local (C+G) content[3,4]. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution, particularly the interplay between viruses and the immune response [5]. More recent studies have revealed that patterns o
Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes  [PDF]
Sameer Hassan,Vasantha Mahalingam,Vanaja Kumar
Advances in Bioinformatics , 2009, DOI: 10.1155/2009/316936
Abstract: Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.
The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern
Ming-ren Ma, Xiao-qin Ha, Hui Ling, Mei-liang Wang, Fang-xin Zhang, Shang-di Zhang, Ge Li, Wei Yan
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-544
Abstract: Relative synonymous codon usage (RSCU) values for the whole HBV coding sequence were studied by Principal component analysis (PCA). The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i) genotyps A and E, (ii) genotype B, (iii) genotypes C, D and G.Codon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.Hepatitis B virus (HBV) disease is one of the main global health problems that two billion people are infected and 350 million people undergo chronic infection as well [1]. HBV belongs to the protyotype member of the family Hepadnaviridae, and has a compact and circular DNA genome of about 3.2 kb in length, with four overlapping open reading frames including large S region (PreS/S), PreC/C, × and P [2,3]. Moreover, the overlapping regions on the genome are helpful to study the evolution of the virus with its point mutations, because the incidence of recombination is rare and any point mutation could effect the genetic characteristics of two overlapped genes [3]. The evolution of HBV should be interactional and constrained by the overlap of genes [4]. In some cases, the evolu
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