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Measure of synonymous codon usage diversity among genes in bacteria
Haruo Suzuki, Rintaro Saito, Masaru Tomita
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-167
Abstract: The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity.We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature.Most amino acids can be encoded by more than one codon (i.e., a triplet of nucleotides); such codons are described as being synonymous, and usually differ by one nucleotide in the third position. In most bacteria, alternative synonymous codons are not used with equal frequencies. Grantham et al. [1] showed that genes from same species often show similar patterns of codon usage, and proposed the 'genome hypothesis' that there exists a species-specific pattern of codon usage. Then, it was shown that in many organisms there are also considerable differences in codon usage among genes within a genome [2]. Previous analyses of codon usage diversity in bacteria have mostly focused on individual genomes, with no quantitative attempt to compare the diversity levels among different genomes. For comparative genomic analysis, it is desirable to quantify the level of codon usage diversity among genes in such a way that the estimates could be compared among genomes.Different factors have been proposed to explain the preferential usage of a subset of synonymous codons, including biased mutation pressure (genome-wide mutational bias toward G/C or
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
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
Maya Botzman, Hanah Margalit
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-10-r109
Abstract: To test this hypothesis we used a simple measure for assessing the extent of codon bias of an organism, and applied it to hundreds of sequenced prokaryotes. Our analysis revealed a large variability in this measure: there are organisms showing very high degrees of codon usage bias and organisms exhibiting almost no differential use of synonymous codons among different genes. Remarkably, we found that the extent of codon usage bias corresponds to the lifestyle of the organism. Especially, organisms able to live in a wide range of habitats exhibit high extents of codon usage bias, consistent with their need to adapt efficiently to different environments. Pathogenic prokaryotes also demonstrate higher extents of codon usage bias than non-pathogenic prokaryotes, in accord with the multiple environments that many pathogens occupy. Our results show that the previously observed correlation between growth rate and metabolic variability is attributed to their individual associations with codon usage bias.Our results suggest that the extent of codon usage bias of an organism plays a role in the adaptation of prokaryotes to their environments.The genetic code is composed of triplets of four nucleotide types for 20 amino acids. This redundancy implies the use of synonymous codons - different codons encoding the same amino acid. Synonymous codons may differ in their frequency of occurrence among different genes within an organism, a phenomenon known as 'codon usage bias' [1]. It was demonstrated that many bacteria and yeast undergo translational selection, with highly expressed genes preferentially using codons assumed to be translated faster and/or more accurately by the ribosome [2,3]. Previous works suggested that these codons are the ones matching abundant tRNAs, which are organism-specific [3-7]. Other works demonstrated additional factors affecting the frequencies of the synonymous codons in an organism, such as the genome GC content [8,9]. Thus, the preferred codons per a
Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants
Qin Zhen,Cai Zhengqiu,Xia Guangmin,Wang Mengcheng
BMC Genomics , 2013, DOI: 10.1186/1471-2164-14-56
Abstract: Background Evidence has been assembled to suggest synonymous codon usage bias (SCUB) has close relationship with intron. However, the relationship (if any) between SCUB and intron number as well as exon position is at present rather unclear. Results To explore this relationship, the sequences of a set of genes containing between zero and nine introns was extracted from the published genome sequences of three algal species, one moss, one fern and six angiosperms (three monocotyledonous species and three dicotyledonous species). In the algal genomes, the frequency of synonymous codons of the form NNG/NNC (codons with G and C at the third position) was positively related to intron number, but that of NNA/NNT was inversely correlated; the opposite was the case in the land plant genomes. The frequency of NNC/NNG was higher and that of NNA/NNT lower in two terminal exons than in the interstitial exons in the land plant genes, but the rule showed to be opposite in the algal genes. SCUB patterns in the interstitial and two terminal exons mirror the different evolutionary relationships between these plant species, while the first exon shows the highest level of conservation is therefore concluded to be the one which experiences the heaviest selection pressure. The phenomenon of SCUB may also be related to DNA methylation induced conversion of CG to AT. Conclusions These data provide some evidence of linkage between SCUB, the evolution of introns and DNA methylation, which brings about a new perspective for understanding how genomic variation is created during plant evolution.
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
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.
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
Codon Usage Bias Measured Through Entropy Approach  [PDF]
Michael G. Sadovsky,Julia A. Putintzeva
Quantitative Biology , 2007,
Abstract: Codon usage bias measure is defined through the mutual entropy calculation of real codon frequency distribution against the quasi-equilibrium one. This latter is defined in three manners: (1) the frequency of synonymous codons is supposed to be equal (i.e., the arithmetic mean of their frequencies); (2) it coincides to the frequency distribution of triplets; and, finally, (3) the quasi-equilibrium frequency distribution is defined as the expected frequency of codons derived from the dinucleotide frequency distribution. The measure of bias in codon usage is calculated for 125 bacterial genomes.
Analysis of codon usage and nucleotide composition bias in polioviruses
Jie Zhang, Meng Wang, Wen-qian Liu, Jian-hua Zhou, Hao-tai Chen, Li-na Ma, Yao-zhong Ding, Yuan-xing Gu, Yong-sheng Liu
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-146
Abstract: The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents and dinucleotides were investigated and a comparative analysis of codon usage pattern for open reading frames (ORFs) among 48 polioviruses isolates including 31 of genotype 1, 13 of genotype 2 and 4 of genotype 3.The result shows that the overall extent of codon usage bias in poliovirus samples is low (mean ENC = 53.754 > 40). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in those polioviruses. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage among three genotypes. Geographic factor also has some effect on the codon usage pattern (exists in the genotype-1 of polioviruses). No significant effect in gene length or vaccine derived polioviruses (DVPVs), wild viruses and live attenuated virus was observed on the variations of synonymous codon usage in the virus genes. The relative abundance of dinucleotide (CpG) in the ORFs of polioviruses are far below expected values especially in DVPVs and attenuated virus of polioviruses genotype 1.The information from this study may not only have theoretical value in understanding poliovirus evolution, especially for DVPVs genotype 1, but also have potential value for the development of poliovirus vaccines.When molecular sequence data started to be accumulated nearly 20 years ago, it was noted that synonymous codons are not used equally in different genomes, even in different genes of the same genome[1-3]. As an important evolutionary phenomenon, it is well known that synonymous codon usage bias exists in a wide range of biological systems from prokaryotes to eukaryotes [4,5]. Codon usage analysis has been applied to prokaryote and eukaryote, such as Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Caenorhabditis el
Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?
Xiufan Shi,Jingfei Huang,Chongrong Liang,Shuqun Liu,Jun Xie,Ciquan Liu
Chinese Science Bulletin , 2001, DOI: 10.1007/BF03183549
Abstract: Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest codon-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature, codon-anticodon binding strength may be closely related to synonymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.
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