Genome-wide analysis of codon usage bias patterns in an enterotoxigenic Escherichia coli F18 strain

Ri Wei Xia,Wen Bin Bao,Xue Mei Yin,Wei Yun Qin,Guo Qiang Zhu,Sheng Long Wu 한국유전학회 2017 Genes & Genomics Vol.39 No.11

Enterogenic Escherichia coli (ETEC) F18 strains are the main pathogenic bacteria causing severe diarrhea in humans and domestic animals. However, the information about synonymous codon usage pattern of ETEC F18 genome remains unclear. We conducted a genome-wide analysis of synonymous codon usage patterns in the ETEC F18 strain SRA: SAMN02471895. After filtering of the complete genome sequence, 4327 coding sequences were analyzed using multivariate statistical methods to calculate synonymous codon usage patterns and to evaluate the influence of various factors in shaping the codon usage. The mean GC content was 51.38%, with a slight preference for G/C-ending codons. Twenty-two codons were determined as ‘‘optimal codons”. ENC plots showed some of the genes were on or close to the expected curve, while only points with low-ENC values were below the curve. PR2 analysis showed that GC and AT were not used proportionally, suggesting major roles for mutational pressure and natural selection in shaping usage. Neutrality plots showed a significant correlation between GC12 and GC3, suggesting that mutational pressure is responsible for nucleotide composition in shaping the strength of codon usage. Translational selection was the main factor shaping the codon usage pattern of ETEC F18 genome, while other factors such as protein length, GRAVY and ARO values also influenced codon usage to some extent. We analyzed the codon usage pattern systematically and identified the factors shaping codon usage bias in the ETEC F18 genome. Such information further elucidates the mechanisms of synonymous codon usage bias and provides the basis of molecular genetic engineering and evolutionary studies.

Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus

Hongju Wang,Tao Meng,Wenqiang Wei 한국유전학회 2018 Genes & Genomics Vol.40 No.7

The helicase gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is not only involved in viral DNA replication, but also plays a role in viral host range. To identify the codon usage bias of helicase of AcMNPV, the codon usage bias of helicase was especially studies in AcMNPV and 41 reference strains of baculoviruses by calculating the codon adaptation index (CAI), effective number of codon (ENc), relative synonymous codon usage (RSCU), and other indices. The helicase of baculovirus is less biased (mean ENc = 50.539 > 40; mean CAI = 0.246). AcMNPV helicase has a strong bias toward the synonymous codons with G and C at the third codon position (GC3s = 53.6%). The plot of GC3s against ENc values revealed that GC compositional constraints are the main factor that determines the codon usage bias of major of helicase. Several indicators supported that the codon usage pattern of helicase is mainly subject to mutation pressure. Analysis of variation in codon usage and amino acid composition indicated AcMNPV helicase shows the significant preference for one or more postulated codons for each amino acid. A cluster analysis based on RSCU values suggested that AcMNPV is evolutionarily closer to members of group I alphabaculovirus. Comparison of the codon usage pattern among E. coli, yeast, mouse, human and AcMNPV showed that yeast is a suitable expression system for AcMNPV helicase. AcMNPV helicase shows weak codon usage bias. This study may help in elucidating the functional mechanism of AcMNPV helicase and the evolution of baculovirus helicases.

Genome-wide comparative analysis of the codon usage patterns in plants

Shizhong Zhang,Jinguang Huang,Ning Li,Yuanyuan Li,Chengchao Zheng 한국유전학회 2016 Genes & Genomics Vol.38 No.8

Codon usage analysis has been a classical area of study for decades and is important for evolution, mRNA translation, and new gene discovery. Recently, genome sequencing has made it possible to perform studies of the entire genome in plant kingdoms. The base composition of the coding sequence, codon usage pattern, codon pairs, and related indicators of relative synonymous codon usage (RSCU), including the Fop, Nc, RSCU, CAI and GC contents, were analyzed. We found that the GC content of single-celled algae is the highest, whereas dicotyledons are the lowest. Moreover, the base composition of plants is similar within the same family. In addition, the GC content of the second base of the codon is lower than the first and third base. In conclusion, the codon usage characteristics are opposite in Gramineae, single-celled algae, fern and dicotyledon, moss, and Pinaceae. Furthermore, the degree of codon usage bias is decreasing with evolution. Therefore, we hypothesize that the lower the plants, the more that they must optimize codons and that higher plants no longer need to optimize codons.

Codon usage bias and evolutionary analyses of Zika virus genomes

Siddiq Ur Rahman,Yuanhui Mao,Shiheng Tao 한국유전학회 2017 Genes & Genomics Vol.39 No.8

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 influenzalike 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.

Insights into the Usage of Nucleobase Triplets and Codon Context Pattern in Five Influenza A Virus Subtypes^s

( Himangshu Deka ),( Supriyo Chakraborty ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.11

Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, an immense number of novel strains have developed astronomically over the years. The present work deals with the codon utilization partialness among five different influenza A viruses isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis showed very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role, which is reflected in the consequential positive correlation between the GC contents at different codon positions. Untangling the codon utilization profile would significantly contribute to identifying novel drug targets that will pacify the search for antivirals against this virus.

The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family

Satyabrata Sahoo,Ria Rakshit Korea Genome Organization 2022 Genomics & informatics Vol.20 No.4

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

Codon Usage Bias of Human Cytomegalovirus Genes with Different Evolutionary Conservancy

김유영,이찬희 대한미생물학회 2013 Journal of Bacteriology and Virology Vol.43 No.4

Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, β-herpes genes are common to β-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. β-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.

Codon Usage Bias of Human Cytomegalovirus Genes with Different Evolutionary Conservancy

Kim, Yu Young,Lee, Chan Hee 대한미생물학회 2013 Journal of Bacteriology and Virology Vol.43 No.4

Human cytomegalovirus (HCMV) is a member of beta-herpesvirus and contains a double-stranded genome with longer than 230 Kbp. HCMV infection of human is mostly asymptomatic, but often causes fatal diseases in immunocompromised people. In this study, codon usages of HCMV genes were analyzed and attempted to correlate with evolutionary conservancy. Core genes are the most conserved genes common among herpesvirus family, ${\beta}$-herpes genes are common to ${\beta}$-herpesviruses, and CMV genes are the least conserved found only in CMVs. Core genes had higher codon adaptation index (CAI) and GC content of silent 3rd codon position (GC3s) values and lower effective number of codons (Nc) and Nc/GC3s values than CMV genes. The average length of core genes was statistically longer than CMV genes, and core genes were found to be less varied than CMV genes. ${\beta}$-herpes genes could be placed between core and CMV genes. Higher CAI and GC3s values along with lower Nc and Nc/GC3s values are suggestive of higher codon usage bias and more adaptation to host cells. Thus it is concluded that core genes of HCMV are more biased in codon usage and adapted to host cells compared to CMV genes.

Synonymous Codon Usage Controls Various Molecular Aspects

임의현,최선심 한국유전체학회 2017 Genomics & informatics Vol.15 No.4

Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.

Synonymous Codon Usage Controls Various Molecular Aspects

Im, Eu-Hyun,Choi, Sun Shim Korea Genome Organization 2017 Genomics & informatics Vol.15 No.4

Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.