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Wu Y, Jin L, Li Y, Zhang D, Zhao Y, Chu Y, Ma ZR, Ma XX, Shang Y. The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis. J Basic Microbiol 2021; 61:133-146. [PMID: 33426673 DOI: 10.1002/jobm.202000592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 11/08/2022]
Abstract
Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.
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Affiliation(s)
- Yaqin Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Li Jin
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yicong Li
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yuefeng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Zhong-Ren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Xiao-Xia Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
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Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA (NEW YORK, N.Y.) 2020; 26:1957-1975. [PMID: 32994183 PMCID: PMC7668247 DOI: 10.1261/rna.077537.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 05/22/2023]
Abstract
To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Julie Zumsteg
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Dimitri Heintz
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Laura Antoine
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Béatrice Chane-Woon-Ming
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Henri Grosjean
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles, Institut Labiris, B-1070, Belgium
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084, Strasbourg, France
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Cao XA, Hu W, Shang YJ, Liu YS, Han SY, Wang YN, Zhao L, Li XR, Zhou JH. Analyses of nucleotide, synonymous codon and amino acid usages at gene levels of Brucella melitensis strain QY1. INFECTION GENETICS AND EVOLUTION 2018; 65:257-264. [PMID: 30092351 DOI: 10.1016/j.meegid.2018.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/20/2018] [Accepted: 08/04/2018] [Indexed: 12/20/2022]
Abstract
Brucella melitensis is the causative pathogen of the zoonotic disease brucellosis in China. This work focused on analyses of genetic features represented by nucleotide, synonymous codon and amino acid usages at gene levels of B. melitensis strain QY1 isolated from China. Although nucleotide usage biases at different codon positions all work on synonymous codon usage bias, nucleotide usage biases at the 1st and 3rd positions play more important roles in codon usages. Mutation pressure caused by nucleotide composition constraint influences the formation of over-representative synonymous codons, but neighboring nucleotides surrounding a codon strongly influence synonymous codon usage bias for B. melitensis strain QY1. There is significant correlation between amino acid usage bias and hydropathicity of proteins for B. melitensis strain QY1. Compared with different Brucella species about synonymous codon usage patterns, synonymous codon usages are not obviously influenced by hosts. Due to nucleotide usage bias at the 1st codon position influencing synonymous codon and amino acid usages, good interactions among nucleotide, synonymous codon and amino acid usages exist in the evolutionary process of B. melitensis.
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Affiliation(s)
- Xiao-An Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Wen Hu
- Gansu Police Vocational College, Lanzhou 730046, Gansu, PR China
| | - You-Jun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Yong-Sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Sheng-Yi Han
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, Gansu, PR China
| | - Yi-Ning Wang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Lu Zhao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xue-Rui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
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Ma XX, Cao X, Ma P, Chang QY, Li LJ, Zhou XK, Zhang DR, Li MS, Ma ZR. Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas. J Basic Microbiol 2018. [PMID: 29537653 DOI: 10.1002/jobm.201700490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.
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Affiliation(s)
- Xiao-Xia Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Xin Cao
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Peng Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Qiu-Yan Chang
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Lin-Jie Li
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Xiao-Kai Zhou
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - De-Rong Zhang
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Ming-Sheng Li
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
| | - Zhong-Ren Ma
- Key Laboratory of Bioengineering & Biotechnology of State Ethnic Affairs Commission, Engineering and Technology Research Center for Animal Cell, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, P.R. China
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Ma XX, Ma P, Chang QY, Liu ZB, Zhang D, Zhou XK, Ma ZR, Cao X. Adaptation ofBorrelia burgdorferito its natural hosts by synonymous codon and amino acid usage. J Basic Microbiol 2018. [DOI: 10.1002/jobm.201700652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiao-Xia Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Peng Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Qiu-Yan Chang
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Zhen-Bin Liu
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Derong Zhang
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Xiao-Kai Zhou
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Zhong-Ren Ma
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
| | - Xin Cao
- Engineering and Technology Research Center for Animal Cell, Gansu; College of Life Science and Engineering; Northwest Minzu University; Gansu P.R. China
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Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. Agalactiae. J Genet 2016; 94:251-60. [PMID: 26174672 DOI: 10.1007/s12041-015-0512-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Because of the low GC content of the gene population, amino acids of the two mycoplasmas tend to be encoded by synonymous codons with an A or T end. Compared with the codon usage of ovine, Mycoplasma capricolum and M. agalactiae tend to select optimal codons, which are rare codons in ovine. Due to codon usage pattern caused by genes with key biological functions, the overall codon usage trends represent a certain evolutionary direction in the life cycle of the two mycoplasmas. The overall codon usage trends of a gene population of M. capricolum subsp. capricolum can be obviously separated from other mycoplasmas, and the overall codon usage trends of M. agalactiae are highly similar to those of M. bovis. These results partly indicate the independent evolution of the two mycoplasmas without the limits of the host cell's environment. The GC and AT skews estimate nucleotide composition bias at different positions of nucleotide triplets and the protein consideration caused by the nucleotide composition bias at codon positions 1 and 2 largely take part in synonymous codon usage patterns of the two mycoplasmas. The correlation between the codon adaptation index and codon usage variation indicates that the effect of codon usage on gene expression in M. capricolum subsp. capricolum is opposite to that of M. agalactiae, further suggesting independence of the evolutionary process influencing the overall codon usage trends of gene populations of mycoplasmas.
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Zhou JH, Ding YZ, He Y, Chu YF, Zhao P, Ma LY, Wang XJ, Li XR, Liu YS. The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. PLoS One 2014; 9:e108949. [PMID: 25350396 PMCID: PMC4211681 DOI: 10.1371/journal.pone.0108949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/26/2014] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains’ genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins.
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Affiliation(s)
- Jian-hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Yao-zhong Ding
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Ying He
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Yue-feng Chu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Ping Zhao
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Li-ya Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Xin-jun Wang
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Xue-rui Li
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
- * E-mail: (XRL); (YSL)
| | - Yong-sheng Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
- * E-mail: (XRL); (YSL)
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Li S, Yang J. System analysis of synonymous codon usage biases in archaeal virus genomes. J Theor Biol 2014; 355:128-39. [PMID: 24685889 PMCID: PMC7094158 DOI: 10.1016/j.jtbi.2014.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 12/30/2022]
Abstract
Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology. The SCUB of archaeal virus genes depends mainly on GC richness of genome. The mutational pressure is the main factor that influences SCUB. The aromaticity of each protein is also critical in affecting SCUB. The translational selection could play a leading role in HRPV1׳s SCUB. The mode is helpful to explore the origin of life and the evolution of biology.
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Affiliation(s)
- Sen Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China.
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