Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases
Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at d...
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| Published in | Biological & pharmaceutical bulletin Vol. 40; no. 7; pp. 1086 - 1091 |
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| Main Authors | , |
| Format | Journal Article |
| Language | English |
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Japan
The Pharmaceutical Society of Japan
01.07.2017
Pharmaceutical Society of Japan Japan Science and Technology Agency |
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| Abstract | Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro. |
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| AbstractList | Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro. Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro.Middle East respiratory syndrome coronavirus (MERS CoV) is a recently evolved fatal respiratory disease that poses a concern for a global epidemic. MERS CoV encodes 2 proteases, 3C-like protease (3CLpro) and papain-like protease (PLpro). These proteases share in processing MERS CoV polyproteins at different sites to yield 16 nonstructural proteins. In this work, we provide evidence that MERS CoV 3CLpro and PLpro are subject to different genetic and evolutionary influences that shape the protein sequence, codon usage pattern, and codon usage bias. Compositional bias is present in both proteins due to a preference for AT nucleotides. Thymidine (T) was highly preferred at the third position of codons, preferred and overrepresented codons in PLpro, but was replaced by guanosine (G) in 3CLpro. Compositional constraints were important in PLpro but not in 3CLpro. Directed mutation pressure seems to have a strong influence on 3CLpro codon usage, which is more than 30-fold higher than that in PLpro. Translational selection was evident with PLpro but not with 3CLpro. Both proteins are less immunogenic by showing low CpG frequencies. Correspondence analysis reveals the presence of 3 genetic clusters based on codon usage in PLpro and 3CLpro. Every protein had one common cluster and 2 different clusters. As revealed by correspondence analysis, the number of influences on codon usage are restricted in MERS CoV 3CLpro. In contrast, PLpro is controlled by a broader range of compositional, mutational, and other influences. This may be due to the multifunctional protease, deubiquitination, and innate immunity suppressing profiles of PLpro. |
| Author | Altaher, Abdallah Kandeel, Mahmoud |
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| CitedBy_id | crossref_primary_10_1016_j_meegid_2020_104471 crossref_primary_10_2174_2666796702666210709115659 crossref_primary_10_1016_j_jviromet_2019_113806 crossref_primary_10_1016_j_eng_2018_11_035 crossref_primary_10_1002_jmv_25754 crossref_primary_10_1080_07391102_2020_1784291 crossref_primary_10_1177_1176934320918861 crossref_primary_10_1016_j_compbiolchem_2018_05_020 |
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| References_xml | – reference: 17) Kandeel M, Kitade Y. In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference. J. Comput. Aided Mol. Des., 27, 605–614 (2013). – reference: 29) Kandeel M, Miyamoto T, Kitade Y. Bioinformatics, enzymologic properties, and comprehensive tracking of Plasmodium falciparum nucleoside diphosphate kinase. Biol. Pharm. Bull., 32, 1321–1327 (2009). – reference: 10) Wang F, Chen C, Tan W, Yang K, Yang H. Structure of main protease from human coronavirus NL63: insights for wide spectrum anti-coronavirus drug design. Scientific Reports, 6, 22677 (2016). – reference: 12) Lei J, Hilgenfeld R. Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin. Virol. Sin., 31, 288–299 (2016). – reference: 7) Shi J, Zhang J, Li S, Sun J, Teng Y, Wu M, Li J, Li Y, Hu N, Wang H, Hu Y. Epitope-based vaccine target screening against highly pathogenic MERS-CoV: an in silico approach applied to emerging infectious diseases. PLOS ONE, 10, e0144475 (2015). – reference: 28) Kandeel M, Kitamura Y, Kitade Y. The exceptional properties of Plasmodium deoxyguanylate pathways as a potential area for metabolic and drug discovery studies. Nucleic acids symposium series. Vol. 53, Oxford Univ. Press, pp. 39–40 (2009). – reference: 18) Bahir I, Fromer M, Prat Y, Linial M. Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences. Mol. Syst. Biol., 5, 311 (2009). – reference: 23) Chen Y, Chen Y-F. Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection. VirusDisease, 25, 285–293 (2014). – reference: 24) Uddin A, Mazumder TH, Choudhury MN, Chakraborty S. Codon bias and gene expression of mitochondrial ND2 gene in chordates. Bioinformation, 11, 407–412 (2015). – reference: 25) Shi S-L, Jiang Y-R, Yang R-S, Wang Y, Qin L. Codon usage in alphabaculovirus and betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected. Infect. Genet. Evol., 44, 412–417 (2016). – reference: 2) Kandeel M, Elaiziz M, Kandeel A, Altaher A, Kitade Y. Association of host tropism of Middle East syndrome coronavirus with the amino acid structure of host cell receptor dipeptidyl peptidase 4. Acta Virol., 58, 359–363 (2014). – reference: 27) Kandeel M, Kato A, Kitamura Y, Kitade Y. Thymidylate kinase: the lost chemotherapeutic target. Nucleic acids symposium series. Vol. 53, Oxford Univ. Press, pp. 283–284 (2009). – reference: 16) Kandeel M, Kitade Y. Computational analysis of siRNA recognition by the Ago2 PAZ domain and identification of the determinants of RNA-induced gene silencing. PLOS ONE, 8, e57140 (2013). – reference: 14) Lin M-H, Chuang S-J, Chen C-C, Cheng S-C, Cheng K-W, Lin C-H, Sun C-Y, Chou C-Y. Structural and functional characterization of MERS coronavirus papain-like protease. J. Biomed. Sci., 21, 54 (2014). – reference: 6) Cowling BJ, Park M, Fang VJ, Wu P, Leung GM, Wu JT. Preliminary epidemiologic assessment of MERS-CoV outbreak in South Korea, May–June 2015. Euro Surveill., 20, 7–13 (2015). – reference: 32) Zhou T, Gu W, Ma J, Sun X, Lu Z. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems, 81, 77–86 (2005). – reference: 5) Su S, Wong G, Liu Y, Gao GF, Li S, Bi Y. MERS in South Korea and China: a potential outbreak threat? Lancet, 385, 2349–2350 (2015). – reference: 20) Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from international DNA sequence databases: status for the year 2000. 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| SubjectTerms | 3C Viral Proteases Amino acid sequence codon usage Codons Computational Biology - methods Coronaviridae coronavirus Coronaviruses CpG islands Cysteine Endopeptidases - chemistry Cysteine Endopeptidases - genetics evolution Evolution, Molecular Food chains Genome, Viral Guanosine Immunogenicity Innate immunity Interferon Middle East Respiratory Syndrome Coronavirus - enzymology Middle East Respiratory Syndrome Coronavirus - genetics Middle East Respiratory Syndrome Coronavirus - physiology Nonstructural proteins Nucleotides Papain Papain - chemistry Papain - genetics Polyproteins protease Protein Processing, Post-Translational Proteinase Proteins Respiratory diseases Silent Mutation - genetics synonymous codon Thymidine Viral Proteins - chemistry Viral Proteins - genetics Virus Replication - genetics |
| Title | Synonymous and Biased Codon Usage by MERS CoV Papain-Like and 3CL-Proteases |
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