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Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade
Enterovirus A (EV-A) species cause hand, foot and mouth disease (HFMD), threatening the health of young children. Understanding the mutual codon usage pattern of the virus and its host(s) has fundamental and applied values. Here, through examining multiple codon usage parameters, we found that the c...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9329520/ https://www.ncbi.nlm.nih.gov/pubmed/35909978 http://dx.doi.org/10.3389/fcimb.2022.941325 |
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author | Zeng, Liyan Chen, Ming Wang, Min Zhu, Liuyao Yan, Jingjing Zhang, Xiaoyan Xu, Jianqing Zhang, Shuye |
author_facet | Zeng, Liyan Chen, Ming Wang, Min Zhu, Liuyao Yan, Jingjing Zhang, Xiaoyan Xu, Jianqing Zhang, Shuye |
author_sort | Zeng, Liyan |
collection | PubMed |
description | Enterovirus A (EV-A) species cause hand, foot and mouth disease (HFMD), threatening the health of young children. Understanding the mutual codon usage pattern of the virus and its host(s) has fundamental and applied values. Here, through examining multiple codon usage parameters, we found that the codon usage bias among EV-A strains varies and is clade-specific. EVA76, EVA89, EVA90, EVA91 and EVA92, the unconventional clade of EV-A strains, show unique codon usage pattern relative to the two conventional clades, including EVA71, CVA16, CVA6 and CVA10, etc. Analyses of Effective Number of Codon (ENC), Correspondence Analysis (COA) and Parity Rule 2 (PR2), etc., revealed that the codon usage patterns of EV-A strains are shaped by mutation pressure and natural selection. Based on the neutrality analysis, we determined the dominant role of natural selection in the formation of the codon usage bias of EV-A. In addition, we have determined the codon usage compatibility of potential hosts for EV-A strains using codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses, and found that EV-A showed host-specific codon adaptation patterns in different clades. Finally, we confirmed that the unique codon usage pattern of the unconventional clade affected protein expression level in human cell lines. In conclusion, we identified novel characteristics of codon usage bias in distinct EV-A clades associated with their host range, transmission and pathogenicity. |
format | Online Article Text |
id | pubmed-9329520 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93295202022-07-29 Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade Zeng, Liyan Chen, Ming Wang, Min Zhu, Liuyao Yan, Jingjing Zhang, Xiaoyan Xu, Jianqing Zhang, Shuye Front Cell Infect Microbiol Cellular and Infection Microbiology Enterovirus A (EV-A) species cause hand, foot and mouth disease (HFMD), threatening the health of young children. Understanding the mutual codon usage pattern of the virus and its host(s) has fundamental and applied values. Here, through examining multiple codon usage parameters, we found that the codon usage bias among EV-A strains varies and is clade-specific. EVA76, EVA89, EVA90, EVA91 and EVA92, the unconventional clade of EV-A strains, show unique codon usage pattern relative to the two conventional clades, including EVA71, CVA16, CVA6 and CVA10, etc. Analyses of Effective Number of Codon (ENC), Correspondence Analysis (COA) and Parity Rule 2 (PR2), etc., revealed that the codon usage patterns of EV-A strains are shaped by mutation pressure and natural selection. Based on the neutrality analysis, we determined the dominant role of natural selection in the formation of the codon usage bias of EV-A. In addition, we have determined the codon usage compatibility of potential hosts for EV-A strains using codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses, and found that EV-A showed host-specific codon adaptation patterns in different clades. Finally, we confirmed that the unique codon usage pattern of the unconventional clade affected protein expression level in human cell lines. In conclusion, we identified novel characteristics of codon usage bias in distinct EV-A clades associated with their host range, transmission and pathogenicity. Frontiers Media S.A. 2022-07-14 /pmc/articles/PMC9329520/ /pubmed/35909978 http://dx.doi.org/10.3389/fcimb.2022.941325 Text en Copyright © 2022 Zeng, Chen, Wang, Zhu, Yan, Zhang, Xu and Zhang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Cellular and Infection Microbiology Zeng, Liyan Chen, Ming Wang, Min Zhu, Liuyao Yan, Jingjing Zhang, Xiaoyan Xu, Jianqing Zhang, Shuye Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title |
Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title_full |
Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title_fullStr |
Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title_full_unstemmed |
Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title_short |
Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade |
title_sort | enterovirus a shows unique patterns of codon usage bias in conventional versus unconventional clade |
topic | Cellular and Infection Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9329520/ https://www.ncbi.nlm.nih.gov/pubmed/35909978 http://dx.doi.org/10.3389/fcimb.2022.941325 |
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