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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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Wu X, Shan K, Zan F, Tang X, Qian Z, Lu J. Optimization and Deoptimization of Codons in SARS-CoV-2 and Related Implications for Vaccine Development. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205445. [PMID: 37267926 PMCID: PMC10427376 DOI: 10.1002/advs.202205445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/08/2023] [Indexed: 06/04/2023]
Abstract
The spread of coronavirus disease 2019 (COVID-19), caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2), has progressed into a global pandemic. To date, thousands of genetic variants have been identified among SARS-CoV-2 isolates collected from patients. Sequence analysis reveals that the codon adaptation index (CAI) values of viral sequences have decreased over time but with occasional fluctuations. Through evolution modeling, it is found that this phenomenon may result from the virus's mutation preference during transmission. Using dual-luciferase assays, it is further discovered that the deoptimization of codons in the viral sequence may weaken protein expression during virus evolution, indicating that codon usage may play an important role in virus fitness. Finally, given the importance of codon usage in protein expression and particularly for mRNA vaccines, it is designed several codon-optimized Omicron BA.2.12.1, BA.4/5, and XBB.1.5 spike mRNA vaccine candidates and experimentally validated their high levels of expression. This study highlights the importance of codon usage in virus evolution and provides guidelines for codon optimization in mRNA and DNA vaccine development.
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Affiliation(s)
- Xinkai Wu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Ke‐jia Shan
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Fuwen Zan
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of PathogensInstitute of Pathogen BiologyChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100176China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene ResearchCenter for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China
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Xiao Y, Huang H, Chen Y, Zheng S, Chen J, Zou Z, Mehmood N, Ullah I, Liao X, Wang J. Insight on genetic features prevalent in five Ipomoea species using comparative codon pattern analysis reveals differences in major codons and reduced GC content at the 5’ end of CDS. Biochem Biophys Res Commun 2023; 657:92-99. [PMID: 37001285 DOI: 10.1016/j.bbrc.2023.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Ipomoea plants possess important commercial, medicinal, and ornamental value. Molecular and morphological studies have confirmed that most species of this genus exhibit similar phenotypes but complex phylogenetic relationships. To date, limited information is available on these evolutionary relationships. In this study, systematic analysis of diverse species from Ipomoea was used to elucidate the relationships in this genus. To this end, we employed the concept of codon usage bias (CUB) to analyze the codon usage bias of five Ipomoea species such as effective number of codons (ENC) and GC content at the third synonym codon position (GC3s). Three types of plots including ENC-GC3s, parity rule 2 (PR2) and neutrality plots were employed to discover the factors determining CUB, and the frequency of hydrogen bonds and nucleotide were calculated to dissect changes in GC content at the 5'-end of the coding sequence. Our results showed little distinctness in CUB among the five species, with a reduction of hydrogen bonds content at the 5'-end (with similar changes in cytosines). In addition, optimal codons of Ipomoea aquatica ended with G or C, different from those of the other four species, which ended in A or T. These results may be useful for exploring the evolutionary relationships among this group, and for understanding the reasons for the variation among Ipomoea species.
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Pouresmaeil M, Dall'Ara M, Salvato M, Turri V, Ratti C. Cauliflower mosaic virus: Virus-host interactions and its uses in biotechnology and medicine. Virology 2023; 580:112-119. [PMID: 36812696 DOI: 10.1016/j.virol.2023.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023]
Abstract
Cauliflower mosaic virus (CaMV) was the first discovered plant virus with genomic DNA that uses reverse transcriptase for replication. The CaMV 35S promoter is a constitutive promoter and thus, an attractive driver of gene expression in plant biotechnology. It is used in most transgenic crops to activate foreign genes which have been artificially inserted into the host plant. In the last century, producing food for the world's population while preserving the environment and human health is the main topic of agriculture. The damage caused by viral diseases has a significant negative economic impact on agriculture, and disease control is based on two strategies: immunization and prevention to contain virus spread, so correct identification of plant viruses is important for disease management. Here, we discuss CaMV from different aspects: taxonomy, structure and genome, host plants and symptoms, transmission and pathogenicity, prevention, control and application in biotechnology as well as in medicine. Also, we calculated the CAI index for three ORFs IV, V, and VI of the CaMV virus in host plants, the results of which can be used in the discussion of gene transfer or antibody production to identify the CaMV.
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Affiliation(s)
- Mahin Pouresmaeil
- Department of Biotechnology, Faculty of Agriculture, Azarbijan Shahid Madani University, Tabriz, Iran.
| | - Mattia Dall'Ara
- Department of Agricultural and Food Sciences, School of Agriculture and Veterinary Medicine, University of Bologna, 40127, Bologna, Italy
| | - Maria Salvato
- University of Maryland, Department of Veterinary Medicine, College Park, MD, 20742, USA
| | - Valentina Turri
- Healthcare Direction, Istituto Scientifico Romagnolo per Lo Studio e La Cura Dei Tumori, IRCCS, 47014, Meldola, FC, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences, School of Agriculture and Veterinary Medicine, University of Bologna, 40127, Bologna, Italy
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Lu X, Chen Y, Zhang G. Functional evolution of SARS-CoV-2 spike protein: Maintaining wide host spectrum and enhancing infectivity via surface charge of spike protein. Comput Struct Biotechnol J 2023; 21:2068-2074. [PMID: 36936817 PMCID: PMC10008190 DOI: 10.1016/j.csbj.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The SARS-CoV-2 virus, which causes the COVID-19, is rapidly accumulating mutations to adapt to the hosts. We collected SARS-CoV-2 sequence data from the end of 2019 to January 2023 to analyze for their evolutionary features during the pandemic. We found that most of the SARS-CoV-2 genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. From the original strain to the alpha, delta and omicron variant types, the Ka/Ks of the S-gene increases, while the Ka/Ks within one variant type decreases over time. During the evolution, the codon usage did not evolve towards optimal translation and protein expression. In contrast, only S-gene mutations showed a remarkable trend on accumulating more positive charges. This facilitates the infection via binding human ACE2 for cell entry and binding furin for cleavage. Such a functional evolution emphasizes the survival strategy of SARS-CoV-2, and indicated new druggable target to contain the viral infection. The nearly fully positively-charged interaction surfaces indicated that the infectivity of SARS-CoV-2 virus may approach a limit.
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Affiliation(s)
- Xiaolong Lu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
- Chi-Biotech Co. Ltd., Shenzhen, China
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A comparative analysis depicting the disease characteristics and phylogenetic signature of human cytomegalovirus infection in Human Immunodeficiency Virus 1 seropositive patients with end-organ retinitis and gastro-enteric diseases. Sci Rep 2022; 12:7617. [PMID: 35538132 PMCID: PMC9091246 DOI: 10.1038/s41598-022-11727-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/11/2022] [Indexed: 11/08/2022] Open
Abstract
During advanced HIV infection, Human Cytomegalovirus (HCMV) has been proven to produce devitalizing end-organ diseases (EOD). The interactive co-existence of HIV and HCMV has been reported by many researchers and has been suggested to be linked with a more aggressive disease state. This study has been designed to bring forward an assessment of the clinical risk factors capable of defining the conditions of HCMV induced retinitis and gastro-enteric diseases among HIV1 seropositive patients. We also intended to analyse the phylogenetic variation if any, among the infecting virus types inducing the two separate clinical conditions. The patients were arranged in three different groups; (Group 1 with 26 individuals and group 2 and group 3 with 25 individuals each) based on their current status of HIV and HCMV infections. Serum ELISA, qualitative and quantitative detection of HCMV DNA, Real time mRNA expression study, sequencing, and phylogenetic analysis were performed. All statistical analyses and graphs were exercised using relevant software. We found that in HIV patients with HCMV induced end-organ diseases the components of the CXCL9, 10, 11-CXCR3 chemokine pathway is highly expressed with significant differences existing among patients with retinitis and gastrointestinal disease. We found that the gL gene sequences from the retinitis (HR) group clustered almost separately from that of the gastroenteritis (HG) group in the phylogenetic tree. It may be suggested that a form of natural selection pressure is working on the clinical HCMV strains creating a slight divergence in their phylogenetic lineage thereby helping them adapt to the particular tissue microenvironment they are colonizing.
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Mogro EG, Bottero D, Lozano MJ. Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic. Virology 2022; 568:56-71. [PMID: 35134624 PMCID: PMC8808327 DOI: 10.1016/j.virol.2022.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.
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Affiliation(s)
- Ezequiel G Mogro
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina
| | - Daniela Bottero
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina.
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation. J Appl Genet 2021; 63:159-167. [PMID: 34655422 PMCID: PMC8520108 DOI: 10.1007/s13353-021-00665-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/24/2021] [Accepted: 10/03/2021] [Indexed: 11/05/2022]
Abstract
During SARS-CoV-2 proliferation, the translation of viral RNAs is usually the rate-limiting step. Understanding the molecular details of this step is beneficial for uncovering the origin and evolution of SARS-CoV-2 and even for controlling the pandemic. To date, it is unclear how SARS-CoV-2 competes with host mRNAs for ribosome binding and efficient translation. We retrieved the coding sequences of all human genes and SARS-CoV-2 genes. We systematically profiled the GC content and folding energy of each CDS. Considering that some fixed or polymorphic mutations exist in SARS-CoV-2 and human genomes, all algorithms and analyses were applied to both pre-mutate and post-mutate versions. In SARS-CoV-2 but not human, the 5-prime end of CDS had lower GC content and less RNA structure than the 3-prime part, which was favorable for ribosome binding and efficient translation initiation. Globally, the fixed and polymorphic mutations in SARS-CoV-2 had created an even lower GC content at the 5-prime end of CDS. In contrast, no similar patterns were observed for the fixed and polymorphic mutations in human genome. Compared with human RNAs, the SARS-CoV-2 RNAs have less RNA structure in the 5-prime end and thus are more favorable of fast translation initiation. The fixed and polymorphic mutations in SARS-CoV-2 are further amplifying this advantage. This might serve as a strategy for SARS-CoV-2 to adapt to the human host.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China. .,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China.
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