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Tikhomirova TS, Matyunin MA, Lobanov MY, Galzitskaya OV. In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein? Proteins 2021; 90:1119-1141. [PMID: 34964171 DOI: 10.1002/prot.26294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022]
Abstract
Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.
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Affiliation(s)
- Tatyana S Tikhomirova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia
| | - Maxim A Matyunin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Michail Yu Lobanov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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3
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Qi X, Wei C, Li Y, Wu Y, Xu H, Guo R, Jia Y, Li Z, Wei Z, Wang W, Jia J, Li Y, Wang A, Gao X. The characteristic of the synonymous codon usage and phylogenetic analysis of hepatitis B virus. Genes Genomics 2020; 42:805-815. [PMID: 32462516 PMCID: PMC7311504 DOI: 10.1007/s13258-020-00932-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/31/2020] [Indexed: 12/18/2022]
Abstract
Background Hepatitis B virus (HBV) infection is a crucial medical issue worldwide. The dependence of HBV replication on host cell machineries and their co-evolutionary interactions prompt the codon usage pattern of viral genes to translation selection and mutation pressure. Objective The evolutionary characteristics of HBV and the natural selection effects of the human genome on the codon usage characteristics were analyzed to provide a basis for medication development for HBV infection. Methods The codon usage pattern of sequences from different HBV genotypes of our isolates and reference HBV genome sequences downloaded from the National Center for Biotechnology Information (NCBI) database were analyzed by computing the relative synonymous codon usage (RSCU), nucleotide content, codon adaptation index (CAI) and the effective number of codons (ENC). Results The highest ENC values were observed in the C genotypes, followed by the B genotypes. The ENC values indicated a weak codon usage bias (CUB) in HBV genome. The number of codons differentially used between the three genotypes was markedly higher than that of similarly used codons. High CAI values indicated a good adaptability of HBV to its host. The ENC plot indicated the occurrence of mutational pressure in the three genotypes. The mean Ka/Ks ratios in the three genotypes were lower than 1, which indicated a negative selection pressure. The CAI and GC3% plot indicated the existence of CUB in the HBV genome. Conclusions Nucleotide composition, mutation bias, negative selection and mutational pressure are key factors influencing the CUB and phylogenetic diversity in HBV genotypes. The data provided here could be useful for developing drugs for HBV infection. Electronic supplementary material The online version of this article (10.1007/s13258-020-00932-w) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoming Qi
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Chaojun Wei
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Yonghong Li
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Yu Wu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Hui Xu
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Rui Guo
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Yanjuan Jia
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Zhenhao Li
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Zhenhong Wei
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Wanxia Wang
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Jing Jia
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Yuanting Li
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Anqi Wang
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China.,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China.,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China
| | - Xiaoling Gao
- The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital, 204 Donggang West Road, Chengguan District, Lanzhou, 730000, China. .,NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, 730000, China. .,Gansu Provincial Biobank and Bioinformation Engineering Research Center, Lanzhou, 730000, China.
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5
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Ulrich K, Wehner S, Bekaert M, Di Paola N, Dilcher M, Muir KF, Taggart JB, Matejusova I, Weidmann M. Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades. J Gen Virol 2018; 99:1567-1581. [PMID: 30358526 DOI: 10.1099/jgv.0.001155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59 % of the IPNV isolates belonged to the persistent type and 32 % to the low-virulent type, and only one highly pathogenic strain (1.79 %) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Under-representation of CpG dinucleotides in the IPNV genome to minimize detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes, together with the assumption of adaptation and immune escape, indicates that IPNV is evolving with the host.
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Affiliation(s)
- Kristina Ulrich
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Michaël Bekaert
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Nicholas Di Paola
- 3Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Meik Dilcher
- 4Canterbury Health Laboratories, Christchurch, New-Zealand
| | | | - John B Taggart
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Manfred Weidmann
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
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