1
|
Prakash JAJ, Jacob JJ, Rachel T, Vasudevan K, Amladi A, Iyadurai R, Manesh A, Veeraraghavan B. Genomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence. Indian J Med Microbiol 2023; 44:100360. [PMID: 37356834 DOI: 10.1016/j.ijmmb.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/17/2023] [Accepted: 02/08/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE Brucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform. METHODS The two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out. RESULTS Phylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes. CONCLUSION Here we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.
Collapse
Affiliation(s)
- John Antony Jude Prakash
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Tanya Rachel
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Anushree Amladi
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Ramya Iyadurai
- Department of General Medicine Unit V, Christian Medical College and Hospital, Vellore 632004, Tamil Nadu, India.
| | - Abi Manesh
- Department of Infectious Diseases, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| |
Collapse
|
2
|
Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [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: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
Collapse
Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| |
Collapse
|
3
|
Wang X, Sun J, Zheng Y, Xie F. Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts. J Basic Microbiol 2022; 62:975-983. [PMID: 35778820 DOI: 10.1002/jobm.202200072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/01/2022] [Accepted: 06/11/2022] [Indexed: 11/09/2022]
Abstract
Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via Vs calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (Vs value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (Vs < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (Vs > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.
Collapse
Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Jing Sun
- Department of Endocrine, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yueyan Zheng
- School of Stomatology, Lanzhou University, Lanzhou, Gansu, China
| | - Fuqiang Xie
- Department of Stomatology, The Second Hospital of Lanzhou University, Lanzhou, Gansu, China
| |
Collapse
|
4
|
Saha J, Bhattacharjee S, Pal Sarkar M, Saha BK, Basak HK, Adhikary S, Roy V, Mandal P, Chatterjee A, Pal A. A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses. GENE REPORTS 2021; 23:101055. [PMID: 33615042 PMCID: PMC7887452 DOI: 10.1016/j.genrep.2021.101055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/20/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
The novel corona virus disease or COVID-19 caused by a positive strand RNA virus (PRV) called SARS-CoV-2 is plaguing the entire planet as we conduct this study. In this study a multifaceted analysis was carried out employing dinucleotide signature, codon usage and codon context to compare and unravel the genomic as well as genic characteristics of the SARS-CoV-2 isolates and how they compare to other PRVs which represents some of the most pathogenic human viruses. The main emphasis of this study was to comprehend the codon biology of the SARS-CoV-2 in the backdrop of the other PRVs like Poliovirus, Japanese encephalitis virus, Hepatitis C virus, Norovirus, Rubella virus, Semliki Forest virus, Zika virus, Dengue virus, Human rhinoviruses and the Betacoronaviruses since codon usage pattern along with the nucleotide composition prevalent within the viral genome helps to understand the biology and evolution of viruses. Our results suggest discrete genomic dinucleotide signature within the PRVs. Some of the genes from the different SARS-CoV-2 isolates were also found to demonstrate heterogeneity in terms of their dinucleotide signature. The SARS-CoV-2 isolates also demonstrated a codon context trend characteristically dissimilar to the other PRVs. The findings of this study are expected to contribute to the developing global knowledge base in countering COVID-19.
Collapse
Key Words
- CAI, Codon Adaptation Index
- CNS, Central Nervous System
- COVID-19
- CRS, Congenital Rubella Syndrome
- CUB, Codon Usage Bias
- Codon context
- Codon usage bias
- Coronaviruses
- Fop, Frequency of optimal codons
- GC1, Guanine and Cytosine content on the first position of the codon
- GC2, Guanine and Cytosine content on the second position of the codon
- GC3, Guanine and Cytosine content on the third position of the codon
- HCV, Hepatitis C Virus
- MERS, Middle East Respiratory Syndrome
- MFE, Minimum Free Energy
- Nc, Effective Number of Codons
- PCA, Principal Component Analysis
- PRV, Positive strand RNA Virus
- Positive strand RNA virus
- RCDI, Relative Codon De-Optimization Index
- RSCU, Relative Synonymous Codon Usage
- SARS, Severe Acute Respiratory Syndrome
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- SCUO, Synonymous Codon Usage Order
- SiD, Similarity Index
Collapse
Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Sukanya Bhattacharjee
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Barnan Kumar Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Hriday Kumar Basak
- Department of Chemistry, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Samarpita Adhikary
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Abhik Chatterjee
- Department of Chemistry, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj PIN-733 134, Uttar Dinajpur, West Bengal, India
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Xu Q, Chen H, Sun W, Zhu D, Zhang Y, Chen JL, Chen Y. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis. Microb Pathog 2021; 150:104732. [PMID: 33429052 DOI: 10.1016/j.micpath.2021.104732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 01/21/2023]
Abstract
Streptococcus suis (S. suis) is a gram-positive coccus that causes disease in humans and animals. The codon usage pattern of bacteria reveals a range of evolutionary changes that assist them to enhance tolerance to environments. To better understand the genetic features during the evolution of S. suis, we performed codon usage analysis. Nine pathogenic strains of different serotypes and different geographical distribution were analyzed to better understand the differences in their evolutionary process. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A/T-ending codons are dominant in S. suis. Neutrality analysis, correspondence analysis and ENC-plot results revealed that natural selection is the predominant element prompting codon usage. Cluster analysis based on RSCU was roughly consistent with the dendrogram rooted genomic BLAST analysis. Comparison of synonymous codon usage pattern between S. suis and susceptible hosts (H. sapiens and S. scrofa) revealed that the codon usage of S. suis is separated from the synonymous codon usage of susceptible hosts. The CAI values implied that S. suis includes a series of predicted highly expressed coding sequences contained in metabolism and transcriptional regulation, revealing the necessity of this pathogen to deal with various environmental conditions. The study of codon usage in S. suis may provide evidence involving the molecular evolution of bacteria and a better understanding of evolutionary relationships between S. suis and its corresponding hosts.
Collapse
Affiliation(s)
- Quanming Xu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Sun
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dewen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongyi Zhang
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ye Chen
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
7
|
A Crosstalk on Codon Usage in Genes Associated with Leukemia. Biochem Genet 2020; 59:235-255. [PMID: 32989646 DOI: 10.1007/s10528-020-10000-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023]
Abstract
Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.
Collapse
|
8
|
Silverj A, Rota-Stabelli O. On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus. Virus Res 2020; 286:198097. [DOI: 10.1016/j.virusres.2020.198097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
|
9
|
Ge Z, Li X, Cao X, Wang R, Hu W, Gen L, Han S, Shang Y, Liu Y, Zhou JH. Viral adaption of staphylococcal phage: A genome-based analysis of the selective preference based on codon usage Bias. Genomics 2020; 112:4657-4665. [PMID: 32818632 DOI: 10.1016/j.ygeno.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/09/2022]
Abstract
Given the high therapeutic value of the staphylococcal phage, the genome co-evolution of the phage and the host has gained great attention. Though the genome-wide AT richness in staphylococcal phages has been well-studied with nucleotide usage bias, here we proved that host factor, lifestyle and taxonomy are also important factors in understanding the phage nucleotide usages bias using information entropy formula. Such correlation is especially prominent when it comes to the synonymous codon usages of staphylococcal phages, despite the overall scattered codon usage pattern represented by principal component analysis. This strong relationship is explained by nucleotide skew which testified that the usage biases of nucleotide at different codon positions are acting on synonymous codons. Therefore, our study reveals a hidden relationship of genome evolution with host limitation and phagic phenotype, providing new insight into phage genome evolution at genetic level.
Collapse
Affiliation(s)
- Zhiyi Ge
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, United States of America
| | - Wen Hu
- Gansu Police Vocational College, Lanzhou 730046, Gansu, PR China
| | - Ling Gen
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China; The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, Gansu Province, PR China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Yongsheng Liu
- 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.
| |
Collapse
|
10
|
Zhou JH, Li H, Li X, Gao J, Xu L, Han S, Liu Y, Shang Y, Cao X. Tracing Brucella evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes. J Biomol Struct Dyn 2020; 39:3986-3995. [PMID: 32448095 DOI: 10.1080/07391102.2020.1773313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The host range of Brucella organisms has expanded from terrestrial and marine mammals to fish and amphibians. The high homology genomes of different Brucella organisms promote us to investigate evolutionary patterns for nucleotide, codon and amino acid usage patterns at gene levels among Brucella species. Although the similar patterns for nucleotide and synonymous codon usages exist in gene population, GC composition at the first codon position has significant correlations to that of the second and third codon positions, respectively, suggesting that nucleotide usages surrounding one codon influence synonymous codon usage patterns. Evolutionary patterns represented by synonymous codon and amino acid usages reflect host factor impacting Brucella speciation. As for genetic variations of important virulent factors involved with different biological functions, genes encoding lipoplysaccharides (LPSs) display more distinctive codon adaptation to Brucella than those of the BvrR/BvrS system and type IV secretion system. By Bayesian analysis, the polygenetic constructions for these genes of virulent factors shared by Brucella species display the purifying/positive selections and partially host factor in mediating genetic variations of these genes. The systemic analyses for nucleotide, synonymous codon and amino acid usages at gene level and genetic variations of important virulent factor genes display that host limitation influences either genetic characterizations at gene level or a particular gene involved in virulent factors of Brucella.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jian-Hua Zhou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Hua Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,China Agricultural Vet Biology and Technology limited liability company, Lanzhou, Gansu, P.R. China
| | - Xuerui Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Jing Gao
- Gansu Center for Animal Disease Prevention and Control, Lanzhou, Gansu, P.R. China
| | - Long- Xu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, P.R. China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, P.R. China
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, 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
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| |
Collapse
|
11
|
Han S, Hu W, Kan W, Ge Z, Song X, Li L, Shang Y, Zeng Q, Zhou JH. Analyses of genetics and pathogenesis of Salmonella enterica QH with narrow spectrum of antibiotic resistance isolated from yak. INFECTION GENETICS AND EVOLUTION 2020; 82:104293. [PMID: 32247035 DOI: 10.1016/j.meegid.2020.104293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 02/06/2023]
Abstract
Salmonella is an important pathogen for public health due to food poisoning and acute infectious intestinal disease by zoonotic trait. We isolated Salmonella enterica QH which represents the normal growth condition in Luria-Bertani culture and displays a wide range of susceptibility for multiple antibiotics. To further investigate genetic and pathogenic traits of S. enterica QH, the sequencing genome of S. enterica QH and oral Salmonella infection in mice were performed in this study. Compared with other Salmonella strains, several large sequences containing prophages and genomic islands were inserted into S. enterica QH genome. Furthermore, nucleotide and synonymous codon usage patterns display mutation pressure and natural selection serving as drivers for the evolutionary trend of S. enterica QH at gene level. The unique codon usage pattern of S. enterica QH probably contributes to adaptation to environmental/host niches and to pathogenicity. In an early oral S. enterica QH infection, the levels of CD4+ and CD8+ lymphocytes significantly reduce in peripheral blood of mice, but the increasing transcription levels of some cytokines (IFN-β1, IFN-γ and CXCL10) might have pleiotypic immune effects against S. enterica QH infection. Of note, IL10 displays significant enhancement at levels of transcription and translation, suggesting that immunosuppressive effects mediated by IL10 may function as an early oral S. enterica QH infection. The systemic investigations, including genomic and genetic characterizations and biological traits of S. enterica QH in vivo and in vitro may reflect the basic lifestyle of S. enterica QH, requiring intestine colonization, undergoing environmental stresses and performing dissemination.
Collapse
Affiliation(s)
- Shengyi Han
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu Province, PR China; State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Wen Hu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China; Gansu Police Vocational College, Lanzhou, 730046, Gansu, PR China
| | - Wei Kan
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu Province, PR China; Qinghai Animal Disease Prevention and Control Center, Xi-ning 810000, PR China
| | - Zhiyi Ge
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Xiangyang Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Lingxia Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, PR China
| | - Qiaoying Zeng
- The College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, Gansu Province, 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.
| |
Collapse
|
12
|
Jin L, Gao H, Cao X, Han S, Xu L, Ma Z, Shang Y, Ma XX. Significance and roles of synonymous codon usage in the evolutionary process of Proteus. J Basic Microbiol 2020; 60:424-434. [PMID: 32162710 DOI: 10.1002/jobm.201900647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/02/2020] [Accepted: 02/15/2020] [Indexed: 12/21/2022]
Abstract
Proteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine-tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.
Collapse
Affiliation(s)
- Li Jin
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Han Gao
- Department of College of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaoan Cao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Shengyi Han
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Long Xu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China.,College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiao-Xia Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| |
Collapse
|
13
|
Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
Collapse
|