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Gong M, Lu X, Zhang C, Ma L, Yan H, Nai G, Lai Y, Li Y, Pu Z, Chen B, Ma S, Li S. Evolutionary analysis of genes from WOX family and their expression profile in grape ( Vitis vinifera) under different stresses. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP24136. [PMID: 39074235 DOI: 10.1071/fp24136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/09/2024] [Indexed: 07/31/2024]
Abstract
The WUSCHEL-related homeobox (WOX) transcription factor family plays critical roles in plant growth, development, and stress adaptation, but the biological functions in response to various stress of the WOX gene family have not been extensively researched in grapevine (Vitis vinifera ). In this study, 12 grapevine WOXs were identified from the grapevine genome. Quantitative PCR and microarray expression profiling found that the expression of WOXs had an obvious tissue-specific pattern. Conjoint analysis between various tissues and treated materials indicated VvWUS1 expression is associated with expression of genes from grapevine rupestris stem pitting-associated virus; and VvWOX3 with grapevine fanleaf virus. The gene expression patterns of the WOXs in grape were different under salt stress, with VvWOX8/9 , VvWUS1 , and VvWOX3 responding more strongly to salt stress than control by 18.20-, 9.50-, and 9.19-fold. This study further improves understanding of the evolution and function of the WOX gene family, and offers a theoretical framework and reference for breeding grapevine to better tolerate adversity and permit cultivation of seedlings free of viruses.
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Affiliation(s)
- Meishuang Gong
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xu Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Congcong Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Lei Ma
- Agronomy College, Gansu Agricultural University, Lanzhou 730070, China
| | - Haokai Yan
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Guojie Nai
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Ying Lai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanyuan Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhihui Pu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaoying Ma
- Laboratory and Base Management Center, Gansu Agricultural University, Lanzhou 730070, China
| | - Sheng Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; and College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China; and Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
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Gao W, Chen X, He J, Sha A, Luo Y, Xiao W, Xiong Z, Li Q. Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains. BMC Genomics 2024; 25:456. [PMID: 38730418 PMCID: PMC11084086 DOI: 10.1186/s12864-024-10374-3] [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: 06/12/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species. The results revealed that the codons of all Pleurotus strains had a preference for ending in A/T. Furthermore, the correlation between codon base compositions and codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) indices was also detected, implying the influence of base composition on codon bias. The two P. ostreatus species were found to have differences in various base bias indicators. The average effective number of codons (ENC) of mitochondrial core PCGs of Pleurotus was found to be less than 35, indicating strong codon preference of mitochondrial core PCGs of Pleurotus. The neutrality plot analysis and PR2-Bias plot analysis further suggested that natural selection plays an important role in Pleurotus codon bias. Additionally, six to ten optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified in eight Pleurotus strains, with UGU and ACU being the most widely used optimal codons in Pleurotus. Finally, based on the combined mitochondrial sequence and RSCU value, the genetic relationship between different Pleurotus strains was deduced, showing large variations between them. This research has improved our understanding of synonymous codon usage characteristics and evolution of this important fungal group.
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Affiliation(s)
- Wei Gao
- Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yingyong Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China.
- School of Food and Biological Engineering, Chengdu University, 2025 # Chengluo Avenue, Longquanyi District, Chengdu, Sichuan, 610106, China.
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Pouresmaeil M, Azizi-Dargahlou S. Investigation of CaMV-host co-evolution through synonymous codon pattern. J Basic Microbiol 2024; 64:e2300664. [PMID: 38436477 DOI: 10.1002/jobm.202300664] [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: 11/13/2023] [Revised: 01/20/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
Cauliflower mosaic virus (CaMV) has a double-stranded DNA genome and is globally distributed. The phylogeny tree of 121 CaMV isolates was categorized into two primary groups, with Iranian isolates showing the greatest genetic variations. Nucleotide A demonstrated the highest percentage (36.95%) in the CaMV genome and the dinucleotide odds ratio analysis revealed that TC dinucleotide (1.34 ≥ 1.23) and CG dinucleotide (0.63 ≤ 0.78) are overrepresented and underrepresented, respectively. Relative synonymous codon usage (RSCU) analysis confirmed codon usage bias in CaMV and its hosts. Brassica oleracea and Brassica rapa, among the susceptible hosts of CaMV, showed a codon adaptation index (CAI) value above 0.8. Additionally, relative codon deoptimization index (RCDI) results exhibited the highest degree of deoptimization in Raphanus sativus. These findings suggest that the genes of CaMV underwent codon adaptation with its hosts. Among the CaMV open reading frames (ORFs), genes that produce reverse transcriptase and virus coat proteins showed the highest CAI value of 0.83. These genes are crucial for the creation of new virion particles. The results confirm that CaMV co-evolved with its host to ensure the optimal expression of its genes in the hosts, allowing for easy infection and effective spread. To detect the force behind codon usage bias, an effective number of codons (ENC)-plot and neutrality plot were conducted. The results indicated that natural selection is the primary factor influencing CaMV codon usage bias.
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Affiliation(s)
- Mahin Pouresmaeil
- Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Seed and Plant Certification and Registration Institute, Ardabil Agricultural and Natural Resources Research Center, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Gao M, Yang X, Wu Y, Wang J, Hu X, Ma Z, Zhou JH. Analysis for codon usage bias in membrane anchor of nonstructural protein 5A from BVDV. J Basic Microbiol 2023; 63:1106-1114. [PMID: 37407515 DOI: 10.1002/jobm.202300080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/23/2023] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
The nonstructural protein 5A (NS5A) of the bovine viral diarrhea virus (BVDV) is a monotopic membrane protein. This protein can anchor to the cell membrane by an in-plane amphipathic ⍺-helix, which participates in the viral replication complex. In this study, the effects of synonymous codon usage pattern of NS5A and the overall transfer RNA (tRNA) abundance in cells on the formation of the in-plane membrane anchor of NS5A were analyzed, based on NS5A coding sequences of different BVDV genotypes. BVDV NS5A coding sequences represent the most potential for BVDV genotyping. Moreover, the nucleotide usage of BVDV NS5A dominates the genotype-specific pattern of synonymous codon usage. There is an obvious relationship between synonymous codon usage bias and the spatial conformation of the in-plane membrane anchor. Furthermore, the overall tRNA abundance profiling displays that codon positions with a high level of tRNA abundance are more than ones with a low level of tRNA abundance in the in-plane membrane anchor, implying that high translation speed probably acts on the spatial conformation of in-plane membrane anchor of BVDV NS5A. These results give a new opinion on the effect of codon usage bias in the formation of the in-plane membrane anchor of BVDV NS5A.
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Affiliation(s)
- Mingyang Gao
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xuanye Yang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yuhu Wu
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zhongren Ma
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
| | - Jian-Hua Zhou
- Key Laboratory of Biotechnology and Bioengineering of State Ethnic Affairs Commission, Biomedical Research Center, Northwest Minzu University, Lanzhou
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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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Li G, Shi L, Zhang L, Xu B. Componential usage patterns in dengue 4 viruses reveal their better evolutionary adaptation to humans. Front Microbiol 2022; 13:935678. [PMID: 36204606 PMCID: PMC9530264 DOI: 10.3389/fmicb.2022.935678] [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: 05/04/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
Abstract
There have been at least four types of dengue outbreaks in the past few years. The evolutionary characteristics of dengue viruses have aroused great concerns. The evolutionary characteristics of dengue 4 viruses are studied in the present study based on their base usage patterns and codon usage patterns. The effective number of codons and relative synonymous codon usage (RSCU) values of four types of dengue viruses were counted or calculated. The Kullback–Leibler (K–L) divergences of relative synonymous codon usage from dengue viruses to humans and the Kullback–Leibler divergences of amino acid usage patterns from dengue viruses to humans were calculated to explore the adaptation levels of dengue viruses. The results suggested that: (1) codon adaptation in dengue 4 viruses occurred through an evolutionary process from 1956 to 2021, (2) overall relative synonymous codon usage values of dengue 4 viruses showed more similarities to humans than those of other subtypes of dengue viruses, and (3) the smaller Kullback–Leibler divergence of amino acid usage and relative synonymous codon usage from dengue viruses to humans indicated that the dengue 4 viruses adapted to human hosts better. All results indicated that both mutation pressure and natural selection pressure contributed to the codon usage pattern of dengue 4 viruses more obvious than to other subtypes of dengue viruses and that the dengue 4 viruses adapted to human hosts better than other types of dengue viruses during their evolutionary process.
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Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'an Technological University, Xi'an, China
- *Correspondence: Gun Li
| | - Liang Shi
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'an Technological University, Xi'an, China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, China
- Liang Shi
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'an Technological University, Xi'an, China
| | - Bingyi Xu
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronic Information Engineering, Xi'an Technological University, Xi'an, China
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Salami Ghaleh S, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Mollapour Sisakht M, Farhadi A, Mousakhan Bakhtiari M, Lee Kuehu D, Deng Y. SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.22.501212. [PMID: 35923310 PMCID: PMC9347281 DOI: 10.1101/2022.07.22.501212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the β-coronavirus . This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus. According to the significant role of non-structural protein 1 (NSP1) in inhibiting host mRNA translation, this study focuses on the link between amino acid sequences of NSP1 and alterations of them spreading around the world. The SARS-CoV-2 NSP1 protein sequences were analyzed and FASTA files were processed by Python language programming libraries. Reference sequences compared with each NSP1 sample to identify every mutation and categorize them were based on continents and frequencies. NSP1 mutations rate divided into continents were different. Based on continental studies, E87D in global vision and also in Europe notably increased. The E87D mutation has significantly risen especially in the last months of the study as the first frequent mutation observed. The remarkable mutations, H110Y and R24C, have the second and third frequencies, respectively. Based on this mutational information, despite NSP1 being a conserved sequence occurrence, these mutations change the rate of flexibility and stability of the NSP1 protein, which can eventually affect inhibiting the host translation. IMPORTANCE In this study, we analyzed 6,510,947 sequences of non-structural protein 1 as a conserved region of SARS-CoV-2. According to the obtained results, 93.4819% of samples had no mutant regions on their amino acid sequences. Heat map data of mutational samples demonstrated high percentages of mutations that occurred in the region of 72 to 126 amino acids indicating a hot spot region of the protein. Increased rates of E87D, H110Y, and R24C mutations in the timeline of our study were reported as significant compared to available mutant samples. Analyzing the details of replacing amino acids in the most frequent E87D mutation reveals the role of this alteration in increasing molecule flexibility and destabilizing the structure of the protein.
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