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Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. BMC PLANT BIOLOGY 2024; 24:424. [PMID: 38764045 PMCID: PMC11103831 DOI: 10.1186/s12870-024-04999-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/08/2024] [Indexed: 05/21/2024]
Abstract
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.
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Affiliation(s)
- Lianwen Shen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, 650224, China
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
- Guizhou Academy of Forestry, Guiyang, 550005, China
| | | | - Mei Liang
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Shang Qu
- Guizhou Academy of Forestry, Guiyang, 550005, China
| | - Shijing Feng
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China.
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, China.
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Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C. Analysis of codon usage patterns in 48 Aconitum species. BMC Genomics 2023; 24:703. [PMID: 37993787 PMCID: PMC10664653 DOI: 10.1186/s12864-023-09650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/05/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found in China. These species are known for their various pharmacological effects and are commonly used to treat joint pain, cold abdominal pain, and other ailments. Codon usage bias (CUB) analysis contributes to evolutionary relationships and phylogeny. Based on protein-coding sequences (PCGs), we selected 48 species of Aconitum for CUB analysis. RESULTS The results revealed that Aconitum species had less than 50% GC content. Furthermore, the distribution of GC content was irregular and followed a trend of GC1 > GC2 > GC3, indicating a bias towards A/T bases. The relative synonymous codon usage (RSCU) heat map revealed the presence of conservative codons with slight variations within the genus. The effective number of codons (ENC)-Plot and the parity rule 2 (PR2)-bias plot analysis indicate that natural selection is the primary factor influencing the variation in codon usage. As a result, we screened various optimal codons and found that A/T bases were preferred as the last codon. Furthermore, our Maximum Likelihood (ML) analysis based on PCGs among 48 Aconitum species yielded results consistent with those obtained from complete chloroplast (cp.) genome data. This suggests that analyzing mutation in PCGs is an efficient method for demonstrating the phylogeny of species at the genus level. CONCLUSIONS The CUB analysis of 48 species of Aconitum was mainly influenced by natural selection. This study reveals the CUB pattern of Aconitum and lays the foundation for future genetic modification and phylogenetic analyses.
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Affiliation(s)
- Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Jiahao Liu
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Wanqing Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Yonglin Hai
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Haizhu Zhang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, Yunnan, 671000, China
| | - Xiaoli Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
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Li ZM, Fan ZL, Wang XY, Wang TY. Factors Affecting the Expression of Recombinant Protein and Improvement Strategies in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2022; 10:880155. [PMID: 35860329 PMCID: PMC9289362 DOI: 10.3389/fbioe.2022.880155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 06/01/2022] [Indexed: 01/20/2023] Open
Abstract
Recombinant therapeutic proteins (RTPs) are important parts of biopharmaceuticals. Chinese hamster ovary cells (CHO) have become the main cell hosts for the production of most RTPs approved for marketing because of their high-density suspension growth characteristics, and similar human post-translational modification patterns et al. In recent years, many studies have been performed on CHO cell expression systems, and the yields and quality of recombinant protein expression have been greatly improved. However, the expression levels of some proteins are still low or even difficult-to express in CHO cells. It is urgent further to increase the yields and to express successfully the “difficult-to express” protein in CHO cells. The process of recombinant protein expression of is a complex, involving multiple steps such as transcription, translation, folding processing and secretion. In addition, the inherent characteristics of molecular will also affect the production of protein. Here, we reviewed the factors affecting the expression of recombinant protein and improvement strategies in CHO cells.
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Affiliation(s)
- Zheng-Mei Li
- School of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
| | - Zhen-Lin Fan
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Institutes of Health Central Plain, Xinxiang Medical University, Xinxiang, China
| | - Xiao-Yin Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang, China
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
- *Correspondence: Tian-Yun Wang,
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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Bhandari BK, Lim CS, Remus DM, Chen A, van Dolleweerd C, Gardner PP. Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites. PLoS Comput Biol 2021; 17:e1009461. [PMID: 34610008 PMCID: PMC8519471 DOI: 10.1371/journal.pcbi.1009461] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/15/2021] [Accepted: 09/19/2021] [Indexed: 12/16/2022] Open
Abstract
Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann's ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.
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Affiliation(s)
- Bikash K. Bhandari
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Daniela M. Remus
- Callaghan Innovation Protein Science and Engineering, University of Canterbury, Christchurch, New Zealand
| | - Augustine Chen
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Craig van Dolleweerd
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
| | - Paul P. Gardner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Biomolecular Interaction Center, University of Canterbury, Christchurch, New Zealand
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Huo X, Liu S, Li Y, Wei H, Gao J, Yan Y, Zhang G, Liu M. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ 2021; 9:e10450. [PMID: 33505783 PMCID: PMC7789865 DOI: 10.7717/peerj.10450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.
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Affiliation(s)
- Xiaowei Huo
- College of Pharmaceutical Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Sisi Liu
- Hunan Academy of Forestry, Changsha, China
| | - Yimin Li
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Hao Wei
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Jing Gao
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Yonggang Yan
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Gang Zhang
- College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Mengmeng Liu
- College of Traditional Chinese Medicine, Hebei University, Baoding, China
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7
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Duan F, Chen J, Yao H, Wang Y, Jia Y, Ling Z, Feng Y, Pan Z, Yin Y, Jiao X. Enhanced therapeutic efficacy of Listeria-based cancer vaccine with codon-optimized HPV16 E7. Hum Vaccin Immunother 2021; 17:1568-1577. [PMID: 33449866 DOI: 10.1080/21645515.2020.1839291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cervical cancer is a leading cause of high mortality in women in developing countries and has a serious impact on women's health. Human papilloma virus (HPV) prophylactic vaccines have been produced and may hold promise for reducing the incidence of cervical cancer. However, the limitations of current HPV vaccine strategies make the development of HPV therapeutic vaccines particularly important for the treatment of HPV related lesions. Our previous work has demonstrated that LM4Δhly::E7 was safe and effective in inducing antitumor effect by antigen-specific cellular immune responses and direct killing of tumor cell on a cervical cancer model. In this study, the codon usage effect of a novel Listeria-based cervical cancer vaccine LM4Δhly::E7-1, was evaluated for effects of codon-optimized E7 expression, cellular immune response and therapeutic efficacy in a tumor-bearing murine model. Our data demonstrated that up-regulated expression of E7 was strikingly elevated by codon usage optimization, and thus induced significantly higher Th1-biased immunity, lymphocyte proliferation, and strong specific CTL activity ex-vivo compared with LM4Δhly::E7-treated mice. Furthermore, LM4Δhly::E7-1 enhanced a remarkable therapeutic effect in establishing tumors. Taken together, our results suggest that codon usage optimization is an important consideration in constructing live bacterial-vectored vaccines and is required for promoting effective T cell responses.
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Affiliation(s)
- Feifei Duan
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Jiaqi Chen
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Hao Yao
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yuting Wang
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yanyan Jia
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Zhiting Ling
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Youwei Feng
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Yuelan Yin
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
| | - Xin'An Jiao
- Jiangsu Key Laboratory of Zoonosis, Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, MOA of China, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou, Jiangsu Province, China
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Khan MS, Guan DL, Ma LB, Xie JY, Xu SQ. Analysis of synonymous codon usage pattern of genes in unique non-blood-sucking leech Whitmania pigra. J Cell Biochem 2019; 120:9850-9858. [PMID: 30681200 DOI: 10.1002/jcb.28267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/19/2018] [Indexed: 12/17/2022]
Abstract
Whitmania pigra is a unique, fluid-sucking ectoparasite and an anticoagulant medical leech. The codon usage bias (CUB) is the nonuniform usage of synonymous codons in which some codons are more preferred than others. Here, we performed a comprehensive analysis of CUB of genes in W. pigra, analyzing 140 780 transcripts, 59 553 unigenes, and 20 304 qualified coding sequences (CDSs) from the transcriptomic data of W. pigra. The effective number of codons values suggested that the CUB was low in these genes. We recognized profoundly favored codons in W. pigra that have a G/C-ending. Parity rule two-bias plots suggested that both mutation pressure and natural selection might have influenced the CUB. However, neutrality plots revealed that natural selection might have played a major role while mutation pressure might have played a minor role in shaping the CUB. We applied principal component analysis to relative synonymous codon usage values for divided CDSs based on GC content and codon-ending bases. Codon usage in W. pigra had a general inclination toward C-ending codons and natural selection rather than mutation pressure is the dominant force in the genetic evolution of W. pigra. To our knowledge, this is the first study to describe a complete codon usage analysis of W. pigra; this will increase the understanding of CUB and evolution in W. pigra. The analysis of codon usage patterns in W. pigra aids in understanding its evolution and genetic architecture.
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Affiliation(s)
- Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, People's Republic of China
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Vito D, Smales CM. Engineering of the cellular translational machinery and non-coding RNAs to enhance CHO cell growth, recombinant product yields and quality. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Guan DL, Ma LB, Khan MS, Zhang XX, Xu SQ, Xie JY. Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. BMC Genomics 2018; 19:542. [PMID: 30016953 PMCID: PMC6050667 DOI: 10.1186/s12864-018-4937-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Background Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. Results We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. Conclusions Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4937-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Xiu-Xiu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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Polysome profiling of mAb producing CHO cell lines links translational control of cell proliferation and recombinant mRNA loading onto ribosomes with global and recombinant protein synthesis. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/07/2017] [Accepted: 05/15/2017] [Indexed: 12/13/2022]
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12
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Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications. World J Microbiol Biotechnol 2016; 33:19. [PMID: 27905091 DOI: 10.1007/s11274-016-2185-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.
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Pan-omics analysis of biological data. Methods 2016; 102:1-2. [DOI: 10.1016/j.ymeth.2016.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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