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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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Gao Y, Lu Y, Song Y, Jing L. Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus. BMC Genom Data 2022; 23:46. [PMID: 35725374 PMCID: PMC9210703 DOI: 10.1186/s12863-022-01064-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The phenomenon of codon usage bias is known to exist in many genomes and is mainly determined by mutation and selection. Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Sunflower (Helianthus annuus L.) is an annual crop that is cultivated worldwide as ornamentals, food plants and for their valuable oil. The WRKY family genes in plants play a central role in diverse regulation and multiple stress responses. Evolutionary analysis of WRKY family genes of H. annuus can provide rich genetic information for developing hybridization resources of the genus Helianthus.
Results
Bases composition analysis showed the average GC content of WRKY genes of H. annuus was 43.42%, and the average GC3 content was 39.60%, suggesting that WRKY gene family prefers A/T(U) ending codons. There were 29 codons with relative synonymous codon usage (RSCU) greater than 1 and 22 codons ending with A and U base. The effective number of codons (ENC) and codon adaptation index (CAI) in WRKY genes ranged from 43.47–61.00 and 0.14–0.26, suggesting that the codon bias was weak and WRKY genes expression level was low. Neutrality analysis found a significant correlation between GC12 and GC3. ENC-plot showed most genes on or close to the expected curve, suggesting that mutational bias played a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that the usage of AT and GC was disproportionate. A total of three codons were identified as the optimal codons.
Conclusion
Apart from natural selection effects, most of the genetic evolution in the H. annuus WRKY genome might be driven by mutation pressure. Our results provide a theoretical foundation for elaborating the genetic architecture and mechanisms of H. annuus and contributing to enrich H. annuus genetic resources.
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Salwan R, Sharma V. Trends in extracellular serine proteases of bacteria as detergent bioadditive: alternate and environmental friendly tool for detergent industry. Arch Microbiol 2019; 201:863-877. [PMID: 31025057 DOI: 10.1007/s00203-019-01662-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/20/2018] [Accepted: 04/15/2019] [Indexed: 02/07/2023]
Abstract
Proteases, one of the largest groups of industrial enzymes occupy a major share in detergent industry. To meet the existing demands, proteases with efficient catalytic properties are being explored from bacteria residing in extreme habitats. Alkaline proteases are also considered as promising candidates for industrial sectors due to the activity and stability under alkaline and harsh environment. Therefore, a systematic review on experimental studies of bacterial proteases was conducted with emphasis on purification, characterization, cloning and expression and their suitability as detergent additive. Relevant searches using a combination of filters/keywords were performed in the online databases; PubMed, Science Direct, Scopus and Web of Science. Over thousands of research papers, 71 articles in Scopus, 48 articles in Science Direct, 18 articles in PubMed and 8 articles in Web of Science were selected with regard to bacterial extracellular proteases till date. Selected articles revealed majority of the studies conducted between the years 2015 and 17 and were focused on purification of proteases from bacteria. Among microbes, a total of 41 bacterial genera have been explored with limited studies from extreme habitats. Majority of the studies have reported the involvement of subtilisin-like serine proteases with effective properties for detergent industries. The studies revealed shifting of trend from purification to cloning to genetic engineering to meet the industrial demands. The present systematic review describes the proteases from extremophilic bacteria and use of biotechnological techniques such as site-directed mutagenesis and codon optimization to engineer enzymes with better hot spots in the active sites to meet industrial challenges.
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Affiliation(s)
- Richa Salwan
- College of Horticulture and Forestry, Dr. YSP- University of Horticulture and Forestry, Neri, Hamirpur, HP, 177 001, India. .,University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, PB, 140 413, India.
| | - Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, PB, 140 413, India.
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Codon optimization significantly enhanced the expression of human 37-kDa iLRP in Escherichia coli. 3 Biotech 2018; 8:210. [PMID: 29651375 DOI: 10.1007/s13205-018-1234-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/02/2018] [Indexed: 01/24/2023] Open
Abstract
37-kDa immature laminin receptor protein (iLRP), the precursor of 67-kDa laminin receptor protein (LRP), is overexpressed on the surface of most cancer cells and recognized as a universal tumor antigen. The role makes it a potential target for cancer immunotherapy, which has been well-studied. Our study aimed to produce high quality of human iLRP in bacteria so that the needs in research of its clinical application could be met. The powerful system for heterologous protein expression, pET system was used. Two types of DNA sequences encoding the same amino acid sequences were separately cloned into the vector pET30a(+). One of the resulting vectors includes the wild-type iLRP, and other one includes the codon-optimized iLRP. The expression by both genes was then compared in Escherichia coli BL21(DE3). Our results revealed that the performance of codon optimization was crucial for the expression of human iLRP in Escherichia coli. The yield was significantly enhanced up to 300 mg/L of bacterial culture by this approach.
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Efficient genetic approaches for improvement of plasmid based expression of recombinant protein in Escherichia coli : A review. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Aghaei S, Saffar B, Ghaedi K, Mobini Dehkordi M. Functional analysis of recombinant codon-optimized bovine neutrophil β-defensin. J Adv Res 2016. [DOI: 10.1016/j.jare.2015.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Jia X, Liu S, Zheng H, Li B, Qi Q, Wei L, Zhao T, He J, Sun J. Non-uniqueness of factors constraint on the codon usage in Bombyx mori. BMC Genomics 2015; 16:356. [PMID: 25943559 PMCID: PMC4422305 DOI: 10.1186/s12864-015-1596-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori. Results A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans). Conclusions The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the “optimal codons” of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1596-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Jia
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Shuyu Liu
- Guangzhou East Campus Lab Centre, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China.
| | - Hao Zheng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Bo Li
- Innovative Drug Research Centre, Chongqing University, Chongqing, 401331, People's Republic of China.
| | - Qi Qi
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Lei Wei
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Taiyi Zhao
- Wageningen University, Wageningen, 6708 PG, Netherlands.
| | - Jian He
- Guangzhou East Campus Lab Centre, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Šnajder M, Mihelič M, Turk D, Ulrih NP. Codon optimisation is key for pernisine expression in Escherichia coli. PLoS One 2015; 10:e0123288. [PMID: 25856104 PMCID: PMC4391949 DOI: 10.1371/journal.pone.0123288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pernisine is an extracellular serine protease from the hyperthermophilic Archaeon Aeropyrum pernix K1. Low yields from the natural host and expression problems in heterologous hosts have limited the potential applications of pernisine in industry. METHODOLOGY/ PRINCIPAL FINDINGS The challenges of pernisine overexpression in Escherichia coli were overcome by codon preference optimisation and de-novo DNA synthesis. The following forms of the pernisine gene were cloned into the pMCSGx series of vectors and expressed in E. coli cells: wild-type (pernisinewt), codon-optimised (pernisineco), and codon-optimised with a S355A mutation of a predicted active site (pernisineS355Aco). The fusion-tagged pernisines were purified using fast protein liquid chromatography equipped with Ni2+ chelate and gel filtration chromatography columns. The identities of the resultant proteins were confirmed with N-terminal sequencing, tandem mass spectrometry analysis, and immunodetection. Pernisinewt was not expressed in E. coli at detectable levels, while pernisineco and pernisineS355Aco were expressed and purified as 55-kDa proforms with yields of around 10 mg per litre E. coli culture. After heat activation of purified pernisine, the proteolytic activity of the mature pernisineco was confirmed using zymography, at a molecular weight of 36 kDa, while the mutant pernisineS355Aco remained inactive. Enzymatic performances of pernisine evaluated under different temperatures and pHs demonstrate that the optimal enzymatic activity of the recombinant pernisine is ca. 100°C and pH 7.0, respectively. CONCLUSIONS/ SIGNIFICANCE These data demonstrate that codon optimisation is crucial for pernisine overexpression in E. coli, and that the proposed catalytic Ser355 has an important role in pernisine activity, but not in its activation process. Pernisine is activated by autoproteolytical cleavage of its N-terminal proregion. We have also confirmed that the recombinant pernisine retains the characteristics of native pernisine, as a calcium modulated thermostable serine protease.
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Affiliation(s)
- Marko Šnajder
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Marko Mihelič
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- Institute Jozef Stefan, Ljubljana, Slovenia
| | - Dušan Turk
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- Institute Jozef Stefan, Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology (CipKeBiP), Ljubljana, Slovenia
- * E-mail:
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