玉米AAP基因密码子偏性与进化分析

doi:10.19640/j.cnki.jtau.2024.03.004

Journal of Tianjin Agricultural University ›› 2024, Vol. 31 ›› Issue (3): 17-22.doi: 10.19640/j.cnki.jtau.2024.03.004

• Researches and Scientific Notes • Previous Articles Next Articles

Codon bias and evolution analysis of maize AAP gene

Wang Yu, Luo Xifan, Ge Junzhu, Chen Shuaijun, Yang Hongpeng, Wu Jiang^{Corresponding Author}

College of Agronomy and Resources Environment, Tianjin Agricultural University, Tianjin 300392, China

Received:2023-08-09 Online:2024-06-30 Published:2024-07-15

Abstract

Abstract: Amino acid permease (AAP) is involved in the absorption and transport of amino acids in plants, thereby altering plant growth and development. The study of codon preference of AAP gene is of guiding significance for heterologous expression of AAP gene, functional verification and improvement of its genetic transformation system. Codon W, EMBOSS, Origin 2021 and SPSS were used to perform clustering, neutral, ENC and PR2-plot of AAP gene codons of 25 species, and the best heteroexpression receptor and genetic transformation receptor of maize AAP were selected. The results showed that CAI, ENc and GC values of maize AAP gene were 0.269, 35.48 and 65.3%, respectively, indicating that the codon preference of maize AAP gene was weak, and the protein encoding process preferred to end in G/C. RSCU clustering analysis showed that maize AAP gene was similar to monocotyledonous grasses in terms of use preference and homologous relationship. The analysis of neutral, ENC and PR2 plots showed that the codon preference of maize AAP was greatly affected by natural selection. The codon frequency analysis showed that Escherichia coli was more suitable as heterologous expression receptor of maize AAP gene than yeast expression system, and rice was more suitable as genetic transformation receptor. This study provides a basis for the functional verification of maize AAP and the cultivation of transgenic plants.

Key words: maize, AAP gene, codon bias, cluster analysis, heterologous expression

CLC Number:

S513

Wang Yu, Luo Xifan, Ge Junzhu, Chen Shuaijun, Yang Hongpeng, Wu Jiang. Codon bias and evolution analysis of maize AAP gene[J]. Journal of Tianjin Agricultural University, 2024, 31(3): 17-22.

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References

[1] BOUDKO D Y.Molecular ontology of amino acid transport[M]// GERENCSER G A. Epithelial Transport Physiology. New York:Springer,2010:379-472.
[2] WIPF D,LUDEWIG U,TEGEDER M,et al.Conservation of amino acid transporters in fungi,plants and animals[J]. Trends Biochem Sci,2002,27(3):139-147.
[3] Rentsch D,Schmidt S,Tegeder M.Transporters for uptake and allocation of organic nitrogen compounds in plants[J]. FEBS Lett,2007,581(12):2281-2289.
[4] Fischer W,André B,Rentsch D,et al.Amino acid transport in plants[J]. Trends in Plant Science,1998,3(5):188-195.
[5] Frommer W B,Hummel S,Riesmeier J W.Expression cloning in yeast of a cDNA encoding a broad specificity amino acid permease from Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences of the United States of America,1993,90(13):5944-5948.
[6] Zhang L Z,Tan Q M,Lee R,et al.Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis[J]. Plant Cell,2010,22(11):3603-3620.
[7] Tegeder M.Transporters involved in source to sink partitioning of amino acids and ureides:opportunities for crop improvement[J]. Journal of Experimental Botany,2014,65:1865-1878.
[8] Schmidt R,Stransky H,Koch W.The amino acid permease AAP8 is important for early seed development in Arabidopsis thaliana[J]. Planta,2007,226(4):805-813.
[9] Okumoto S,Schmidt R,Tegeder M,et al.High affinity amino acid transporters specifically expressed in xylem parenchyma and developing seeds of Arabidopsis[J]. Journal of Biological Chemistry,2002,277(47):45338-45346.
[10] Lu Y,Song Z,Lü K,et al.Molecular characterization, expression and functional analysis of the amino acid transporter gene family(OsAATs)in rice[J]. Acta Physiologiae Plantarum,2012,34(5):1943-1962.
[11] Taylor M R,Reinders A,Ward J M.Transport function of rice amino acid permeases(AAPs)[J]. Plant & Cell Physiology,2015,56(7):1355.
[12] Zhao H,Ma H,Li Y,et al.Genome-wide survey and expression analysis of amino acid transporter gene family in rice(Oryza sativa L.)[J]. Plos One,2012,7(11):e49210.
[13] Tschaplinski T J, Standaert R F, Engle N L,et al.Down-regulation of the caffeic acid O- methyltransferase gene in switchgrass reveals a novel monolignol analog[J]. Biotechnol Biofuels,2012,5(1):71.
[14] Liu H M,He R,Zhang H Y,et al.Analysis of synonymous codon usage in Zea mays[J]. Molecular Biology Reports,2010,37(2):677-684.
[15] Ikemura T.Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes:a proposal for a synonymous codon choice that is optimal for the E. coli translational system[J]. Journal of Molecular Biology,1981,151(3):389-409.
[16] Sharp P M,Li W H.The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias[J]. Molecular Biology ＆ Evolution,1987,4(3):222-230.
[17] Chen S Y,Zhang H,Wang X,et al.Analysis of Codon usage bias in the chloroplast genome of Helianthus annuus J-01[J]. IOP Conference Series:Earth and Environmental Science,2021,792(1):9-12.
[18] Zhang W J,Zhou J,Li Z F,et al.Comparative analysis of Codon usage patterns among mitochondrion,chloroplast and nuclear genes in Triticum aestivum L[J]. Journal of Integrative Plant Biology,2007,49(2):246-254.
[19] Noboru S.Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position[J]. Gene,1999,238(1):53-58.
[20] 张晓元,郝荣华,刘飞,等. 密码子优化提高海藻糖合成酶基因在大肠杆菌中的表达水平[J]. 食品与药品,2019,21(1):1-6.
[21] 张建楼,徐瑞涛,霍珊珊,等. 猪细小病毒NS1基因的克隆、表达及密码子优化提高表达水平[J]. 中国兽医学报,2018,38(10):1840-1845.
[22] 孙鹏,朱爱臣,梁天,等. 鸡IL-17基因的克隆、序列分析及密码子优化提高表达水平[J]. 农业生物技术学报,2023,31(7):1464-1476.
[23] 王占军,李豹,姜行舟,等. 两种茶树全基因组数据的密码子偏好性比较分析[J]. 中国细胞生物学学报,2018,40(12):2028-2039.
[24] 周茜,王玉州,陈芸,等. 独行菜LaAP2基因密码子偏性与进化分析[J]. 生物学杂志,2021,38(6):15-19,30.
[25] He X,Li B,Shao Y,et al.Cell fusion between gastric epithelial cells and mesenchymal stem cells results in epithelial-to-mesenchymal transition and malignant transformation[J]. BMC Cancer,2015,15(1):24.
[26] Larue L,Bellacosa A.Epithelial-mesenchymal transition in development and cancer:role of phosphatidylinositol 3 kinase/AKT pathways[J]. Oncogene,2005,24(50):7443-7454.
[27] 吴宪明,吴松锋,任大明,等. 密码子偏性的分析方法及相关研究进展[J]. 遗传,2007,29(4):420-426.

Codon bias and evolution analysis of maize AAP gene

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