Bioinformatics Analysis of Casbene Synthase Genes in Different Plants

doi:10.7525/j.issn.1673-5102.2016.04.017

Abstract

Abstract: We used bioinformatics to study 13 casbene synthase (CS; EC 4.6.1.7) full-length gene sequences registered in the GenBank from Euphorbia esula, Jatropha curcas L., Ricinus communis and Triadica sebifera, and predicted the composition of nucleic acid and amino acid sequences, leader peptides, signal peptide, trans-membrane topological structure, hydrophobicity or hydrophilicity, the secondary and tertiary structure as well as the function domains. The 13 genes encoding ORFs were 1647-1845 bp, the molecular weight of the 13 predicted proteins were 63.0-70.8 kD, and the termination codons were TGA or TAA. The theoretical isoelectric points of the 13 proteins were lower than 7.0, which suggested that CS proteins were acidic. Leu was the most contented amino acid. By the homologous alignment of nucleic acid, CS genes were divided into two groups. The prediction of leading peptides showed that at least 6 CSs had leader peptide (chloroplast leader peptide mainly) in common. All 13 CSs had no signal peptide and trans-membrane topological structure in and the peptide chains were hydrophilicity. α-helix was the dominant secondary structure constructional element of the 13 proteins which contained two terpenoid synthases function domains.

Key words: tigliane, casbene synthase, bioinformatics

CLC Number:

S565.6

LIU Hong-Wei, YANG Yan-Fang, XIONG Wang-Dan, WU Ping-Zhi, WU Guo-Jiang, QIU De-You. Bioinformatics Analysis of Casbene Synthase Genes in Different Plants[J]. Bulletin of Botanical Research, 2016, 36(4): 605-612.

References

1.Adolf W,Opferkuch H J,Hecker E.Irritant phorbol derivatives from four Jatropha species[J].Phytochemistry,1984,23(1):129-132.
2.Gustafson K R,Cardellina J H,McMahon J B,et al.Non-promoting phorbol from the Samoan medicinal plant,Homalanthus nutans,inhibits cell killing by HIV-1[J].J Med Chem,1992,35(11):1978-1986.
3.Schmidt R J.The biosynthesis of tigliane and related diterpenoids:an intriguing problem[J].Bot J Linn Soc,1987,94(1):221-230.
4.Kirby J,Nishimoto M,Park J G,et al.Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae[J].Phytochemistry,2010,71(13):1466-1473.
5.Sato S,Hirakawa H,Isobe S,et al.Sequence Analysis of the Genome of an Oil-Bearing Tree[J].Jatropha curcas L.DNA Res,2011,18(1):65-76.
6.徐建华,朱家勇.生物信息学在蛋白质结构与功能预测中的应用[J].医学分子生物学杂志,2005,2(3):227-232.
Xu J H,Zhu J Y.Bioinformatics and Its Application on Protein Structure and Function Prediction[J].J Med Mol Biol,2005,2(3):227-232.
7.许忠能.生物信息学[M].北京:清华大学出版社,2008:3-10.
Xu Z N.Bioinformatics[M].Beijing:Tsinghua University Press,2008:3-10.
8.Gasteiger E,Gattiker A,Hoogland C,et al.ExPASy:the proteomics server for in-depth protein knowledge and analysis[J].Nucl Acids Res,2003,31(13):3784-3788.
9.Tamura K,Dudley J,Nei M,et al.MEGA4:Molecular evolutionary genetics analysis(MEGA) software version 4.0[J].Mol Biol Evol,2007,24(8):1596-1599.
10.翟中和,王喜忠,丁明孝.细胞生物学[M].北京:高等教育出版社,2000:79-240.
Zhai Z H,Wang X Z,Ding M X.Cell biology[M].Beijing:Higher Education Press,2000:79-240.
11.董娇,周军,辛培尧等.不同植物LDOX/ANS基因的生物信息学分析[J].基因组学与应用生物学,2010,29(5):815-822.
Dong J,Zhou J,Xin P Y,et al.Bioinformatics Analysis of LDOX/ANS Gene in Different Plants[J].Genomics and Applied Biology,2010,29(5):815-822.
12.Emanuelsson O,Nielsen H,Brunak S,et al.Predicting subcellular localization of proteins based on their N-terminal amino acid sequence[J].J Mol Biol,2000,300(4):1005-1016.
13.Emanuelsson O,Nielsen H,Heijne G V.ChloroP,a neural network-based method for predicting chloroplast transit peptides and their cleavage sites[J].Protein Science,1999,8(5):978-984.
14.Bendtsen J D,Nielsen H,Heijne G V,et al.Improved prediction of signal peptides:SingalP 3.0[J].J Mol Biol,2004,340(4):783-795.
15.Iked A M,Arai M,Lao D M.Transmembrane topology prediction methods:a reassessment and improvement by a consensus method using a dataset of experimentally characterized transmembrane topologies[J].In Silico Bio,2002,2(1):19-33.
16.薛庆中.DNA和蛋白质序列数据分析工具[M].第2版.北京:科学出版社,2009:72-109.
Xue Q Z.Data analysis tools of DNA and Protein[M].2ed edition.Beijing:Science Press,2009:72-109.
17.Kyce J,Doolittle R F.A simple method for displaying the hydropathic character of a protein[J].J Mol Biol,1982,157(6):105-132.
18.Geourjon C,Deleage G.SOPMA:Significant improvement in protein secondary structure prediction by consensus prediction from multiple alignments[J].Bioinformatics,1995,11(6):681-684.
19.王镜岩,朱圣庚,徐长发.生物化学[M].第3版.北京:高等教育出版社,2002.
Wang J Y,Zhu S G,Xu C F.Biochemistry[M].The third edition.Beijing:Higher Education Press,2002.
20.薛永常,聂会忠,刘长斌.木质素合酶C3H基因的生物信息学分析[J].生物信息学,2009,7(1):13-17.
Xue Y C,Nie H Z,Liu C B.Bioinformatics analysis on C3H in different plants[J].Bioinformatics,2009,7(1):13-17.
21.Schultz J,Milpetz F,Bork P,et al.SMART,a simple modular architecture research tool:identification of signaling domains[J].Proc Natl Acad Sci,1998,95(11):5857-5864.
22.Bohlmann J,Steele C L,Croteau R.Monoterpene synthases from grand fir(Abies grandis):cDNA isolation,characterization, and functional expression of myrcene synthase,(-)-(4S)-limonene synthase,and(-)-(1S,5S)-pinene synthase[J].J Biol Chem,1997,272(35):21784-21792.
23.Lambert C,Leonard N,De Bolle X,et al.ESyPred3D:Prediction of proteins 3D structures[J].Bioinformatics,2002,18(9):1250-1256.
24.Cao R,Zhang Y H,Mann F M,et al.Diterpene cyclases and the nature of the isoprene fold[J].Proteins:Struct Funct Bioinf,2010,78(11):2417-2432.
25.Köksal M,Jin Y,Coates R M,et al.Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis[J].Nature,2011,469(6):116-120.
26.Wendt K U,Poralla K,Schulz G E.Structure and function of a squalene cyclase[J].Science,1997,277(19):1811-1815.
27.Laskowski R A,Macarthur M W,Moss D,et al.PROCHECK:A program to check the stereo chemical quality of protein structures[J].J Appl Cryst,1993,26(2):283-291.

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