Bioinformatics Analysis of the Structure and Function of CG17196 Protein of Drosophila Melanogaster
American Journal of Life Sciences
Volume 3, Issue 4, August 2015, Pages: 268-273
Received: May 25, 2015;
Accepted: Jun. 6, 2015;
Published: Jul. 1, 2015
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Hongchao Liu, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Xianming Zou, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Yiming Wang, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Xuanlong Du, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Qian Wang, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Junbao Xie, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Xinming Tu, Medical College, Henan University of Science and Technology, Luoyang, Henan, China
Recent studies have suggested that chimeric genes may account for the formation and evolution of new genes and functional divergence. However, the biological function of the new chimeric gene CG17196 of Drosophila melanogaster remains unknown, therefore, this study aims to analyze the structure and function of CG17196 protein using bioinformatics methods. Based on the amino acid sequence of CG17196 protein from NCBI database, the bioinformatics analyses were performed, including protein physical and chemical properties, transmembrane region, signal peptide, subcellular localization, domain, tertiary structure, and the phylogenetic tree of CG17196 related proteins from different species. The results showed that CG17196 protein was an unstable hydrophobic protein, performing biological function in the endoplasmic reticulum. It contained DHHC-type zinc finger domain and three transmembrane regions, but without signal peptide. The prediction result of gene ontology showed that the chance that the CG17196 protein actually had palmitoyltransferase activity was 70%. CG17196 protein and its related proteins in Schizosaccharomyces pombe, Ashbya gossypii, Dictyostelium discoideum and Arabidopsis thaliana showed high homology. In conclusion, CG17196 protein belongs to DHHC protein family and contains palmitoyltransferase activity, which may participate in the protein palmitoylation in the endoplasmic reticulum of Drosophila melanogaster, providing theoretical references for further systematic research on the function and evolution of new chimera CG17196.
Bioinformatics Analysis of the Structure and Function of CG17196 Protein of Drosophila Melanogaster, American Journal of Life Sciences.
Vol. 3, No. 4,
2015, pp. 268-273.
Zhang J, Dean AM, Brunet F, Long M. Evolving protein functional diversity in new genes of Drosophila. Proc Natl Acad Sci U S A, 2004, 101, 16246-16250.
Long M, VanKuren NW, Chen S, Vibranovski MD. New gene evolution: little did we know. Annu Rev Genet, 2013, 47, 307-333.
Assis R, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila. Proc Natl Acad Sci U S A, 2013, 110, 17409-17414.
Arguello JR, Chen Y, Yang S, Wang W, Long M. Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. PLoS Genet, 2006, 2, e77.
Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W. On the origin of new genes in Drosophila. Genome Res, 2008, 18, 1446-1455.
Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genet, 2013, 9, e1003860.
Zhou Q, Wang W. On the origin and evolution of new genes--a genomic and experimental perspective. J Genet Genomics, 2008, 35, 639-648.
Rogers RL, Bedford T, Hartl DL. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics, 2009, 181, 313-322.
Rogers RL, Hartl DL. Chimeric genes as a source of rapid evolution in Drosophila melanogaster. Mol Biol Evol, 2012, 29, 517-529.
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science, 2000, 290, 1151-1155.
Santos ME, Athanasiadis A, Leitão AB, DuPasquier L, Sucena E. Alternative splicing and gene duplication in the evolution of the FoxP gene subfamily. Mol Biol Evol, 2011, 28, 237-247.
Ding Y, Zhao L, Yang S, Jiang Y, Chen Y, Zhao R, Zhang Y, Zhang G, Dong Y, Yu H, Zhou Q, Wang W. A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet, 2010, 6, e1001255.
Chen S, Zhang YE, Long M. New genes in Drosophila quickly become essential. Science, 2010, 330, 1682-1685.
Kemkemer C, Long M. New genes important for development. EMBO Reports, 2014, 15, 460-461.
Ross BD, Rosin L, Thomae AW, Hiatt MA, Vermaak D, de la Cruz AF, Imhof A, Mellone BG, Malik HS. Stepwise evolution of essential centromere function in a Drosophila neogene. Science, 2013, 340, 1211-1214.
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server, In: John M. Walker, ed., The Proteomics Protocols Handbook, Humana Press 2005, pp. 571-607.
Möller S, Croning MD, Apweiler R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 2001, 17, 646-653.
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods, 2011, 8, 785-786.
Horton P, Nakai K. Better prediction of protein cellular localization sites with the k nearest neighbors classifier. Proc Int Conf Intell Syst Mol Biol, 1997, 5, 147-152.
Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Res, 2014, 42, W337-343.
Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 2006, 22, 195-201.
Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res, 2014, 42, W252-258.
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res, 2011, 39, D225-229.
Hamp T, Kassner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Rost B. Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics, 2013, 14, S7.
Benkert P, Biasini M, Schwede T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 2011, 27, 343-350.
Fukata M, Fukata Y, Adesnik H, Nicoll RA, Bredt DS. Identification of PSD-95 palmitoylating enzymes. Neuron, 2004, 44, 987-996.
Zhan ZB, Zhang Y, Zhao RP, Wang W. Evolutionary fate and expression patterns of chimeric new genes in Drosophila melanogaster. Dongwuxue Yanjiu, 2011, 32, 585-595. (in Chinese).
Bannan BA, Van Etten J, Kohler JA, Tsoi Y, Hansen NM, Sigmon S, Fowler E, Buff H, Williams TS, Ault JG, Glaser RL, Korey CA. The Drosophila protein palmitoylome: characterizing palmitoyl-thioesterases and DHHC palmitoyl-transferases. Fly (Austin), 2008, 2, 198-214.
Mesilaty-Gross S, Reich A, Motro B, Wides R. The Drosophila STAM gene homolog is in a tight gene cluster, and its expression correlates to that of the adjacent gene ial. Gene, 1999, 231, 173-186.
Resh MD. Trafficking and signaling by fatty-acylated and prenylated proteins. Nat Chem Biol, 2006, 2, 584-590.
Linder ME, Deschenes RJ. Palmitoylation: policing protein stability and traffic. Nat Rev Mol Cell Biol, 2007, 8, 74-84.
Greaves J, Chamberlain LH. Palmitoylation-dependent protein sorting. J Cell Biol, 2007,176, 249-254.