CREST - a large and diverse superfamily of putative transmembrane hydrolases

Biology Direct

Volumn 6, Issue , 2011, Pages

  Pei, Jimin ^a   Millay, Douglas P ^a   Olson, Eric N ^a   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

CELL SURFACE RECEPTOR; CERAMIDE; HYDROLASE; MEMBRANE PROTEIN; SPHINGOSINE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM; CELL MEMBRANE; CHEMISTRY; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYMOLOGY; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; BACTERIA; CATALYTIC DOMAIN; CELL MEMBRANE; CERAMIDES; ENZYME ACTIVATION; HUMANS; HYDROLASES; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; RECEPTORS, CELL SURFACE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; SPHINGOSINE;

EID: 79960893835     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-6-37     Document Type: Article

References (76)

1. Fagerberg L, Jonasson K, von Heijne G, Uhlen M, Berglund L. Prediction of the human membrane proteome. Proteomics 2010, 10:1141-1149. 10.1002/pmic.200900258, 20175080.
2. Hurwitz N, Pellegrini-Calace M, Jones DT. Towards genome-scale structure prediction for transmembrane proteins. Philos Trans R Soc Lond B Biol Sci 2006, 361:465-475. 10.1098/rstb.2005.1804, 1609336, 16524835.
3. Urban S, Shi Y. Core principles of intramembrane proteolysis: comparison of rhomboid and site-2 family proteases. Curr Opin Struct Biol 2008, 18:432-441. 10.1016/j.sbi.2008.03.005, 2572676, 18440799.
4. Martinez Molina D, Eshaghi S, Nordlund P. Catalysis within the lipid bilayer-structure and mechanism of the MAPEG family of integral membrane proteins. Curr Opin Struct Biol 2008, 18:442-449. 10.1016/j.sbi.2008.04.005, 18550357.
5. Mao C, Obeid LM. Ceramidases: regulators of cellular responses mediated by ceramide, sphingosine, and sphingosine-1-phosphate. Biochim Biophys Acta 2008, 1781:424-434. 2614331, 18619555.
6. Fyrst H, Saba JD. An update on sphingosine-1-phosphate and other sphingolipid mediators. Nat Chem Biol 2010, 6:489-497. 3001344, 20559316.
7. Villa NY, Kupchak BR, Garitaonandia I, Smith JL, Alonso E, Alford C, Cowart LA, Hannun YA, Lyons TJ. Sphingolipids function as downstream effectors of a fungal PAQR. Mol Pharmacol 2009, 75:866-875. 10.1124/mol.108.049809, 2684929, 19066337.
8. Holland WL, Miller RA, Wang ZV, Sun K, Barth BM, Bui HH, Davis KE, Bikman BT, Halberg N, Rutkowski JM, Wade MR, Tenorio VM, Kuo MS, Brozinick JT, Zhang BB, Birnbaum MJ, Summers SA, Scherer PE. Receptor-mediated activation of ceramidase activity initiates the pleiotropic actions of adiponectin. Nat Med 2011, 17:55-63. 10.1038/nm.2277, 21186369.
9. Baida GE, Kuzmin NP. Mechanism of action of hemolysin III from Bacillus cereus. Biochim Biophys Acta 1996, 1284:122-124. 10.1016/S0005-2736(96)00168-X, 8962879.
10. Fujita M, Umemura M, Yoko-o T, Jigami Y. PER1 is required for GPI-phospholipase A2 activity and involved in lipid remodeling of GPI-anchored proteins. Mol Biol Cell 2006, 17:5253-5264. 10.1091/mbc.E06-08-0715, 1679688, 17021251.
11. Maeda Y, Tashima Y, Houjou T, Fujita M, Yoko-o T, Jigami Y, Taguchi R, Kinoshita T. Fatty acid remodeling of GPI-anchored proteins is required for their raft association. Mol Biol Cell 2007, 18:1497-1506. 10.1091/mbc.E06-10-0885, 1838968, 17314402.
12. Winston WM, Molodowitch C, Hunter CP. Systemic RNAi in C. elegans requires the putative transmembrane protein SID-1. Science 2002, 295:2456-2459. 10.1126/science.1068836, 11834782.
13. Feinberg EH, Hunter CP. Transport of dsRNA into cells by the transmembrane protein SID-1. Science 2003, 301:1545-1547. 10.1126/science.1087117, 12970568.
14. Su Z, Wang X, Shen S, Wang L, Li Y, Li N, Li Z. Expression of 2 transcripts of NGX6 gene in colorectal cancer and the correlation with carcinoembryonic antigen. Zhong Nan Da Xue Xue Bao Yi Xue Ban 2010, 35:401-408.
15. Li J, Tan C, Xiang Q, Zhang X, Ma J, Wang JR, Yang J, Li W, Shen SR, Liang S, Li G. Proteomic detection of changes in protein synthesis induced by NGX6 transfected in human nasopharyngeal carcinoma cells. J Protein Chem 2001, 20:265-271. 10.1023/A:1010912311564, 11565907.
16. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
17. Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33:W244-248. 10.1093/nar/gki408, 1160169, 15980461.
18. Biegert A, Soding J. Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA 2009, 106:3770-3775. 10.1073/pnas.0810767106, 2645910, 19234132.
19. Frickey T, Lupas A. CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 2004, 20:3702-3704. 10.1093/bioinformatics/bth444, 15284097.
20. Pei J, Grishin NV. Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases. Protein Sci 2003, 12:1131-1135. 10.1110/ps.0240803, 2323883, 12717035.
21. Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda HM, Tani M, Sueyoshi N, Kambayashi K, Matsumura H, Kai Y, Ito M. Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. J Biol Chem 2009, 284:9566-9577. 10.1074/jbc.M808232200, 2666609, 19088069.
22. Xu R, Sun W, Jin J, Obeid LM, Mao C. Role of alkaline ceramidases in the generation of sphingosine and its phosphate in erythrocytes. FASEB J 2010, 24:2507-2515. 10.1096/fj.09-153635, 2887272, 20207939.
23. Aerts AM, Zabrocki P, Francois IE, Carmona-Gutierrez D, Govaert G, Mao C, Smets B, Madeo F, Winderickx J, Cammue BP, Thevissen K. Ydc1p ceramidase triggers organelle fragmentation, apoptosis and accelerated ageing in yeast. Cell Mol Life Sci 2008, 65:1933-1942. 10.1007/s00018-008-8129-8, 18500447.
24. Yang Q, Gong ZJ, Zhou Y, Yuan JQ, Cheng J, Tian L, Li S, Lin XD, Xu R, Zhu ZR, Mao C. Role of Drosophila alkaline ceramidase (Dacer) in Drosophila development and longevity. Cell Mol Life Sci 2010, 67:1477-1490. 10.1007/s00018-010-0260-7, 20112046.
25. Tang YT, Hu T, Arterburn M, Boyle B, Bright JM, Emtage PC, Funk WD. PAQR proteins: a novel membrane receptor family defined by an ancient 7-transmembrane pass motif. J Mol Evol 2005, 61:372-380. 10.1007/s00239-004-0375-2, 16044242.
26. Zhu Y, Rice CD, Pang Y, Pace M, Thomas P. Cloning, expression, and characterization of a membrane progestin receptor and evidence it is an intermediary in meiotic maturation of fish oocytes. Proc Natl Acad Sci USA 2003, 100:2231-2236. 10.1073/pnas.0336132100, 151323, 12574519.
27. Fernandes MS, Brosens JJ, Gellersen B. Honey, we need to talk about the membrane progestin receptors. Steroids 2008, 73:942-952. 10.1016/j.steroids.2007.12.004, 18221973.
28. Yamauchi T, Kamon J, Ito Y, Tsuchida A, Yokomizo T, Kita S, Sugiyama T, Miyagishi M, Hara K, Tsunoda M, Murakami K, Ohteki T, Uchida S, Takekawa S, Waki H, Tsuno NH, Shibata Y, Terauchi Y, Froguel P, Tobe K, Koyasu S, Taira K, Kitamura T, Shimizu T, Nagai R, Kadowaki T. Cloning of adiponectin receptors that mediate antidiabetic metabolic effects. Nature 2003, 423:762-769. 10.1038/nature01705, 12802337.
29. Yamauchi T, Kadowaki T. Physiological and pathophysiological roles of adiponectin and adiponectin receptors in the integrated regulation of metabolic and cardiovascular diseases. Int J Obes (Lond) 2008, 32(Suppl 7):S13-18.
30. Ouchi N, Parker JL, Lugus JJ, Walsh K. Adipokines in inflammation and metabolic disease. Nat Rev Immunol 2011, 11:85-97. 10.1038/nri2921, 21252989.
31. Zhu Y, Bond J, Thomas P. Identification, classification, and partial characterization of genes in humans and other vertebrates homologous to a fish membrane progestin receptor. Proc Natl Acad Sci USA 2003, 100:2237-2242. 10.1073/pnas.0436133100, 151324, 12601167.
32. Lyons TJ, Villa NY, Regalla LM, Kupchak BR, Vagstad A, Eide DJ. Metalloregulation of yeast membrane steroid receptor homologs. Proc Natl Acad Sci USA 2004, 101:5506-5511. 10.1073/pnas.0306324101, 397413, 15060275.
33. Hsieh MH, Goodman HM. A novel gene family in Arabidopsis encoding putative heptahelical transmembrane proteins homologous to human adiponectin receptors and progestin receptors. J Exp Bot 2005, 56:3137-3147. 10.1093/jxb/eri311, 16263907.
34. Karpichev IV, Cornivelli L, Small GM. Multiple regulatory roles of a novel Saccharomyces cerevisiae protein, encoded by YOL002c, in lipid and phosphate metabolism. J Biol Chem 2002, 277:19609-19617. 10.1074/jbc.M202045200, 11916977.
35. Kupchak BR, Garitaonandia I, Villa NY, Mullen MB, Weaver MG, Regalla LM, Kendall EA, Lyons TJ. Probing the mechanism of FET3 repression by Izh2p overexpression. Biochim Biophys Acta 2007, 1773:1124-1132. 10.1016/j.bbamcr.2007.04.003, 1994572, 17553578.
36. Chen YC, Chang MC, Chuang YC, Jeang CL. Characterization and virulence of hemolysin III from Vibrio vulnificus. Curr Microbiol 2004, 49:175-179.
37. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39:D561-568. 10.1093/nar/gkq973, 3013807, 21045058.
38. Kall L, Krogh A, Sonnhammer EL. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res 2007, 35:W429-432. 10.1093/nar/gkm256, 1933244, 17483518.
39. Gonez LJ, Naselli G, Banakh I, Niwa H, Harrison LC. Pancreatic expression and mitochondrial localization of the progestin-adipoQ receptor PAQR10. Mol Med 2008, 14:697-704. 2527345, 18769639.
40. Paidhungat M, Garrett S. Cdc1 and the vacuole coordinately regulate Mn2+ homeostasis in the yeast Saccharomyces cerevisiae. Genetics 1998, 148:1787-1798. 1460059, 9560393.
41. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. Global mapping of the yeast genetic interaction network. Science 2004, 303:808-813. 10.1126/science.1091317, 14764870.
42. Duxbury MS, Ashley SW, Whang EE. RNA interference: a mammalian SID-1 homologue enhances siRNA uptake and gene silencing efficacy in human cells. Biochem Biophys Res Commun 2005, 331:459-463. 10.1016/j.bbrc.2005.03.199, 15850781.
43. Wolfrum C, Shi S, Jayaprakash KN, Jayaraman M, Wang G, Pandey RK, Rajeev KG, Nakayama T, Charrise K, Ndungo EM, Zimmermann T, Koteliansky V, Manoharan M, Stoffel M. Mechanisms and optimization of in vivo delivery of lipophilic siRNAs. Nat Biotechnol 2007, 25:1149-1157. 10.1038/nbt1339, 17873866.
44. Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D, Bucher G. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol 2008, 9:R10. 10.1186/gb-2008-9-1-r10, 2395250, 18201385.
45. Huvenne H, Smagghe G. Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: a review. J Insect Physiol 2010, 56:227-235. 10.1016/j.jinsphys.2009.10.004, 19837076.
46. Miller JD, Arteca RN, Pell EJ. Senescence-associated gene expression during ozone-induced leaf senescence in Arabidopsis. Plant Physiol 1999, 120:1015-1024. 10.1104/pp.120.4.1015, 59334, 10444084.
47. De Rosa M, Gambacorta A, Gliozzi A. Structure, biosynthesis, and physicochemical properties of archaebacterial lipids. Microbiol Rev 1986, 50:70-80. 373054, 3083222.
48. Sun W, Jin J, Xu R, Hu W, Szulc ZM, Bielawski J, Obeid LM, Mao C. Substrate specificity, membrane topology, and activity regulation of human alkaline ceramidase 2 (ACER2). J Biol Chem 2010, 285:8995-9007. 10.1074/jbc.M109.069203, 2838321, 20089856.
49. Rosenbaum DM, Rasmussen SG, Kobilka BK. The structure and function of G-protein-coupled receptors. Nature 2009, 459:356-363. 10.1038/nature08144, 19458711.
50. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
51. Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res 2009, 37:D310-314. 10.1093/nar/gkn877, 2686597, 18996897.
52. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-222. 10.1093/nar/gkp985, 2808889, 19920124.
53. Rawlings ND, Barrett AJ, Bateman A. MEROPS: the peptidase database. Nucleic Acids Res 2010, 38:D227-233. 10.1093/nar/gkp971, 2808883, 19892822.
54. Saier MH, Yen MR, Noto K, Tamang DG, Elkan C. The Transporter Classification Database: recent advances. Nucleic Acids Res 2009, 37:D274-278. 10.1093/nar/gkn862, 2686586, 19022853.
55. Sun W, Xu R, Hu W, Jin J, Crellin HA, Bielawski J, Szulc ZM, Thiers BH, Obeid LM, Mao C. Upregulation of the human alkaline ceramidase 1 and acid ceramidase mediates calcium-induced differentiation of epidermal keratinocytes. J Invest Dermatol 2008, 128:389-397.
56. Mayor S, Riezman H. Sorting GPI-anchored proteins. Nat Rev Mol Cell Biol 2004, 5:110-120. 10.1038/nrm1309, 15040444.
57. Kupchak BR, Garitaonandia I, Villa NY, Smith JL, Lyons TJ. Antagonism of human adiponectin receptors and their membrane progesterone receptor paralogs by TNFalpha and a ceramidase inhibitor. Biochemistry 2009, 48:5504-5506. 10.1021/bi9006258, 2789275, 19453184.
58. Burke JE, Dennis EA. Phospholipase A2 biochemistry. Cardiovasc Drugs Ther 2009, 23:49-59. 10.1007/s10557-008-6132-9, 2823292, 18931897.
59. Funk CD. Prostaglandins and leukotrienes: advances in eicosanoid biology. Science 2001, 294:1871-1875. 10.1126/science.294.5548.1871, 11729303.
60. Noguchi K, Herr D, Mutoh T, Chun J. Lysophosphatidic acid (LPA) and its receptors. Curr Opin Pharmacol 2009, 9:15-23. 10.1016/j.coph.2008.11.010, 19119080.
61. Ferguson JF, Phillips CM, Tierney AC, Perez-Martinez P, Defoort C, Helal O, Lairon D, Planells R, Shaw DI, Lovegrove JA, Gjelstad IM, Drevon CA, Blaak EE, Saris WH, Leszczynska-Golabek I, Kiec-Wilk B, Riserus U, Karlstrom B, Miranda JL, Roche HM. Gene-nutrient interactions in the metabolic syndrome: single nucleotide polymorphisms in ADIPOQ and ADIPOR1 interact with plasma saturated fatty acids to modulate insulin resistance. Am J Clin Nutr 2010, 91:794-801. 10.3945/ajcn.2009.28255, 20032495.
62. Shih JD, Fitzgerald MC, Sutherlin M, Hunter CP. The SID-1 double-stranded RNA transporter is not selective for dsRNA length. RNA 2009, 15:384-390. 10.1261/rna.1286409, 2657005, 19155320.
63. Matthews BW, Colman PM, Jansonius JN, Titani K, Walsh KA, Neurath H. Structure of thermolysin. Nat New Biol 1972, 238:41-43. 10.1038/238041a0, 18663850.
64. Christianson DW, David PR, Lipscomb WN. Mechanism of carboxypeptidase A: hydration of a ketonic substrate analogue. Proc Natl Acad Sci USA 1987, 84:1512-1515. 10.1073/pnas.84.6.1512, 304464, 3470737.
65. Dideberg O, Charlier P, Dive G, Joris B, Frere JM, Ghuysen JM. Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution. Nature 1982, 299:469-470. 10.1038/299469a0, 7121588.
66. Feng L, Yan H, Wu Z, Yan N, Wang Z, Jeffrey PD, Shi Y. Structure of a site-2 protease family intramembrane metalloprotease. Science 2007, 318:1608-1612. 10.1126/science.1150755, 18063795.
67. Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009, 23:205-211.
68. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007, 2:953-971. 10.1038/nprot.2007.131, 17446895.
69. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659. 10.1093/bioinformatics/btl158, 16731699.
70. Pei J, Grishin NV. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 2007, 23:802-808. 10.1093/bioinformatics/btm017, 17267437.
71. Adachi J, Hasegawa M. MOLPHY version 2.3, programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs (The Institute of Statistical Mathematics) 1996, 28:1-150.
72. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
73. Hasegawa M, Kishino H, Saitou N. On the maximum likelihood method in molecular phylogenetics. J Mol Evol 1991, 32:443-445. 10.1007/BF02101285, 1904100.
74. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321. 10.1093/sysbio/syq010, 20525638.
75. Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006, 55:539-552. 10.1080/10635150600755453, 16785212.
76. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25:1307-1320. 10.1093/molbev/msn067, 18367465.