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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Mao C, Obeid LM: Ceramidases: regulators of cellular responses mediated by ceramide, sphingosine, and sphingosine-1-phosphate. Biochim Biophys Acta. 2008, 1781: 424-434.
Article
PubMed
CAS
PubMed Central
Google Scholar
Fyrst H, Saba JD: An update on sphingosine-1-phosphate and other sphingolipid mediators. Nat Chem Biol. 2010, 6: 489-497.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Feinberg EH, Hunter CP: Transport of dsRNA into cells by the transmembrane protein SID-1. Science. 2003, 301: 1545-1547. 10.1126/science.1087117.
Article
PubMed
CAS
Google Scholar
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.
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
Biegert A, Soding J: Sequence context-specific profiles for homology searching. Proc Natl Acad Sci USA. 2009, 106: 3770-3775. 10.1073/pnas.0810767106.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
CAS
Google Scholar
Ouchi N, Parker JL, Lugus JJ, Walsh K: Adipokines in inflammation and metabolic disease. Nat Rev Immunol. 2011, 11: 85-97. 10.1038/nri2921.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen YC, Chang MC, Chuang YC, Jeang CL: Characterization and virulence of hemolysin III from Vibrio vulnificus. Curr Microbiol. 2004, 49: 175-179.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Paidhungat M, Garrett S: Cdc1 and the vacuole coordinately regulate Mn2+ homeostasis in the yeast Saccharomyces cerevisiae. Genetics. 1998, 148: 1787-1798.
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
De Rosa M, Gambacorta A, Gliozzi A: Structure, biosynthesis, and physicochemical properties of archaebacterial lipids. Microbiol Rev. 1986, 50: 70-80.
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rosenbaum DM, Rasmussen SG, Kobilka BK: The structure and function of G-protein-coupled receptors. Nature. 2009, 459: 356-363. 10.1038/nature08144.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Rawlings ND, Barrett AJ, Bateman A: MEROPS: the peptidase database. Nucleic Acids Res. 2010, 38: D227-233. 10.1093/nar/gkp971.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Mayor S, Riezman H: Sorting GPI-anchored proteins. Nat Rev Mol Cell Biol. 2004, 5: 110-120. 10.1038/nrm1309.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
Burke JE, Dennis EA: Phospholipase A2 biochemistry. Cardiovasc Drugs Ther. 2009, 23: 49-59. 10.1007/s10557-008-6132-9.
Article
PubMed
CAS
PubMed Central
Google Scholar
Funk CD: Prostaglandins and leukotrienes: advances in eicosanoid biology. Science. 2001, 294: 1871-1875. 10.1126/science.294.5548.1871.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
PubMed Central
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Eddy SR: A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009, 23: 205-211.
PubMed
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
Pei J, Grishin NV: PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics. 2007, 23: 802-808. 10.1093/bioinformatics/btm017.
Article
PubMed
CAS
Google Scholar
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.
Google Scholar
Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992, 8: 275-282.
PubMed
CAS
Google Scholar
Hasegawa M, Kishino H, Saitou N: On the maximum likelihood method in molecular phylogenetics. J Mol Evol. 1991, 32: 443-445. 10.1007/BF02101285.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
CAS
Google Scholar
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.
Article
PubMed
Google Scholar
Le SQ, Gascuel O: An improved general amino acid replacement matrix. Mol Biol Evol. 2008, 25: 1307-1320. 10.1093/molbev/msn067.
Article
PubMed
CAS
Google Scholar