PAP IB, a new member of the Reg gene family: Cloning, expression, structural properties, and evolution by gene duplication

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1727, Issue 3, 2005, Pages 177-187

  Laurine, Emmanuelle ^a,b,c,h   Manival, Xavier ^d,i   Montgelard, Claudine ^e   Bideau, Chantal ^f   Bergé Lefranc, Jean Louis ^f   Érard, Monique ^g   Verdier, Jean Michel ^a,b,c  

^a University of Montpellier   (France)

^b UNIV MONTPELLIER   (France)

^c PSL RESEARCH UNIVERSITY   (France)

^d Lab 'Rythmes Biologiques C   (France)

^e INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^f AIX MARSEILLE UNIVERSITY   (France)

^g INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

^h PARKINSON S INSTITUTE   (United States)

ⁱ Biopôle de l Université de Lorraine   (France)

Author keywords

Charge distribution; Homology modeling; PAP IB; Phylogeny; Reg; Structure function relationship

Indexed keywords

PANCREATITIS ASSOCIATED PROTEIN IB; PROTEIN; REGENERATION PROTEIN IALPHA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE EXPRESSION; LIGAND BINDING; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PANCREAS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; SURFACE CHARGE; X RAY;

EID: 14644387472     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2005.01.011     Document Type: Article

References (54)

1. J.P. Bernard, Z. Adrich, G. Montalto, A. De Caro, M. De Reggi, H. Sarles, and J.C. Dagorn Inhibition of nucleation and crystal growth of calcium carbonate by human lithostathine Gastroenterology 103 1992 1277 1284
2. S. Geider, A. Baronnet, C. Cerini, S. Nitsche, J.P. Astier, R. Michel, R. Boistelle, Y. Berland, J.C. Dagorn, and J.M. Verdier Pancreatic lithostathine as a calcite habit modifier J. Biol. Chem. 271 1996 26302 26306
3. E. Anastasi, E. Ponte, R. Gradini, A. Bulotta, P. Sale, C. Tiberti, H. Okamoto, F. Dotta, and U.D. Mario Expression of Reg and cytokeratin 20 during ductal cell differentiation and proliferation in a mouse model of autoimmune diabetes Eur. J. Endocrinol. 141 1999 644 652
4. H. Okamoto The Reg gene family and Reg proteins: with special attention to the regeneration of pancreatic beta-cells J. Hepato-Biliary-Pancr. Surg. 6 1999 254 262
5. M.E. Zenilman, J. Chen, and T.H. Magnuson Effect of reg protein on rat pancreatic ductal cells Pancreas 17 1998 256 261
6. J.L. Levine, K.J. Patel, Q. Zheng, A.R. Shuldiner, and M.E. Zenilman A recombinant rat regenerating protein is mitogenic to pancreatic derived cells J. Surg. Res. 89 2000 60 65
7. H. Nishimune, S. Vasseur, S. Wiese, M.C. Birling, B. Holtmann, M. Sendtner, J.L. Iovanna, and C.E. Henderson Reg-2 is a motoneuron neurotrophic factor and a signalling intermediate in the CNTF survival pathway Nat. Cell Biol. 2 2000 906 914
8. C. Lasserre, L. Christa, M.T. Simon, P. Vernier, and C. Bréchot A novel gene (HIP) activated in human primary liver cancer Cancer Res. 52 1992 5089 5095
9. T. Itoh, N. Sawabu, Y. Motoo, A. Funakoshi, and H. Teraoka The human pancreatitis-associated protein (PAP)-encoding gene generates multiple transcripts through alternative use of 5′ exons Gene 155 1995 283 287
10. H. Rechreche, G. Montalto, G.V. Mallo, S. Vasseur, L. Marasa, P. Soubeyran, J.C. Dagorn, and J.L. Iovanna pap, reg Ialpha and reg Ibeta mRNAs are concomitantly up-regulated during human colorectal carcinogenesis Int. J. Cancer 81 1999 688 694
11. T. Watanabe, Y. Yonemura, H. Yonekura, Y. Suzuki, H. Miyashita, K. Sugiyama, S. Moriizumi, M. Unno, O. Tanaka, and H. Kondo Pancreatic beta-cell replication and amelioration of surgical diabetes by Reg protein Proc. Natl. Acad. Sci. U. S. A. 91 1994 3589 3592
12. D.J. Gross, L. Weiss, I. Reibstein, J. van den Brand, H. Okamoto, A. Clark, and S. Slavin Amelioration of diabetes in nonobese diabetic mice with advanced disease by linomide-induced immunoregulation combined with Reg protein treatment Endocrinology 139 1998 2369 2374
13. L. Duplan, B. Michel, J. Boucraut, S. Barthellemy, S. Desplat-Jego, V. Marin, D. Gambarelli, D. Bernard, P. Berthezene, B. Alescio-Lautier, and J.M. Verdier Lithostathine and pancreatitis-associated protein are involved in the very early stages of Alzheimer's disease Neurobiol. Aging 22 2001 79 88
14. E. Laurine, C. Gregoire, M. Fandrich, S. Engemann, S. Marchal, L. Thion, M. Mohr, B. Monsarrat, B. Michel, C.M. Dobson, E. Wanker, M. Erard, and J.M. Verdier Lithostathine quadruple-helical filaments form proteinase K-resistant deposits in Creutzfeldt-Jakob disease J. Biol. Chem. 278 2003 51770 51778
15. E.V. Koonin, L. Aravind, and A.S. Kondrashov The impact of comparative genomics on our understanding of evolution Cell 101 2000 573 576
16. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
17. C. Bartoli, J.C. Dagorn, M. Fontes, and J.L. Bergé-Lefranc A limited genomic region contains the human REG and REG-related genes Eur. J. Hum. Genet. 3 1995 344 350
18. K. Nata, Y. Liu, L. Xu, T. Ikeda, T. Akiyama, N. Noguchi, S. Kawaguchi, A. Yamauchi, I. Takahashi, N.J. Shervani, T. Onogawa, S. Takasawa, and H. Okamoto Molecular cloning, expression and chromosomal localization of a novel human REG family gene, REG III Gene 340 2004 161 170
19. Y. Narushima, M. Unno, K. Nakagawara, M. Mori, H. Miyashita, Y. Suzuki, N. Noguchi, S. Takasawa, T. Kumagai, H. Yonekura, and H. Okamoto Structure, chromosomal localization and expression of mouse genes encoding type III Reg, RegIII alpha, RegIII beta, RegIII gamma Gene 185 1997 159 168
20. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J.F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, and M. Frazier Initial sequencing and analysis of the human genome Nature 409 2001 860 921
21. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L. Gabor Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R.R. Ji, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, B. Neelam, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, and C. Yan The sequence of the human genome Science 291 2001 1304 1351
22. H. Philippe MUST, a computer package of management utilities for sequences and trees Nucleic Acids Res. 21 1993 5264 5272
23. R. Rafaeloff, G.L. Pittenger, S.W. Barlow, X.F. Qin, B. Yan, L. Rosenberg, W.P. Duguid, and A.I. Vinik Cloning and sequencing of the pancreatic islet neogenesis associated protein (INGAP) gene and its expression in islet neogenesis in hamsters J. Clin. Invest. 99 1997 2100 2109
24. D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences Comput. Appl. Biosci. 8 1992 275 282
25. S. Guindon, and O. Gascuel A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 52 2003 696 704
26. J.P. Huelsenbeck, and F. Ronquist MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 17 2001 754 755
27. J. Greer Comparative modeling of homologous proteins Methods Enzymol. 202 1991 239 252
28. A.L. Morris, M.W. MacArthur, E.G. Hutchinson, and J.M. Thornton Stereochemical quality of protein structure coordinates Proteins 12 1992 345 364
29. R.A. Laskowski, D.S. Moss, and J.M. Thornton Main-chain bond lengths and bond angles in protein structures J. Mol. Biol. 231 1993 1049 1067
30. L. Wesson, and D. Eisenberg Atomic solvation parameters applied to molecular dynamics of proteins in solution Protein Sci. 1 1992 227 235
31. J.A. Blake, M.T. Davisson, J.T. Eppig, L.J. Maltais, S. Povey, J.A. White, and J.E. Womack A report on the international nomenclature workshop held may 1997 at the Jackson Laboratory, Bar Harbor, Maine, USA Genomics 45 1997 464 468
32. X. Huang A contig assembly program based on sensitive detection of fragment overlaps Genomics 14 1992 18 25
33. K. Drickamer Two distinct classes of carbohydrate-recognition domains in animal lectins J. Biol. Chem. 263 1988 9557 9560
34. K. Drickamer, and M.E. Taylor Biology of animal lectins Annu. Rev. Cell Biol. 9 1993 237 264
35. J.A. Bertrand, D. Pignol, J.P. Bernard, J.M. Verdier, J.C. Dagorn, and J.C. Fontecilla-Camps Crystal structure of human lithostathine, the pancreatic inhibitor of stone formation EMBO J. 15 1996 2678 2684
36. B.I. Lee, D. Mustafi, W. Cho, and Y. Nakagawa Characterization of calcium binding properties of lithostathine J. Biol. Inorg. Chem. 8 2003 341 347
37. S. Kumar, K. Tamura, and M. Nei MEGA: molecular evolutionary genetics analysis software for microcomputers Comput. Appl. Biosci. 10 1994 189 191
38. W.J. Murphy, E. Eizirik, S.J. O'Brien, O. Madsen, M. Scally, C.J. Douady, E. Teeling, O.A. Ryder, M.J. Stanhope, W.W. de Jong, and M.S. Springer Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294 2001 2348 2351
39. V. Gerbaud, D. Pignol, E. Loret, J.A. Bertrand, Y. Berland, J.C. Fontecilla-Camps, J.P. Canselier, N. Gabas, and J.M. Verdier Mechanism of calcite crystal growth inhibition by the N-terminal undecapeptide of lithostathine J. Biol. Chem. 275 2000 1057 1064
40. A.G. Clark Invasion and maintenance of a gene duplication Proc. Natl. Acad. Sci. U. S. A. 91 1994 2950 2954
41. J. Zhang Evolution by gene duplication: an update Trends Ecol. Evol. 18 2003 292 298
42. C.A. Orengo, A.E. Todd, and J.M. Thornton From protein structure to function Curr. Opin. Struct. Biol. 9 1999 374 382
43. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
44. B. Rost, B. Honig, and A. Valencia Bioinformatics in structural genomics Bioinformatics 18 2002 897 898
45. C.A. Wilson, J. Kreychman, and M. Gerstein Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores J. Mol. Biol. 297 2000 233 249
46. L. Thion, and M. Erard Structure/function relationships within the RNA recognition motif family applied to the hermes gene product Prot. Peptide Letters 9 2002 127 132
47. M.A. Andrade, S.I. O'Donoghue, and B. Rost Adaptation of protein surfaces to subcellular location J. Mol. Biol. 276 1998 517 525
48. O. Lichtarge, H.R. Bourne, and F.E. Cohen An evolutionary trace method defines binding surfaces common to protein families J. Mol. Biol. 257 1996 342 358
49. K. Pawlowski, and A. Godzik Surface map comparison: studying function diversity of homologous proteins J. Mol. Biol. 309 2001 793 806
50. D.R. Livesay, P. Jambeck, A. Rojnuckarin, and S. Subramaniam Conservation of electrostatic properties within enzyme families and superfamilies Biochemistry 42 2003 3464 3473
51. F.E. May, S.T. Church, S. Major, and B.R. Westley The closely related estrogen-regulated trefoil proteins TFF1 and TFF3 have markedly different hydrodynamic properties, overall charge, and distribution of surface charge Biochemistry 42 2003 8250 8259
52. H. Nielsen, J. Engelbrecht, S. Brunak, and G. von Heijne Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Eng. 10 1997 1 6
53. A.M. De Caro, Z. Adrich, B. Fournet, C. Capon, J.J. Bonicel, J.D. De Caro, and M. Rovery N-terminal sequence extension in the glycosylated forms of human pancreatic stone protein. The 5-oxoproline N-terminal chain is O-glycosylated on the 5th amino acid residue Biochim. Biophys. Acta 994 1989 281 284
54. H. Okamoto, and S. Takasawa Recent advances in the Okamoto model: the CD38-cyclic ADP-ribose signal system and the regenerating gene protein (Reg)-Reg receptor system in beta-cells Diabetes 51 Suppl. 3 2002 S462 S473