Comparative genomic analysis of the clade B serpin cluster at human chromosome 18q21: Amplification within the mouse squamous cell carcinoma antigen gene locus

Genomics

Volumn 84, Issue 1, 2004, Pages 176-184

  Askew, David J ^a   Askew, Yuko S ^a   Kato, Yukari ^a   Turner, Russell F ^a   Dewar, Ken ^b   Lehoczky, Jessica ^b   Silverman, Gary A ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

Chromosome 18; EST; expressed sequence tag; National Center for Biotechnology Information; NCBI; percentage identity plots; PIP; Proteinases; reactive site loop; RSL; SCCA; serine proteinase inhibitor; serpin; Serpins; squamous cell carcinoma antigen; STS

Indexed keywords

GENOMIC DNA; SERINE PROTEINASE INHIBITOR; SQUAMOUS CELL CARCINOMA ANTIGEN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CHROMOSOME 18Q; CLADISTICS; DNA DETERMINATION; DNA SEQUENCE; FEMALE; GENE AMPLIFICATION; GENE CLUSTER; GENE LOCUS; GENE MAPPING; GENE NUMBER; GENE ORDER; GENETIC ANALYSIS; HUMAN; MOLECULAR CLONING; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PSEUDOGENE;

AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, NEOPLASM; CHROMOSOMES, HUMAN, PAIR 18; CYSTEINE ENDOPEPTIDASES; HUMANS; MICE; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PROTEASE INHIBITORS; QUANTITATIVE TRAIT LOCI; SEQUENCE HOMOLOGY, AMINO ACID; SERINE ENDOPEPTIDASES; SERPINS;

PRIMATES; RODENTIA;

EID: 2942625830     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ygeno.2004.01.015     Document Type: Article

References (32)

1. Gettins P.G. Serpin structure, mechanism, and function. Chem. Rev. 102:2002;4751-4803
2. Silverman G.A., Bird P.I., Carrell R.W., Coughlin P.B., Gettins P.G., Irving J.I., Lomas D.A., Luke C.J., Moyer R.W., Pemberton P.A., Remold-O'Donnell E., Salvesen G.S., Travis J., Whisstock J.C. The serpins are an expanding superfamily of structurally similar but funtionally diverse proteins: evolution, mechanism of inhibition, novel functions, and a revised nomenclature. J. Biol. Chem. 276:2001;33293-33296
3. Huntington J.A., Read R.J., Carrell R.W. Structure of a serpin-protease complex shows inhibition by deformation. Nature. 407:2000;923-926
4. Irving J.A., Pike R.N., Lesk A.M., Whisstock J.C. Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function. Genome Res. 10:2000;1845-1864
5. Silverman G.A., Askew D.J., Irving J.A., Luke C.J., Kaiserman D., Bird P.I., Whisstock J.C. Serpins: Evolution. 2003;Nature Publ. Group, London
6. Bird P.I., Silverman G.A. Ovalbumin Serpins. 2003;Nature Publ. Group, London
7. Remold-O'Donnell E. The ovalbumin family of serpin proteins. FEBS Lett. 315:1993;105-108
8. G.A. Silverman, J.C. Whisstock, D.J. Askew, S.C. Pak, C. Luke, S. Cataltepe, J.A. Irving, and P.I. Bird, Human clade B serpins (ov-serpins) belong to a cohort of evolutionarily-dispersed intracellular proteinase inhibitor clades that protect cells from promiscuous proteolysis, Cell. Mol. Life Sci. (in press).
9. Benarafa C., Cooley J., Zeng W., Bird P.I., Remold-O'Donnell E. Characterization of four murine homologs of the human ov-serpin monocyte neutrophil elastase inhibitor MNEI (SERPINB1). J. Biol. Chem. 277:2002;42028-42033
10. Al-Khunaizi M., Luke C.J., Askew Y.S., Pak S.C., Askew D.J., Cataltepe S., Miller D., Mills D.R., Tsu C., Bromme D., Irving J.A., Whisstock J.C., Silverman G.A. The serpin SQN-5 is a dual mechanistic-class inhibitor of serine and cysteine proteinases. Biochemistry. 41:2002;3189-3199
11. Bartuski A.J., Kamachi Y., Schick C., Massa H., Trask B.J., Silverman G.A. A murine ortholog of the human serpin SCCA2 maps to chromosome 1 and inhibits chymotrypsin-like serine proteinases. Genomics. 54:1998;297-306
12. Kaiserman D., Knaggs S., Scarff K.L., Gillard A., Mirza G., Cadman M., McKeone R., Denny P., Cooley J., Benarafa C., Remold-O'Donnell E., Ragoussis J., Bird P.I. Comparison of human chromosome 6p25 with mouse chromosome 13 reveals a greatly expanded ov-serpin gene repertoire in the mouse. Genomics. 79:2002;349-362
13. Forsyth S., Horvath A., Coughlin P. A review and comparison of the murine alpha(1)-antitrypsin and alpha(1)-antichymotrypsin multigene clusters with the human clade A serpins. Genomics. 81:2003;336-345
14. Morris E.C., Dafforn T.R., Forsyth S.L., Missen M.A., Horvath A.J., Hampson L., Hampson I.N., Currie G., Carrell R.W., Coughlin P.B. Murine serpin 2A is a redox-sensitive intracellular protein. Biochem. J. 371:2003;165-173
15. Scott F.L., Eyre H.J., Lioumi M., Ragoussis J., Irving J.A., Sutherland G.A., Bird P.I. Human ovalbumin serpin evolution: phylogenic analysis, gene organization, and identification of new PI8-related genes suggest that two interchromosomal and several intrachromosomal duplications generated the gene clusters at 18q21-q23 and 6p25. Genomics. 62:1999;490-499
16. Schneider S.S., Schick C., Fish K.E., Miller E., Pena J.C., Treter S.D., Hui S.M., Silverman G.A. A serine proteinase inhibitor locus at 18q21.3 contains a tandem duplication of the human squamous cell carcinoma antigen gene. Proc. Natl. Acad. Sci. USA. 92:1995;3147-3151
17. Askew Y.S., Pak S.C., Luke C.J., Askew D.J., Cataltepe S., Mills D.R., Kato H., Lehoczky J., Dewar K., Birren B., Silverman G.A. SERPINB12 is a novel member of the human ov-serpin family that is widely expressed and inhibits trypsin-like serine proteinases. J. Biol. Chem. 276:2001;49320-49330
18. Osoegawa K., Tateno M., Woon P.Y., Frengen E., Mammoser A.G., Catanese J.J., Hayashizaki Y., de Jong P.J. Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res. 10:2000;116-128
19. Schwartz S., Zhang Z., Frazer K.A., Smit A., Riemer C., Bouck J., Gibbs R., Hardison R., Miller W. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10:2000;577-586
20. Lane R.P., Cutforth T., Axel R., Hood L., Trask B.J. Sequence analysis of mouse vomeronasal receptor gene clusters reveals common promoter motifs and a history of recent expansion. Proc. Natl. Acad. Sci. USA. 99:2002;291-296
21. Deininger P.L., Batzer M.A. Mammalian retroelements. Genome Res. 12:2002;1455-1465
22. Welss T., Sun J., Irving J.A., Blum R., Smith A.I., Whisstock J.C., Pike R.N., Von Mikecz A., Ruzicka T., Bird P.I., Abts H.F. Hurpin is a selective inhibitor of lysosomal cathepsin L and protects keratinocytes from ultraviolet-induced apoptosis. Biochemistry. 42:2003;7381-7389
23. Jayakumar A., Kang Y., Frederick M.J., Pak S.C., Henderson Y., Holton P.R., Mitsudo K., Silverman G.A., AK E.L.-N., Bromme D., Clayman G.L. Inhibition of the cysteine proteinases cathepsins K and L by the serpin headpin (SERPINB13): a kinetic analysis. Arch. Biochem. Biophys. 409:2003;367-374
24. D.J. Askew, Y.S. Askew, Y. Kato, C.J. Luke, S.C. Pak, D. Bromme, and G.A. Silverman, The amplified mouse squamous cell carcinoma antigen gene locus contains a serpin (Serpinb3b) that inhibits both papain-like cysteine and trypsin-like serine proteinases, Genomics (in press).
25. Bartuski A.J., Kamachi Y., Schick C., Overhauser J., Silverman G.A. Cytoplasmic antiproteinase 2 (PI8) and bomapin (PI10) map to the serpin cluster at 18q21.3. Genomics. 43:1997;321-328
26. Borriello F., Krauter K.S. Multiple murine alpha 1-protease inhibitor genes show unusual evolutionary divergence. Proc. Natl. Acad. Sci. USA. 88:1991;9417-9421
27. Tardiff J., Krauter K.S. Divergent expression of alpha1-protease inhibitor genes in mouse and human. Nucleic Acids Res. 26:1998;3794-3799
28. Craik C.S., Largman C., Fletcher T., Roczniak S., Barr P.J., Fletterick R., Rutter W.J. Redesigning trypsin: alteration of substrate specificity. Science. 228:1985;291-297
29. McPherson J.D., Marra M., Hillier L., Waterston R.H., Chinwalla A., Wallis J., Sekhon M., Wylie K., Mardis E.R., Wilson R.K., Fulton R., Kucaba T.A., Wagner-McPherson C., Barbazuk W.B., Gregory S.G., Humphray S.J., French L., Evans R.S., Bethel G., Whittaker A., Holden J.L., McCann O.T., Dunham A., Soderlund C., Scott C.E., Bentley D.R., Schuler G., Chen H.C., Jang W., Green E.D., Idol J.R., Maduro V.V., Montgomery K.T., Lee E., Miller A., Emerling S., Kucherlapati, Gibbs R., Scherer S., Gorrell J.H., Sodergren E., Clerc-Blankenburg K., Tabor P., Naylor S., Garcia D., de Jong P.J., Catanese J.J., Nowak N., Osoegawa K., Qin S., Rowen L., Madan A., Dors M., Hood L., Trask B., Friedman C., Massa H., Cheung V.G., Kirsch I.R., Reid T., Yonescu R., Weissenbach J., Bruls T., Heilig R., Branscomb E., Olsen A., Doggett N., Cheng J.F., Hawkins T., Myers R.M., Shang J., Ramirez L., Schmutz J., Velasquez O., Dixon K., Stone N.E., Cox D.R., Haussler D., Kent W.J., Furey T., Rogic S., Kennedy S., Jones S., Rosenthal A., Wen G., Schilhabel M., Gloeckner G., Nyakatura G., Siebert R., Schlegelberger B., Korenberg J., Chen X.N., Fujiyama A., Hattori M., Toyoda A., Yada T., Park H.S., Sakaki Y., Shimizu N., et al. A physical map of the human genome. Nature. 409:2001;934-941
30. Higgins D.G., Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 73:1988;237-244
31. Felsenstein J. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol. 266:1996;418-427
32. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425