| Record 10327 View: Standard | Glossary HistCite Guide |
|
Author(s): Ragg H (Ragg, Hermann); Kumar A (Kumar, Abhishek); Koster K (Koester, Katharina); Bentele C (Bentele, Caterina); Wang YJ (Wang, Yunjie); Frese MA (Frese, Marc-Andre); Prib N (Prib, Natalie); Kruger O (Krueger, Olaf)
Title: Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes
Source: BMC EVOLUTIONARY BIOLOGY 9: Art. No. 208
Date: 2009 AUG 22
Document Type: Journal : Article
DOI: 10.1186/1471-2148-9-208
Language: English
Comment:
Address: Univ Bielefeld, Dept Biotechnol, Fac Technol, D-33501 Bielefeld, Germany.
Univ Bielefeld, Ctr Biotechnol, D-33501 Bielefeld, Germany. Med Univ Vienna, Inst Med Chem, Ctr Physiol & Pathophysiol, A-1090 Vienna, Austria. Reprint: Ragg, H, Univ Bielefeld, Dept Biotechnol, Fac Technol, D-33501
Bielefeld, Germany. E-mail: hr@zellkult.techfak.uni-bielefeld.de
abhishek.abhishekkumar@gmail.com kko@zellkult.techfak.uni-bielefeld.de caterina.bentele@meduniwien.ac.at Yunjie.Wang@gmx.net marc-andre_frese@gmx.de natalieprib@online.de o.krueger@cellca.de Author Keywords:
KeyWords Plus: GENOME EVOLUTION; THROMBIN INHIBITOR; SECRETORY PATHWAY; CHICKEN
GENOME; TELEOST FISH; SERPINS; EXPRESSION; ORIGIN; FUGU; ORGANIZATION
Abstract: Background: Intron gains reportedly are very rare during evolution of vertebrates, and the mechanisms underlying their creation are largely unknown. Previous investigations have shown that, during metazoan radiation, the exon-intron patterns of serpin superfamily genes were subject to massive changes, in contrast to many other genes. Results: Here we investigated intron dynamics in the serpin superfamily in lineages pre-and postdating the split of vertebrates. Multiple intron gains were detected in a group of ray-finned fishes, once the canonical groups of vertebrate serpins had been established. In two genes, cooccurrence of non-standard introns was observed, implying that intron gains in vertebrates may even happen concomitantly or in a rapidly consecutive manner. DNA breakage/repair processes associated with genome compaction are introduced as a novel factor potentially favoring intron gain, since all non-canonical introns were found in a lineage of ray-finned fishes that experienced genomic downsizing. Conclusion: Multiple intron acquisitions were identified in serpin genes of a lineage of ray-finned fishes, but not in any other vertebrates, suggesting that insertion rates for introns may be episodically increased. The co-occurrence of non-standard introns within the same gene discloses the possibility that introns may be gained simultaneously. The sequences flanking the intron insertion points correspond to the proto-splice site consensus sequence MAG up arrow N, previously proposed to serve as intron insertion site. The association of intron gains in the serpin superfamily with a group of fishes that underwent genome compaction may indicate that DNA breakage/repair processes might foster intron birth.
Cited References: APARICIO S, 2002, SCIENCE, V297, P1301 BABENKO VN, 2004, NUCLEIC ACIDS RES, V32, P3724, DOI 10.1093/nar/gkh686 BARBOUR KW, 2002, MOL BIOL EVOL, V19, P718 BENARAFA C, 2005, P NATL ACAD SCI USA, V102, P11367, DOI 10.1073/pnas.0502934102 BENTELE C, 2006, BIOCHEM J 3, V395, P449, DOI 10.1042/BJ20051947 BIRNEY E, 2004, GENOME RES, V14, P988, DOI 10.1101/gr.1865504 COLLINS L, 2005, MOL BIOL EVOL, V22, P1053, DOI 10.1093/molbev/msi091 COULOMBEHUNTINGTON J, 2007, GENOME RES, V17, P23, DOI 10.1101/gr.5703406 DIBB NJ, 1989, EMBO J, V8, P2015 FIGUEROA F, 1995, P ROY SOC LOND B BIO, V259, P325 FLICEK P, 2008, NUCLEIC ACIDS RES, V36, PD707, DOI 10.1093/nar/gkm988 FORSYTH S, 2003, GENOMICS, V81, P336, DOI 10.1016/S0888-7543(02)00041-1 FRUGOLI JA, 1998, GENETICS, V149, P355 GESS RW, 2006, NATURE, V443, P981, DOI 10.1038/nature05150 GLADYSHEV EA, 2008, SCIENCE, V320, P1210, DOI 10.1126/science.1156407 GREGORY TR, 2008, ANIMAL GENOME SIZE D HILLIER LW, 2004, NATURE, V432, P695, DOI 10.1038/nature03154 HINEGARDNER R, 1968, AM NAT, V102, P517 IRIMIA M, 2008, TRENDS GENET, V24, P378, DOI 10.1016/j.tig.2008.05.007 JAILLON O, 2004, NATURE, V431, P946, DOI 10.1038/nature03025 KAMP PB, 1999, GENE, V229, P137 KAROLCHIK D, 2008, NUCLEIC ACIDS RES, V36, PD773, DOI 10.1093/nar/gkm966 KASAHARA M, 2007, NATURE, V447, P714, DOI 10.1038/nature05846 KOBORI H, 2007, PHARMACOL REV, V59, P251, DOI 10.1124/pr.59.3.3 KOHANY O, 2006, BMC BIOINFORMATICS, V7, AR474 KOONIN EV, 2006, BIOL DIRECT, V1, AR22 KRUGER O, 2002, GENE, V293, P97 KUMAR A, 2008, BMC EVOL BIOL, V8, AR250 LOH YH, 2008, MOL BIOL EVOL, V25, P526, DOI 10.1093/molbev/msm278 MEYER A, 2005, BIOESSAYS, V27, P937, DOI 10.1002/bies.20293 MORIYAMA S, 2008, ZOOL SCI, V25, P604, DOI 10.2108/zsj.25.604 NAGATA K, 2003, SEMIN CELL DEV BIOL, V14, P275, DOI 10.1016/j.semcdb.2003.09.020 OMILIAN AR, 2008, MOL BIOL EVOL, V25, P2129, DOI 10.1093/molbev/msn164 PONTING CP, 2008, NAT REV GENET, V9, P689, DOI 10.1038/nrg2413 PUTNAM NH, 2007, SCIENCE, V317, P86, DOI 10.1126/science.1139158 PUTNAM NH, 2008, NATURE, V453, P1064, DOI 10.1038/nature06967 RAGG H, 1988, J BIOL CHEM, V263, P12129 RAGG H, 1990, J BIOL CHEM, V265, P5211 RAGG H, 2001, MOL BIOL EVOL, V18, P577 RAGG H, 2007, CELL MOL LIFE SCI, V64, P2763, DOI 10.1007/s00018-007-7157-0 RAIBLE F, 2005, SCIENCE, V310, P1325, DOI 10.1126/science.1119089 RODRIGUEZTRELLES F, 2006, GENE, V366, P201, DOI 10.1016/j.gene.2005.09.004 ROGERS JH, 1989, TRENDS GENET, V5, P213 ROY SW, 2006, NAT REV GENET, V7, P211, DOI 10.1038/nrg1807 ROY SW, 2007, MOL BIOL EVOL, V24, P1579, DOI 10.1093/molbev/msm082 SAITOU N, 1987, MOL BIOL EVOL, V4, P406 SCHIOTH HB, 2005, ANN NY ACAD SCI, V1040, P460, DOI 10.1196/annals.1327.090 SILVERMAN GA, 2001, J BIOL CHEM, V276, P33293 SVERDLOV AV, 2004, CURR BIOL, V14, P1505, DOI 10.1016/j.cub.2004.08.027 SVERDLOV AV, 2004, GENE, V338, P85, DOI 10.1016/j.gene.2004.05.027 TAMURA K, 2007, MOL BIOL EVOL, V24, P1596, DOI 10.1093/molbev/msm092 TARRIO R, 2008, P NATL ACAD SCI USA, V105, P7223, DOI 10.1073/pnas.0802941105 THOMPSON JD, 1997, NUCLEIC ACIDS RES, V25, P4876 VANDEPOELE K, 2004, P NATL ACAD SCI USA, V101, P1638, DOI 10.1073/pnas.0307968100 VENKATESH B, 1999, P NATL ACAD SCI USA, V96, P10267 VOLFF JN, 2003, TRENDS GENET, V19, P674, DOI 10.1016/j.tig.2003.10.006 VOLFF JN, 2004, TRENDS GENET, V20, P176 VOLFF JN, 2005, HEREDITY, V94, P280, DOI 10.1038/sj.hdy.6800635 WESTRUP D, 1994, BBA-GENE STRUCT EXPR, V1217, P93 ZANG XX, 2001, TRENDS BIOCHEM SCI, V26, P191 ZHUO DG, 2007, P NATL ACAD SCI USA, V104, P882, DOI 10.1073/pnas.0604777104 |