Multiple domain insertions and losses in the evolution of the Rab prenylation complex.
BACKGROUND
Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase - RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear.


RESULTS
We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains.


CONCLUSIONS
We found different domain insertions in different taxa, in alpha-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.
Rasteiro
Rita
R
Instituto Gulbenkian de Ciência, Apartado 14, P-2781-901 Oeiras, Portugal. rrasteiro@igc.gulbenkian.pt
Pereira-Leal
Jose B
JB
D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics; D019883:Alkyl and Aryl Transferases / Q000235:genetics; D000595:Amino Acid Sequence; D000818:Animals; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020440:Gene Duplication; D006801:Humans; D017368:Protein Prenylation; D017434:Protein Structure, Tertiary; D020691:rab GTP-Binding Proteins / Q000235:genetics*
D048868:Adaptor Proteins, Signal Transducing; D019883:Alkyl and Aryl Transferases; C075607:Rab geranylgeranyltransferase; D020691:rab GTP-Binding Proteins
Nucleic Acids Res. 2002 Jan 1;30(1):268-72
11752312
Protein Sci. 2002 Apr;11(4):739-56
11910019
Curr Opin Plant Biol. 2002 Dec;5(6):518-28
12393015
J Theor Biol. 2003 Jan 7;220(1):19-25
12453447
Mol Cell. 2003 Feb;11(2):483-94
12620235
Genome Biol. 2003;4(4):212
12702202
Structure. 2000 Mar 15;8(3):241-51
10745007
Trends Genet. 2000 Jun;16(6):276-7
10827456
Proteins. 2000 Aug 15;40(3):502-11
10861942
J Cell Biol. 2000 Jul 10;150(1):89-103
10893259
FEBS Lett. 2001 Jun 8;498(2-3):197-200
11412856
Traffic. 2001 Aug;2(8):532-43
11489211
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
1438297
Nature. 1993 Nov 4;366(6450):84-6
8232542
Proc Natl Acad Sci U S A. 1994 May 10;91(10):4377-81
8183917
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
Protein Eng. 1994 Dec;7(12):1407-10
7716150
J Mol Biol. 1995 Apr 7;247(4):536-40
7723011
Nature. 1996 May 2;381(6577):42-8
8609986
J Biol Chem. 1996 Mar 8;271(10):5289-92
8621375
Protein Sci. 1996 Dec;5(12):2375-90
8976547
Trends Biochem Sci. 1996 Dec;21(12):472-6
9009830
Science. 1997 Mar 21;275(5307):1800-4
9065406
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Science. 1997 Sep 19;277(5333):1811-5
9295270
Bioinformatics. 1998;14(10):892-3
9927721
Protein Sci. 1999 Aug;8(8):1658-67
10452610
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D247-51
15608188
J Biol Chem. 2005 Jan 14;280(2):1641-51
15528213
J Mol Biol. 2005 Feb 11;346(1):355-65
15663950
Bioinformatics. 2005 Feb 1;21(3):410-2
15353450
Trends Genet. 2005 Jan;21(1):25-30
15680510
Nat Biotechnol. 2005 Feb;23(2):253-60
15696156
Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208
15738986
Genome Res. 2005 Apr;15(4):552-9
15805495
Bioinformatics. 2005 Apr 15;21(8):1464-71
15585523
Cell. 2005 Apr 22;121(2):271-80
15851033
Proteins. 2006 Jan 1;62(1):24-45
16287116
Cell Mol Life Sci. 2006 Feb;63(3):255-67
16378247
Physiol Genomics. 2006 Feb 14;24(3):235-51
16332933
J Lipid Res. 2006 Mar;47(3):467-75
16401880
Mol Biol Evol. 2006 Apr;23(4):734-43
16431849
J Lipid Res. 2006 Apr;47(4):681-99
16477080
FEBS J. 2006 May;273(9):2037-47
16640566
Trends Genet. 2006 Dec;22(12):642-4
17045359
Nucleic Acids Res. 2007 Jan;35(Database issue):D308-13
17098927
J Proteome Res. 2007 May;6(5):1882-98
17391014
Bioinformatics. 2001 Aug;17(8):754-5
11524383
Plant Mol Biol. 2003 Apr;51(6):859-66
12777046
Science. 2003 Jun 13;300(5626):1703-6
12805537
Nucleic Acids Res. 2003 Jul 1;31(13):3701-8
12824398
Nature. 2003 Jul 10;424(6945):194-7
12853957
Bioinformatics. 2003 Aug 12;19(12):1572-4
12912839
BMC Evol Biol. 2002 Mar 12;2:3
11914127
EMBO J. 2003 Nov 17;22(22):5963-74
14609943
J Biol Chem. 2003 Nov 21;278(47):46798-804
12941939
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41
14681378
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D226-9
14681400
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D235-9
14681402
Bioinformatics. 2004 Feb 12;20(3):426-7
14960472
J Mol Biol. 2004 May 7;338(4):633-41
15099733
J Mol Biol. 1981 Mar 25;147(1):195-7
7265238
Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11373-7
1763050
J Proteome Res. 2007 May;6(5):1917-32
17391016
Genome Biol. 2007;8(4):R51
17411433
Nucleic Acids Res. 2000 Jan 1;28(1):10-4
10592169
J Struct Biol. 2001 May-Jun;134(2-3):117-31
11551174
Mol Biol Cell. 2001 Oct;12(10):2907-20
11598180
J Mol Biol. 2001 Nov 2;313(4):889-901
11697911
Curr Opin Struct Biol. 2001 Dec;11(6):725-32
11751054