The domain architecture of large guanine nucleotide exchange factors for the small GTP-binding protein Arf.
BACKGROUND
Small G proteins, which are essential regulators of multiple cellular functions, are activated by guanine nucleotide exchange factors (GEFs) that stimulate the exchange of the tightly bound GDP nucleotide by GTP. The catalytic domain responsible for nucleotide exchange is in general associated with non-catalytic domains that define the spatio-temporal conditions of activation. In the case of small G proteins of the Arf subfamily, which are major regulators of membrane trafficking, GEFs form a heterogeneous family whose only common characteristic is the well-characterized Sec7 catalytic domain. In contrast, the function of non-catalytic domains and how they regulate/cooperate with the catalytic domain is essentially unknown.


RESULTS
Based on Sec7-containing sequences from fully-annotated eukaryotic genomes, including our annotation of these sequences from Paramecium, we have investigated the domain architecture of large ArfGEFs of the BIG and GBF subfamilies, which are involved in Golgi traffic. Multiple sequence alignments combined with the analysis of predicted secondary structures, non-structured regions and splicing patterns, identifies five novel non-catalytic structural domains which are common to both subfamilies, revealing that they share a conserved modular organization. We also report a novel ArfGEF subfamily with a domain organization so far unique to alveolates, which we name TBS (TBC-Sec7).


CONCLUSIONS
Our analysis unifies the BIG and GBF subfamilies into a higher order subfamily, which, together with their being the only subfamilies common to all eukaryotes, suggests that they descend from a common ancestor from which species-specific ArfGEFs have subsequently evolved. Our identification of a conserved modular architecture provides a background for future functional investigation of non-catalytic domains.
Mouratou
Barbara
B
Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, avenue de la Terrasse, 91198 Gif sur Yvette cedex, France. mouratou@lebs.cnrs-gif.fr
Biou
Valerie
V
Joubert
Alexandra
A
Cohen
Jean
J
Shields
David J
DJ
Geldner
Niko
N
Jürgens
Gerd
G
Melançon
Paul
P
Cherfils
Jacqueline
J
D020727:ADP-Ribosylation Factors / Q000737:chemistry*; D000465:Algorithms; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D002384:Catalysis; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods; D016785:Cryptosporidium parvum / Q000378:metabolism; D030541:Databases, Genetic; D019143:Evolution, Molecular; D019204:GTP-Binding Proteins / Q000737:chemistry*; D016678:Genome; D006056:Golgi Apparatus / Q000378:metabolism; D006147:Guanine / Q000737:chemistry; D020662:Guanine Nucleotide Exchange Factors / Q000737:chemistry*; D008954:Models, Biological; D008969:Molecular Sequence Data; D010247:Paramecium / Q000378:metabolism; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012326:RNA Splicing; D017386:Sequence Homology, Amino Acid; D012984:Software; D016808:Tetrahymena thermophila / Q000378:metabolism; D013997:Time Factors
D020662:Guanine Nucleotide Exchange Factors; C066755:Sec7 guanine nucleotide exchange factors; D006147:Guanine; D019204:GTP-Binding Proteins; D020727:ADP-Ribosylation Factors
Plant Cell. 2000 Mar;12(3):343-56
10715321
Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2567-72
10716990
J Cell Sci. 2000 Jun;113 ( Pt 11):1883-9
10806099
Genomics. 2000 Jul 1;67(1):40-7
10945468
J Mol Biol. 2000 Sep 8;302(1):205-17
10964570
EMBO J. 2000 Oct 2;19(19):5105-13
11013213
Curr Biol. 2000 Nov 30;10(23):R876-8
11114537
Nature. 2000 Dec 14;408(6814):796-815
11130711
J Cell Sci. 2001 Jun;114(Pt 12):2241-53
11493664
Mol Biol Cell. 2002 Jan;13(1):119-33
11809827
Science. 2002 Jan 25;295(5555):679-82
11809974
Biochemistry. 2002 May 28;41(21):6573-82
12022860
Mol Cell Biol. 2002 Jul;22(13):4914-28
12052896
J Cell Sci. 2002 Jul 15;115(Pt 14):2867-79
12082148
Traffic. 2002 Sep;3(9):605-13
12191012
J Biol Chem. 2002 Aug 30;277(35):32302-9
12052827
Cell. 2003 Jan 24;112(2):219-30
12553910
Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1627-32
12571360
Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2322-7
12606707
EMBO Rep. 2003 Mar;4(3):320-5
12634853
Mol Biol Cell. 2003 Jun;14(6):2357-71
12808035
Cell. 2003 Sep 19;114(6):751-62
14505574
J Biol Chem. 2003 Oct 24;278(43):41573-6
12912991
Nature. 2003 Dec 4;426(6966):525-30
14654833
J Cell Sci. 2004 Feb 15;117(Pt 5):711-22
14734650
Mol Biol Cell. 2004 Apr;15(4):1487-505
14742722
J Neurochem. 2004 Jul;90(1):173-89
15198677
J Biol Chem. 1988 Aug 25;263(24):11711-7
3042778
Nature. 1996 Dec 5;384(6608):479-81
8945477
Nature. 1996 Dec 5;384(6608):481-4
8945478
Cell. 1998 Oct 16;95(2):237-48
9790530
Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):7968-73
10393931
J Cell Biol. 1999 Jul 12;146(1):71-84
10402461
Trends Cell Biol. 2000 Feb;10(2):60-7
10652516
Genetics. 1999 Aug;152(4):1543-56
10430582
Trends Biochem Sci. 1999 Aug;24(8):306-11
10431174
Curr Opin Cell Biol. 1999 Aug;11(4):466-75
10449335
Mol Biol Cell. 2004 Dec;15(12):5283-94
15385626
J Biol Chem. 2005 Mar 18;280(11):10128-34
15644318