Molecular characterisation of the SAND protein family: a study based on comparative genomics, structural bioinformatics and phylogeny.
The activities of vertebrate lysosomes are critical to many essential cellular processes. The yeast vacuole is analogous to the mammalian lysosome and is used as a tool to gain insights into vesicle mediated vacuolar/lysosome transport. The protein SAND, which does not contain a SAND domain (PFAM accession number PF01342), has recently been shown to function at the tethering/docking stage of vacuole fusion as a critical component of the vacuole SNARE complex. In this publication we have identified SAND in diverse eukaryotes, from single celled organisms such as the yeasts to complex multi-cellular chordates such as mammals. We have demonstrated subfamily divisions in the SAND proteins and show that in vertebrates, a duplication event gave rise to two SAND sequences. This duplication appears to have occurred during early vertebrate evolution and conceivably with the evolution of lysosomes. Using bioinformatics we predict a secondary structure, solvent accessibility profile and protein fold for the SAND proteins and determine conserved sequence motifs, present in all SAND proteins and those that are specific to subsets. A comprehensive evaluation of yeast and human functional studies in conjunction with our in silico analysis has identified potential roles for some of these motifs.
Cottage
Amanda
A
MRC Rosalind Franklin Centre for Genomic Research, Genome Campus, Hinxton, Cambridge, CB10 1SB, UK.
Mullan
Lisa
L
Portela
Miriam B D
MB
Hellen
Elizabeth
E
Carver
Tim
T
Patel
Sunil
S
Vavouri
Tanya
T
Elgar
Greg
G
Edwards
Yvonne J K
YJ
D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D005658:Fungi / Q000235:genetics; D023281:Genomics; D006801:Humans; D008247:Lysosomes / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000235:genetics; D017433:Protein Structure, Secondary; D050600:SNARE Proteins; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014617:Vacuoles / Q000235:genetics; D033921:Vesicular Transport Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics*
D050600:SNARE Proteins; D033921:Vesicular Transport Proteins