MBE Advance Access published online on November 28, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn274
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Research Article |
Molecular evolution, functional variation and proposed nomenclature of the gene family that includes sphingomyelinase D in sicariid spider venoms
* Department of Biology, Lewis and Clark College, Portland, OR 97219
Department of Biochemistry and Molecular Physics, University of Arizona, Tucson, AZ 85721
Cleveland High School, Portland, OR 97202
¶ Correspondence: Dr. Greta Binford, Lewis and Clark College, 0615 SW Palatine Hill Rd. Department of Biology, Portland, OR 97219 (503) 768-7653 office (503) 768-7658 FAX binford{at}lclark.edu
Received for publication July 10, 2008. Revision received October 27, 2008. Accepted for publication November 17, 2008.
The venom enzyme sphingomyelinase D (SMase D) in the spider family Sicariidae (brown, or fiddleback spiders (Loxosceles) and six-eyed sand spiders (Sicarius)) causes dermonecrosis in mammals. SMase D is in a gene family with multiple venom-expressed members that vary in functional specificity. We analyze molecular evolution of this family, and variation in SMase D activity among crude venoms using a dataset that represents the phylogenetic breadth of Loxosceles and Sicarius. We isolated a total of 190 non-redundant nucleotide sequences encoding 168 non-redundant amino acid sequences of SMase D homologs from 21 species. Bayesian phylogenies support 2 major clades, that we name 
and β, within which we define 7 and 3 subclades respectively. Sequences in the clade are exclusively from New World Loxosceles and L. rufescens and include published genes for which expression products have SMase D and dermonecrotic activity. The β clade includes paralogs from New World Loxosceles that have no, or reduced, SMase D and no dermonecrotic activity, and also paralogs from Sicarius and African Loxosceles of unknown activity. Gene duplications are frequent, consistent with a birth-and-death model, and there is evidence of purifying selection with episodic positive directional selection. Despite having venom-expressed SMase D homologs, venoms from New World Sicarius have reduced, or no, detectable SMase D activity, and Loxosceles in the Southern African spinulosa group have low SMase D activity. Sequence conservation mapping shows >98% conservation of proposed catalytic residues of the active site and around a plug motif at the opposite end of the TIM barrel, but and β clades differ in conservation of key residues surrounding the apparent substrate binding pocket. Based on these combined results we propose an inclusive nomenclature for the gene family, renaming it SicTox, and discuss emerging patterns of functional diversification.
Key Words: Loxosceles • Sicarius • duplication • toxin
1 current address: Department of Zoology, University of British Columbia, Vancouver, B.C. V6T 164
2 current address: Department of Cellular and Molecular Biology, University of Wisconsin, Madison, Madison, WI 53706
3 current address: Department of Genome Sciences, University of Washington, Seattle, WA 98195