Regulation and role of purine nucleotide synthesis genes in animal development From studies of purine disorders in humans, it is clear that the maintenance of the correct level of purine nucleotides is essential for normal growth and development. Using the fruit fly Drosophila melanogaster as a model system, we are exploring how the expression of purine synthesis genes is regulated during animal development. We are currently examining the relationship between purine gene regulation and pathways involved in cell proliferation, stress, and aging. In addition, the cellular and developmental effects of purine depletion are being examined. We use the tools of genetic analysis, transgenic technology, and molecular biology to study cis-regulatory DNA sequences and trans-regulatory gene products important for regulation of purine gene expression. A second research program arose from our studies on a duplicated pair of purine synthesis genes, Prat and Prat2, which both encode the enzyme amidophosphoribosyltransferase, yet are not redundant in function. Both are essential genes for fly development and they have diversified with respect to their expression patterns in development, where Prat is exclusively expressed in the female germline and imaginal tissue and Prat2 is expressed in the fat body. The analysis of this gene duplication, which appears to have occured by a retrotransposition event, served as a starting point for our second research program focusing on the functional analysis of gene duplication by retrotransposition in Drosophila. Functional analysis of RNA-based gene duplications We are examining both the mechanism and consequences of gene duplication by retrotransposition in Drosophila species. Gene duplication by retrotransposition occurs by reverse transcription of mRNAs and insertion of the cDNA into a new site to generate a retrogene copy. Since retrogenes are “not born equal” to their parent genes, they are good candidates for functional diversification as protein coding genes or regulatory RNA genes. Using genetics, bioinformatics, and cell and molecular biology, we have three main research objectives which address fundamental questions about the significance of retroduplication in genome evolution. These objectives are to examine 1) the functional divergence of existing retrogenes; 2) the function of transcribed pseudoretrogenes; and 3) the mechanism of retroduplication in the germ-line.

O'Neill, R.S. and Clark D.V. (2013) The Drosophila melanogaster septin gene Sep2 has a redundant function with the retrogene Sep5 in imaginal cell proliferation but is essential for oogenesis. Genome Dec;56(12):753-8. Pubmed O’Neill, R.S. and Clark, D.V. (2013) Evolution of three parent genes and their retrogene copies in Drosophila species. International Journal of Evolutionary Biology, Int J Evol Biol. 2013;2013:693085. Pubmed Merzetti, E., Hackett, J.M., and Clark, D.V. (2013) Transcriptional regulation of the purine de novo synthesis gene Prat in Drosophila melanogaster. Gene Apr 15;518(2):280-6. Pubmed Holland, C., Lipsett, D.B., and Clark, D.V. (2011) A link between impaired purine nucleotide synthesis and apoptosis in Drosophila melanogaster. Genetics Jun;188(2):359-67. Pubmed Hackett, J.M. and Clark, D.V. (2009) Modifiers of Prat, a de novo purine synthesis gene, in Drosophila melanogaster. Genome 52(11): 957-967. Pubmed Penney, J., Bosse, J. and Clark, D.V. (2008) Expression pattern diversity and functional conservation between retroposed PRAT genes from Drosophila melanogaster and Drosophila virilis. J Mol. Evol. May;66(5):457-471. Pubmed Langille, Morgan G. I., and Clark, D.V. (2007) Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles. Genomics, Sep;90(3):334-43. Pubmed Ji, Y. and Clark, D.V. (2006) The purine synthesis gene Prat2 is required for Drosophila metamorphosis, as revealed by inverted-repeat-mediated RNA interference. Genetics, Mar;172(3):1621-31. Pubmed Malmanche, N., and Clark, D.V. (2004) Drosophila melanogaster Prat, a purine de novo synthesis gene, has a pleiotropic maternal effect phenotype. Genetics, Dec;168(4):2011-23. Pubmed Malmanche, N., and Clark, D.V. (2003) Identification of trans-dominant modifiers of Prat expression in Drosophila melanogaster. Genetics, Aug;164(4):1419-33. Pubmed Malmanche, N., Drapeau, D., Cafferty, P., Ji, Y., and Clark, D.V. (2003) The PRAT purine synthesis gene duplication in Drosophila melanogaster and Drosophila virilis is associated with a retrotransposition event and diversification of expression patterns. J. Mol. Evol. 56:630-42. Pubmed