The PRAT Purine Synthesis Gene Duplication in Drosophila melanogaster and Drosophila virilis Is Associated with a Retrotransposition Event and Diversification of Expression Patterns

Abstract

The Drosophila melanogaster Prat gene encodes amidophosphoribosyltransferase (PRAT; EC 2.4.2.14), which performs the first step in de novo purine nucleotide synthesis. Prat mutations have a recessive lethal phenotype that is found for other genes encoding enzymes in this pathway. The D. melanogaster genome project has revealed a second gene, CG10078 or Prat2, encoding a protein with 76% amino acid sequence identity with Prat. The two genes map to different arms of chromosome 3 and have different intron/exon organizations, as we confirmed by cDNA sequence analysis of Prat2. With the goal to determine the functional significance of this gene duplication, we isolated and sequenced two PRAT-encoding genes from Drosophila virilis. We find that the two D. virilis genes are orthologous to the two D. melanogaster genes in terms of intron/exon organization, amino acid coding sequence, and 5' noncoding sequence. The absence of introns in both DmelPrat and DvirPrat genes suggests that Prat originated from a retrotransposition of Prat2 and that the gene duplication has been preserved in the two species since their divergence approximately 40 million years ago. Analysis of mRNA expression in development shows that maternal expression, detected in adult ovaries and embryos prior to the onset of zygotic transcription, is present for Prat but not Prat2 in both species. Taken together, these findings support the notion that two PRAT-encoding genes have evolved distinct functions in both Drosophila species.

Molecular evolution of the insect Halloween family of cytochrome P450s: Phylogeny, gene organization and functional conservation

“…This could explain the distinct spatial and temporal expression of Cyp307a1 and Cyp307a2 (Ono et al, 2006). In D. melanogaster, retrotransposition has generated two copies of amidophosphoribosyltransferase (Malmanche et al, 2003). These two paralogs are, like Cyp307a1 and Cyp307a2, expressed at different developmental stages.…”

Wolbachiaand virus alter the host transcriptome at the interface of nucleotide metabolism pathways

“…Interestingly, there are a few genes that differentially respond to Wolbachia and virus, such as prat2. prat2 is a gene involved in the de novo synthesis of purine nucleotides (Ji and Clark, 2006;Malmanche et al, 2003), and one of the most strongly downregulated in the virus-responsive gene set, expressed at <0.01% of the level of expression in PBS-injected flies ( Figure 6B). While prat2 did not meet the threshold for statistical significance in the Wolbachia-responsive RNA-Seq analysis, prat2 was upregulated in Wolbachia-colonized flies 1.7-fold ( Figure 6B).…”

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

“…At the level of protein-coding function, retrotransposition has been identified as a minor but important mechanism for the creation of novel combinations of functional domains (Babushok et al 2007) and has also been identified as having the potential to create protein-coding loci de novo (Kaessmann et al 2009). However, while it has been estimated that more than 100 human protein-coding loci might have arisen by this route (Vinckenbosch et al 2006), very few retrotransposed loci have evidence of function at the protein level; notable exceptions include human GLUD2 (Shashidharan et al 1994) and Drosophila Prat (Malmanche et al 2003). While the increasing number of transcribed retrotransposed genes creates additional candidate protein-coding loci (Baertsch et al 2008), there is no evidence that proteins originate from such loci.…”