Phylogeny of related functions: the case of polyamine biosynthetic enzymes

Genome annotation requires explicit identification of gene function. This t ask frequently uses protein sequence alignments with examples having a know n function. Genetic drift, co-evolution of subunits in protein complexes an d a variety of other constraints interfere with the relevance of alignments . Using a specific class of proteins, it is shown that a simple data analys is approach can help solve some of the problems posed. The origin of ureohy drolases has been explored by comparing sequence similarity trees, maximizi ng amino acid alignment conservation. The trees separate agmatinases from a rginases but suggest the presence of unknown biases responsible for unexpec ted positions of some enzymes. Using factorial correspondence analysis, a d istance tree between sequences was established, comparing regions with gaps in the alignments. The gap tree gives a consistent picture of functional k inship, perhaps reflecting some aspects of phylogeny, with a clear domain o f enzymes encoding two types of ureohydrolases (agmatinases and arginases) and activities related to, but different from ureohydrolases, Several annot ated genes appeared to correspond to a wrong assignment if the trees were s ignificant. They were cloned and their products expressed and identified bi ochemically. This substantiated the validity of the gap tree, its organizat ion suggests a very ancient origin of ureohydrolases. Some enzymes of eukar yotic origin are spread throughout the arginase part of the trees: they mig ht have been derived from the genes found in the early symbiotic bacteria t hat became the organelles. They were transferred to the nucleus when symbio tic genes had to escape Muller's ratchet. This work also shows that arginas es and agmatinases share the same two manganese-ion-binding sites and exhib it only subtle differences that can be accounted for knowing the three-dime nsional structure of arginases. In the absence of explicit biochemical data , extreme caution is needed when annotating genes having similarities to ur eohydrolases.