Purine biosynthesis and the case of the “missing” genes

Abstract

This work is a survey of known and suspected purine biosynthesis genes in sequenced archaea. We searched existing sequence databases for genes for the 11 steps (17 distinct genes) of de novo purine biosynthesis in 65 sequenced archaea, and carefully inspected each hit for the presence of active site residues and other residues known or suspected to be required for function. We found a number of problems with existing annotations, such as missing active site residues, fusions, and incorrect initiation sites. There is also evidence that the pathway has been shaped by horizontal gene transfer, duplication, and gene loss. Two groups of archaea lack a gene normally required for purine biosynthesis, suggesting that there are at least two more variants in this pathway to discover. We propose the existence of a gene encoding a GAR transformylase enzyme that is structurally unrelated to either known GAR transformylase, expected to be present in seven of the 65 archaea studied. A second proposed gene encodes a novel IMP cyclohydrolase function and is expected to be present in the Crenarchaea and Pyrococci.Functional characterization of some purine biosynthesis enzymes will also be reported.