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J. Bacteriol. doi:10.1128/JB.01381-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase

Biotech Center and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901; Department of Molecular Biology, Princeton University, Princeton, NJ 08544

^* To whom correspondence should be addressed. Email: LEUSTEK{at}AESOP.RUTGERS.EDU.

	Abstract

A variant of the diaminopimelate (DAP)/lysine biosynthesis pathway uses an LL-diaminopimelate aminotransferase (DapL, EC 2.6.1.83) to catalyze the direct conversion of L-2,3,4,5-tetrahydrodipicolinate to LL-diaminopimelate. Comparative genomic analysis and experimental verification of DapL candidates revealed the existence of two diverged forms of DapL (DapL1 and DapL2). DapL orthologs were identified in eubacteria and archaea. In some species the corresponding dapL gene was found to lie in genomic contiguity with other dap genes, suggestive of a polycistronic structure. The DapL candidate enzymes were found to cluster into two classes sharing approximately 30% amino acid identity. The function of selected enzymes from each class was studied. Both were able to functionally complement Escherichia coli dapD and dapE mutants, and to catalyze LL-diaminopimelate transamination, providing functional evidence for a role in DAP/lysine biosynthesis. In all cases the occurrence of dapL in a species correlated with the absence of genes for dapD and dapE representing the acyl DAP pathway variants and only in a few cases was dapL coincident with ddh encoding m-DAP dehydrogenase. The results indicate that the DapL pathway is restricted to specific lineages of eubacteria including the Cyanobacteria, Desulfuromonadales, Firmicutes, Bacteroidetes, Chlamydiae, Spirochaeta, Chloroflexi; and two archaeal groups the Methanobacteriaceae and Archaeoglobaceae.