Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase.
A variant of the diaminopimelate (DAP)-lysine biosynthesis pathway uses an LL-DAP aminotransferase (DapL, EC 2.6.1.83) to catalyze the direct conversion of L-2,3,4,5-tetrahydrodipicolinate to LL-DAP. 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 classes were able to functionally complement Escherichia coli dapD and dapE mutants and to catalyze LL-DAP 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 meso-DAP dehydrogenase. The results indicate that the DapL pathway is restricted to specific lineages of eubacteria including the Cyanobacteria, Desulfuromonadales, Firmicutes, Bacteroidetes, Chlamydiae, Spirochaeta, and Chloroflexi and two archaeal groups, the Methanobacteriaceae and Archaeoglobaceae.
Hudson
André O
AO
Biotech Center and Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901, USA.
Gilvarg
Charles
C
Leustek
Thomas
T
D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D003960:Diaminopimelic Acid / Q000378:metabolism*; D005816:Genetic Complementation Test; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D007700:Kinetics; D008239:Lysine / Q000096:biosynthesis; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D000637:Transaminases / Q000737:chemistry / Q000145:classification* / Q000235:genetics*
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D003960:Diaminopimelic Acid; D000637:Transaminases; D008239:Lysine