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.2008 May;190(9):3256-63.
doi: 10.1128/JB.01381-07. Epub 2008 Feb 29.

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

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

André O Hudson et al. J Bacteriol.2008 May.

Abstract

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.

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Figures

FIG. 1.
FIG. 1.
The known variants of the DAP-lysine biosynthesis pathways. The chemical structures of intermediates are shown on the left. The name of the pathway is indicated at the top of the diagram, and the individual steps including enzyme symbol are shown below. In the DAP dehydrogenase and DAP aminotransferase diagrams, only the step(s) that differs from the succinyl and acetyl-DAP pathways is shown.
FIG. 2.
FIG. 2.
Phylogenetic analysis of DapL orthologs. The diagram is of a neighbor-joining tree produced by alignment with Clustal W using a gap penalty of 10 and a gap length penalty of 0.2. The tree was constructed by bootstrap analysis using MEGA, version 3.1. Locus tags are indicated. The identities of enzyme clusters are indicated. Homologous proteins that cannot be DapL proteins are marked with an asterisk. The same proteins are indicated in Table S2 in the supplemental material.
FIG. 3.
FIG. 3.
Complementation assay. Complementation was tested in the indicated mutant under inducing and repressing conditions. The vector was pBAD33, and sll0480 was thedapL ortholog fromSynechocystis cloned into pBAD33. The constructs were tested for complementation of thedapD mutant anddapD dapE double mutant. Each construct was serially diluted in 0.85% (wt/vol) saline (from the left, optical density at 600 nm of 0.1, 0.01, and 0.001), and 5 μl was plated onto the indicated medium. Gene expression from the constructs was induced on medium containing 0.2% (wt/vol) arabinose (Ara) or was repressed on medium containing 0.2% (wt/vol) glucose (Glc). DAP was added when indicated at 50 μg ml−1.
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References

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