Elucidation of the D-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima.

Various D-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional D-alanine (D-Ala) and D-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both L-lysine (L-Lys) and D-Lys, but not meso-diaminopimelate (meso-Dpm). D-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterised a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the D-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward D- and L-Lys, and also had relatively high activity toward D- and L-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerisation activity toward LL- and meso-Dpm, and also measurably racemised certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of D-Lys and D-Ala for use as peptidoglycan components, and that Dpm epimerase converts LL-Dpm to meso-Dpm, a precursor in the L-Lys biosynthetic pathway. This article is protected by copyright. All rights reserved.