Background Hydroxy-l-lysines are versatile chiral building blocks and can be obtained by hydroxylation of the amino acid l-lysine. The conversion is catalyzed by α-ketoglutarate-dependent lysine dioxygenases (KDOs), which belong to the superfamily of Fe2+/α-ketoglutarate-dependent oxygenases. These enzymes are highly regio- and stereoselective; however, they require α-ketoglutarate (α-KG) as a cosubstrate. Apart from the costly direct addition of α-KG, it can be generated via cellular metabolism from inexpensive and renewable carbon sources, such as d-xylose. Therefore, we engineered a Pseudomonas taiwanensis VLB120 chassis to efficiently convert l-lysine to hydroxy-l-lysine using KDOs with the supply of α-KG from d-xylose as the sole carbon source via the Weimberg pathway. Results For the generation of a suitable whole-cell biocatalyst, we investigated the l-lysine catabolism of P. taiwanensis VLB120 and created a mutant strain that is deficient in l-lysine catabolism to minimize l-lysine degradation and to facilitate complete conversion via the biotransformation reaction. Next, a library of KDO genes was heterologously expressed in the engineered chassis strain P. taiwanensis VLB120∆C∆3. The hydroxylation of l-lysine was assessed in biotransformations with growing cells and d-xylose to supply α-KG via the Weimberg pathway. Hydroxy-l-lysine was successfully produced by strains harboring KDOs that hydroxylate the C-4 position of l-lysine. We further explored the three most promising whole-cell biocatalysts and investigated the influence of increased concentrations of the substrate l-lysine and the metal cofactor Fe2+. Finally, the engineered strain expressing a KDO from Flavobacterium species was grown in stirred-tank bioreactors and was able to produce 8.7 ± 0.3 g L−1 hydroxy-l-lysine with a space-time yield of 98.6 ± 3.4 mg L h−1 and a specific product yield on biocatalyst (YHyl/X) of 1.68 ± 0.07 g gCDW−1. The supply of α-KG via the Weimberg pathway proved very efficient, as approximately every second molecule of d-xylose which was converted and entered the central carbon metabolism was used for the biotransformation reaction (YHyl/Xyl,net = 0.48 ± 0.02 mol mol−1). Conclusions We successfully established a whole-cell biocatalyst for the synthesis of hydroxy-l-lysine from l-lysine and d-xylose and demonstrated multigram-scale production with our engineered strain. Our work lays the foundation for whole-cell bioprocesses utilizing Fe2+/α-ketoglutarate-dependent oxygenases fueled by the Weimberg pathway.

Engineering Pseudomonas taiwanensis VLB120 for regio- and stereospecific hydroxylation of l-lysine fueled by the Weimberg pathway

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2026年2月19日

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Philipp Nerke,
Julian Handke,
Georg Hubmann,
Stephan Lütz

摘要

Background

Hydroxy-l-lysines are versatile chiral building blocks and can be obtained by hydroxylation of the amino acid l-lysine. The conversion is catalyzed by α-ketoglutarate-dependent lysine dioxygenases (KDOs), which belong to the superfamily of Fe²⁺/α-ketoglutarate-dependent oxygenases. These enzymes are highly regio- and stereoselective; however, they require α-ketoglutarate (α-KG) as a cosubstrate. Apart from the costly direct addition of α-KG, it can be generated via cellular metabolism from inexpensive and renewable carbon sources, such as d-xylose. Therefore, we engineered a Pseudomonas taiwanensis VLB120 chassis to efficiently convert l-lysine to hydroxy-l-lysine using KDOs with the supply of α-KG from d-xylose as the sole carbon source via the Weimberg pathway.

Results

For the generation of a suitable whole-cell biocatalyst, we investigated the l-lysine catabolism of P. taiwanensis VLB120 and created a mutant strain that is deficient in l-lysine catabolism to minimize l-lysine degradation and to facilitate complete conversion via the biotransformation reaction. Next, a library of KDO genes was heterologously expressed in the engineered chassis strain P. taiwanensis VLB120∆C∆3. The hydroxylation of l-lysine was assessed in biotransformations with growing cells and d-xylose to supply α-KG via the Weimberg pathway. Hydroxy-l-lysine was successfully produced by strains harboring KDOs that hydroxylate the C-4 position of l-lysine. We further explored the three most promising whole-cell biocatalysts and investigated the influence of increased concentrations of the substrate l-lysine and the metal cofactor Fe²⁺. Finally, the engineered strain expressing a KDO from Flavobacterium species was grown in stirred-tank bioreactors and was able to produce 8.7 ± 0.3 g L⁻¹ hydroxy-l-lysine with a space-time yield of 98.6 ± 3.4 mg L h⁻¹ and a specific product yield on biocatalyst (Y_Hyl/X) of 1.68 ± 0.07 g g_CDW⁻¹. The supply of α-KG via the Weimberg pathway proved very efficient, as approximately every second molecule of d-xylose which was converted and entered the central carbon metabolism was used for the biotransformation reaction (Y_Hyl/Xyl,net = 0.48 ± 0.02 mol mol⁻¹).

Conclusions

We successfully established a whole-cell biocatalyst for the synthesis of hydroxy-l-lysine from l-lysine and d-xylose and demonstrated multigram-scale production with our engineered strain. Our work lays the foundation for whole-cell bioprocesses utilizing Fe²⁺/α-ketoglutarate-dependent oxygenases fueled by the Weimberg pathway.