Researchers identified the LYS2 gene as responsible for biosynthesis of the bioactive cyclic dipeptide cyclo(Pro-Val) in a marine probiotic yeast, and overexpressing it increased production by 45.5%.
45.5% production increaseCyclo(Pro-Val) output increase from overexpressing the LYS2 gene in a marine probiotic yeast
What the researchers found
The NRPS-like gene LYS2 (3,825 bp, encoding 1,274 amino acids) was identified as essential for cyclo(Pro-Val) biosynthesis in the marine probiotic yeast M. guilliermondii GXDK6. The encoded enzyme (Lys2p, an L-2-amino-hexanedioic acid reductase) utilizes a novel macrocyclization mechanism involving peptide N-terminal and C-terminal imines through nucleophilic reactions.
Overexpressing LYS2 increased cyclo(Pro-Val) production by 45.5%, while knocking out LYS2 completely eliminated synthesis — confirming it as the essential biosynthetic gene. This establishes a new metabolic regulatory pathway for cyclic peptide production in yeast.
Why it matters
Cyclic peptides (diketopiperazines) are increasingly recognized for their bioactive properties, but efficient production methods have been lacking. By identifying the exact gene and mechanism responsible for cyclic peptide biosynthesis in a probiotic yeast, this study opens the door to scalable biotechnological production. Using a probiotic organism as the production platform adds potential food-safety advantages. The 45.5% production increase from a single gene overexpression demonstrates practical engineering potential.
How the study worked
The marine probiotic yeast M. guilliermondii GXDK6 was used as the chassis organism. The LYS2 gene was identified through genomic analysis and functionally characterized using overexpression and knockout experiments. Cyclo(Pro-Val) production was quantified under both conditions. The macrocyclization mechanism was characterized at the molecular level, revealing the novel imine-mediated nucleophilic reaction pathway.
What this study cannot tell us
The study focuses on a single cyclic dipeptide (cyclo(Pro-Val)) in a single yeast strain. Whether LYS2 can be leveraged to produce other diketopiperazines or more complex cyclic peptides is unknown. The 45.5% increase in production, while significant, may not be sufficient for commercial-scale manufacturing without further optimization. The bioactivities of cyclo(Pro-Val) mentioned are referenced but not experimentally validated in this study. Scale-up from laboratory to industrial production was not demonstrated.
How to read the evidence
This is a well-designed preclinical biotechnology study with strong functional validation (overexpression and knockout experiments). The gene-to-function relationship is conclusively demonstrated, though translation to practical applications requires further engineering and scale-up work.
When this study was published
Published in 2025, this study represents current advances in peptide biosynthesis and marine natural product biotechnology.
The bigger picture
This study advances the field of peptide biotechnology by connecting nonribosomal peptide synthase (NRPS) biology to practical cyclic peptide manufacturing. NRPS enzymes are responsible for producing many therapeutically important peptides (including antibiotics like vancomycin and antifungals like cyclosporine), but their mechanisms in yeast have been poorly understood. Elucidating how a marine probiotic yeast produces cyclic peptides expands the toolkit for peptide biosynthesis and supports the growing bioeconomy around marine-derived natural products.
Questions still open
- Can the LYS2 overexpression system be engineered to produce different cyclic peptides beyond cyclo(Pro-Val)?
- What are the specific bioactivities of cyclo(Pro-Val) that make it valuable for agricultural and food applications?
- Could this probiotic yeast production system be scaled up for industrial manufacturing of bioactive cyclic peptides?
Common questions
What are diketopiperazines and why are they interesting?
Why use yeast to produce peptides?
Read the original research
NRPS-like Gene LYS2 Contributed to the Biosynthesis of Cyclo(Pro-Val) in a Multistress-Tolerant Aromatic Probiotic, Meyerozyma guilliermondii GXDK6.
Journal of agricultural and food chemistry, 73(1), 507-520
Citation
Bu, Ru; Li, Zhenze; Qin, Qiyu; Bai, Huashan; Meng, Can; Wei, Ruihang; Chen, Xinglin; Wu, Shanguang; Kashif, Muhammad; He, Sheng; Jiang, Chengjian. (2025). NRPS-like Gene LYS2 Contributed to the Biosynthesis of Cyclo(Pro-Val) in a Multistress-Tolerant Aromatic Probiotic, Meyerozyma guilliermondii GXDK6.. Journal of agricultural and food chemistry, 73(1), 507-520. https://doi.org/10.1021/acs.jafc.4c08573