Knocking out three transporters reshapes selenium metabolism in engineered Bacillus subtilis

Seleno-amino acids are valued as organic selenium supplements with potential anti-cancer activity, and the soil bacterium Bacillus subtilis can be engineered to synthesize and secrete one of them, Se-methylselenocysteine (SeMCys). A new study in AMB Express, published on 17 September 2026, set out to answer a basic question that had remained unclear: which proteins actually transport SeMCys in this bacterium.

Because transporters strongly influence amino acid metabolism, the researchers first screened for differentially expressed transporter genes using transcriptome analysis of B. subtilis during SeMCys fermentation. This approach allowed them to identify candidate transporters whose activity might shape how much SeMCys the cells take up and how much the fermentation ultimately produces.

The team then tested three of these transporter-encoding genes, ycgH, ywoD and yrdR, by deleting them from the genome. Knockout of any of the three reduced SeMCys uptake by more than 50 percent, and genetic complementation, in which the deleted gene was restored, brought the uptake capacity back. This pattern supports the conclusion that each of these proteins contributes to moving SeMCys into the cell.

The knockouts also changed the fermentation outcome. Deleting the transporter genes lowered SeMCys yield by at least one quarter while raising the levels of SeMCys inside the cells, a result consistent with the cells losing less of the compound to internal transport dynamics.

Overexpression told the opposite story. When each of the three transporters was individually overproduced, SeMCys production improved, and yrdR overexpression delivered the largest gain, a 53.3 percent rise in titer. This makes yrdR a particularly interesting target for future strain engineering aimed at higher SeMCys output.

An unexpected finding emerged when the transporter genes were knocked out: selenomethionine (SeMet) appeared as a new product during SeMCys fermentation. The study therefore documents not only which proteins move SeMCys but also how removing them redirects selenium metabolism toward a different seleno-amino acid.

Transcript-level data helped explain this shift. Genes belonging to the SeMet biosynthetic pathway showed elevated transcription after transporter knockout, while metK, which is responsible for SeMet consumption, and mccB, which facilitates selenocysteine biosynthesis, were down regulated. Together these changes are consistent with carbon and selenium flux being rerouted toward SeMet accumulation.

The authors describe the work as delivering novel insights into amino acid transportation and selenium metabolism. Because the study was conducted in engineered B. subtilis during fermentation, its findings concern microbial production systems rather than human health outcomes, and the anti-cancer potential of seleno-amino acids remains a subject of ongoing research. Even so, the identification of ycgH, ywoD and yrdR as SeMCys transporters, and the demonstration that their deletion triggers SeMet synthesis, gives metabolic engineers a clearer map of how transporter activity shapes selenium-amino acid profiles in fermenter cultures.

Subject of Research: Identification of SeMCys transporters in Bacillus subtilis and the metabolic effects of their knockout

Article Title: Identification of proteins that transport SeMCys and the SeMet synthesis caused by their knockout

Article References: Zhao, M., Ren, H., Yang, S., Deng, S., Wang, F., & Yin, X. (2026). Identification of proteins that transport SeMCys and the SeMet synthesis caused by their knockout. AMB Express. https://doi.org/10.1186/s13568-026-02121-6

Image Credits: AI Generated

DOI: 10.1186/s13568-026-02121-6

Keywords: Bacillus subtilis, Se-methylselenocysteine, selenomethionine, transporters, metabolic engineering, transcriptomics, fermentation, selenium metabolism, gene knockout, protein overexpression, Identification, proteins