Transcriptomic Insights into Selenite Response and Biotransformation in a Novel Selenium-Enriching Lactic Acid Bacterium

Many microorganisms are capable of surviving selenium (Se)-rich environments and efficiently transforming inorganic Se into organic Se, enabling them to act as a potent biocatalyst for the synthesis of organic Se. Here, we isolated a novel selenium-enriching lactic acid bacterium, Pediococcus acidilactici 03W, from the selenium-rich soil. The growth experiment showed that glucose is the optimal carbon source for P. acidilactici 03W when grown in 1000 µg·mL−1 sodium selenite at pH 6. RNA-seq analysis revealed that a total of 761 genes exhibited altered expression in response to selenite exposure. Downregulation of the phosphate transporter operon (pstA/B/C) and TauE/SafE-type exporters signaled a flux-throttling program that curtailed transmembrane anion flow—limiting high-affinity phosphate uptake and modulating sulfur/selenite export—thereby aligning net anion influx with the cell’s available reductive capacity. In contrast, the expression of the key genes responsible for NAD(P)H or FMN-dependent oxidoreductases and thiol-based redox systems (e.g., trxA/B, tpx, gor, and garB) was induced, together with cysteine desulfurases and sulfurtransferases, supporting the enzymatic reduction of selenite. Interestingly, Fe–S cluster assembly genes (e.g., sufU) were suppressed (not induced), suggesting a shift away from de novo Fe–S biogenesis toward sulfur–selenium transfer and detoxification under oxidative stress. Also, some key genes involved in central carbon metabolism, including the glycolytic pathway (e.g., pfkA) and the pentose phosphate pathway (PPP) (e.g., zwf), were downregulated, which is consistent with reallocating resources from rapid growth to redox homeostasis. Collectively, selenium assimilation in P. acidilactici 03W proceeds through anion transport, enzymatic reduction to Se0 or H2Se, and incorporation into seleno-amino acids (selenocysteine and selenomethionine). Our findings provide a basis for microbial selenium transformation and highlight the potential of P. acidilactici 03W for developing selenium-enriched probiotic foods.