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

Abstract

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 μgꞏmL⁻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 selenoamino 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.

Keywords

Pediococcus acidilactici / Selenium metabolism / Selenite reduction / Redox regulation / Transcriptome analysis / Selenium-enriching probiotics

Supplementary Materials

The following supporting information can be found at: https://www.sciepublish.com/article/pii/861, Table S1: Composition of MRS basal medium; Table S2: Primers for 16S rRNA gene amplification; Table S3: PCR reaction mixture and thermocycling program for 16S rRNA gene amplification; Table S4: RNA extraction, library preparation, and sequencing; Table S5: Key selenium-related genes highlighted by RNAseq; Table S6: GO enrichment analysis of selenium-responsive genes (top terms); Table S7: KEGG pathway enrichment of selenium-responsive genes (top 15). Supplementary Data S1: Complete list of differentially expressed genes (DEGs) identified by RNA-seq in response to selenium treatment, including gene annotation and differential expression statistics; Supplementary Data S2: Complete Gene Ontology (GO) enrichment results of selenium-responsive genes, including enriched biological process (BP), molecular function (MF), and cellular component (CC) terms; Supplementary Data S3: Complete KEGG pathway enrichment results of selenium-responsive genes, showing significantly enriched metabolic and signaling pathways.

Author Contributions

Conceptualization: X.L.; Methodology: K.C., X.T.; Investigation: K.C., X.T., G.L.; Formal analysis: K.C., X.T.; Data curation: K.C.; Writing—original draft: K.C.; Writing—review & editing: X.L.; Visualization: K.C.; Supervision: Y.Z., X.L.; Project administration: X.L.; Funding acquisition: X.L.

Ethics Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data will be made available on request.

Funding

This study was supported by the Fundamental Research Funds for the Central Universities (Grant Nos. 30922010305 and 1225011021289).

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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