Selenite Reduction by Proteus sp. YS02: New Insights Revealed by Comparative Transcriptomics and Antibacterial Effectiveness of the Biogenic Se0 Nanoparticles

Abstract

Biotransformation of selenite by microorganisms is an effective detoxification (in cases of dissimilatory reduction, e.g., to Se⁰) and assimilation process (when Se is assimilated by cells). However, the current knowledge of the molecular mechanism of selenite reduction remains limited. In this study, a selenite-resistant bacterium was isolated and identified as Proteus sp. YS02. Strain YS02 reduced 93.2% of 5.0 mM selenite to selenium nanoparticles (SeNPs) within 24 h, and the produced SeNPs were spherical and localized intracellularly or extracellularly, with an average dimension of 140 ± 43 nm. The morphology and composition of the isolated and purified SeNPs were characterized using dynamic light scattering (DLS), scanning electron microscopy (SEM) with energy-dispersive X-ray (EDX) spectrometry, and Fourier transform infrared (FTIR) spectroscopy. FTIR spectroscopy indicated the presence of proteins, polysaccharides, and lipids on the surface of the isolated SeNPs. Furthermore, the SeNPs showed excellent antimicrobial activity against several Gram-positive and Gram-negative pathogenic bacteria. Comparative transcriptome analysis was performed to elucidate the selenite reduction mechanism and biosynthesis of SeNPs. It is revealed that 197 genes were significantly upregulated, and 276 genes were significantly downregulated under selenite treatment. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that genes associated with ABC transporters, sulfur metabolism, pentose phosphate pathway (PPP), and pyruvate dehydrogenase were significantly enhanced, indicating selenite is reduced by sulfite reductase with PPP and pyruvate dehydrogenase supplying reducing equivalents and energy. This work suggests numerous genes are involved in the response to selenite stress, providing new insights into the molecular mechanisms of selenite bioreduction with the formation of SeNPs.

Keywords: Proteus sp. YS02; antibacterial effectiveness; biogenic selenium nanoparticles; selenite biotransformation; transcriptome.

Figure 1

Maximum likelihood tree inferred through MEGA 7 software based on 16S rRNA gene sequence of strain YS02 and related representative strains. Sphingobacterium zeae (KU201960) was used as the out-group member. The scale bars represent 0.05 substitutions per site.

Figure 2

Growth of bacterial strain YS02 in liquid YEP medium containing 5.0 mM selenite. (A) Images of cultures with 5.0 mM selenite (on the left) and without selenite (on the right) aerobically grown for 9 h and (B) the growth curve, time courses of SeO₃²⁻ reduction, and Se⁰ production by strain YS02. Each test was performed in triplicate, and data were presented as the mean ± standard deviation.

Figure 3

TEM analysis of Proteus sp. YS02 (A) cultured without Na₂SeO₃ and (B,C) cultured with 5 mM Na₂SeO₃ after 24 h of incubation. White arrows show nanoparticles inside (B) or outside (C) the cells. Empty ghost cells are indicated by red arrows (C). The bar represents 1 μm.

Figure 4

SEM analysis of Proteus sp. YS02 (A) cultured without Na₂SeO₃ and (B) cultured with 5 mM Na₂SeO₃ for 24 h. White arrows indicate the produced extracellularly located nanoparticles. The bar represents 1 μm.

Figure 5

SEM–EDX analysis of purified SeNPs produced by Proteus sp. YS02. The bar represents 5 μm.

Figure 6

Fourier transform infrared spectrum of isolated SeNPs produced by Proteus sp. YS02.

Figure 7

The antibacterial effect of isolated SeNPs (produced by Proteus sp. YS02) on E. coli, P. aeruginosa, B. subtilis, and S. epidermidis screened by the plate antibacterial test. The red colored disks represented SeNPs and the white disks represented the standard antibiotic.

Figure 8

The volcano plots of genes for Proteus sp. YS02 between the control and Se treatment. Red and blue dots represent genes that were significantly upregulated and downregulated, respectively. Gray dots indicate the genes without significant differential expression.

Figure 9

GO classifications of (A) downregulated DEGs and (B) upregulated DEGs. The X axis presents the number of DEGs belonging to specific categories. The Y axis presents three major functional categories of GO terms.

Figure 10

Enriched KEGG pathways for (A) upregulated DEGs and (B) downregulated DEGs in the presence of selenite. The X axis corresponds to the percentage of DEGs belonging to a specific pathway. The Y axis presents the names of the top 20 pathways.

Figure 11

A hypothesized mechanism of selenite biotransformation and biosynthesis of SeNPs in strain Proteus sp. YS02. Yet unidentified processes are shown in dotted lines or question mark.