Structural determinants and distribution of phosphate specificity in ribonucleotide reductases

Transcriptomic and Metabolomic Insights Into the Prebiotic Potential of Camellia Seed Oil for Enhancing Akkermansia muciniphila Proliferation In Vitro

Camellia seed oil (CSO), a potential prebiotic agent, can significantly increase the relative abundance of Akkermansia muciniphila (A. muciniphila) in mice gut microbiota following oral administration, this study aims to investigate the enhancing effect in vitro. The results showed that after 24-h co-cultivation with 0.5% (v/v) CSO, the growth of A. muciniphila increased from 11.61 ± 0.04 Log10CFU/mL to 12.17 ± 0.10 Log10CFU/mL (p < 0.05), accompanied by a reduction in the oxidation-reduction potential (ORP) value of the media from -126.67 ± 1.78 mV to -117.33 ± 0.72 mV (p < 0.05). Additionally, squalene and (+)-α-tocopherol, bioactive compounds present in CSO, were found to promote A. muciniphila proliferation (squalene OD600: 1.086 ± 0.002, tocopherol OD600: 1.100 ± 0.003, DMSO control OD600: 0.991 ± 0.003, p < 0.0001). Transcriptomic and metabolomic profiling revealed 464, 121, and 194 differentially expressed genes (DEGs) and 212, 160, and 156 differentially expressed metabolites (DEMs) in A. muciniphila co-cultivated with CSO after 4, 16, and 24 h, respectively (p < 0.05). The upregulated DEGs and DEMs were primarily enriched in pathways associated with energy generation (e.g., gap, icd, sucC, GOZ73_RS04175, succinate, phosphoenolpyruvate), nucleotide metabolism (e.g., mazG, deoxyguanosine), amino acid metabolism (e.g., argF, metK, L-tyrosine), translation (e.g., rplO, rpmC), and environmental adaptation (e.g., murA, katE, reduced nicotinamide adenine dinucleotide). These findings suggest that various bioactive compounds present in CSO exhibit prebiotic effects on the in vitro proliferation of A. muciniphila by facilitating nutrient utilization and environmental adaptation. This study provides insights into the extended utilization of CSO.

HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from Rhodobacter sphaeroides reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.