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PubMed2026

Integrative Multi-Omics Mendelian Randomization Analysis Identifies NIT2 as a Potential Metabolic Risk Gene in Hepatocellular Carcinoma.

BACKGROUND: Metabolic pathways are crucial in hepatocellular carcinoma (HCC) pathogenesis, but causal metabolic genes remain unclear. This study used Summary data-based Mendelian Randomization (SMR) and colocalization to identify metabolism-related genetic loci influencing HCC risk. METHODS: Differentially expressed genes in hepatic malignancy phenotype versus normal tissues from TCGA and GTEx were analyzed. Metabolism-related candidates were examined via SMR and colocalization using multi-omics data: methylation (mQTL), expression (eQTL), and protein (pQTL) quantitative trait loci. RESULTS: Multi-omics integration identified NIT2 as a key metabolic regulator for HCC. The cg13016775 locus of NIT2 was associated with elevated HCC risk at gene (OR = 1.618, 95% CI: 1.199-2.182) and protein (OR = 4.432, 95% CI: 1.783-11.018) levels. Colocalization supported a shared causal variant (PPH4 > 0.6), linking NIT2 to hepatocarcinogenesis via metabolic regulation. CONCLUSIONS: This study provides multi-omics evidence for NIT2 as a potential causal gene in HCC, enhancing understanding of metabolic contributions to HCC pathogenesis and highlighting integrative genomics for uncovering causal relationships.

Carcinoma, Hepatocellular↗
PubMed2026

Nitrilase-mediated degradation of insecticides flonicamid and thiacloprid by immobilized engineered Escherichia coli with a novel pathway.

The nitrile‑containing insecticides flonicamid (FLO) and thiacloprid (THI) are widely used in agriculture, posing risks to the environment and animal health. Nitrilase is a key catalyst for the degradation of nitrile compounds, and immobilized engineered bacteria are preferred in wastewater treatment. However, immobilized engineered bacteria expressing nitrilase have never been investigated for pollutant degradation. Here, engineered Escherichia coli pET28a‑VbNitA harboring the nitrilase gene VbNitA was immobilized by calcium alginate encapsulation. FLO was degraded into N-(4-trifluoromethylnicotinoyl)glycinamide and 4-(trifluoromethyl)nicotinol glycine by the immobilized cells via VbNitA. THI was converted to THI‑amide and THI‑imine using the same system. Notably, this is the first report of a nitrilase converting THI to THI‑amide and of THI‑imine as a biodegradation intermediate. Compared with free cells, the immobilized E. coli pET28a‑VbNitA showed higher tolerance to high temperature, alkaline, and acidic environments, and better long-term storage stability. The substrate inhibition model showed that the optimal initial concentrations of FLO and THI for degradation by immobilized E. coli pET28a‑VbNitA were 45.13 and 127.50 μmol/L, respectively. FLO was degraded more rapidly than THI by the immobilized cells. Molecular docking revealed that both FLO and THI formed stable interactions with VbNitA, with FLO positioned closer to Cys165 of the catalytic triad. This study presents a novel THI degradation pathway and provides a new, efficient immobilized biocatalyst for the remediation of wastewater with nitrile‑containing insecticides.

Escherichia coli↗
PubMed2026

A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti.

Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large reverse transcriptase (RT)-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with podovirus-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.IMPORTANCEIn this study, we report the functional characterization of a UG5-large reverse transcriptase-associated defense system (DRT11) encoded on the pSymA megaplasmid of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Using a combination of phylogenetic, metagenomic, genomic, and experimental approaches, we demonstrate that DRT11 functions as a bona fide antiviral defense module, providing protection against naturally occurring rhizosphere phages through a minimal reverse transcriptase-nitrilase architecture. This work establishes direct functional evidence for antiviral activity within the UG5 family and clarifies the evolutionary placement of UG5-associated systems within the broader UG radiation.

Phylogeny↗