A Novel Indigoidine-like NRPS Gene from Arthrobacter antioxidans QL17 Enhances Oxidative Stress Resistance Through Radical Scavenging and Transcriptional Reprogramming

Complete genome sequence and mass spectrometry assist mining siderophore turnerbactin analogs in a non-model Pseudoduganella strain with biocontrol potential

Findings indicate that Pseudoduganella sp.

A conserved vdcBCD cluster encoding a vanillate/p-hydroxybenzoate decarboxylase catalyzes the formation of phenol from p-hydroxybenzoate in the cork-associated Streptomyces graminifolii B37 strain

Cork affected by yellow stain contains aromatic acids and volatile phenols, although the microbial reactions contributing to their formation are still poorly characterized. Streptomyces sp. B37, isolated from yellow-stained cork, was previously shown to convert p -hydroxybenzoate into phenol, but both its precise taxonomic placement and the genetic basis of this bioconversion were unknown. We combined whole-genome comparison, pangenome analysis, and heterologous expression to identify and validate the aromatic acid decarboxylation system underlying this phenotype. Phylogenomic analysis assigned strain B37 to Streptomyces graminifolii species. Comparative genomics showed that B37 belongs to a subclade of closely related Vanillate Decarboxylase (VDC)-positive genomes with an accessory repertoire enriched in functions related to aromatic compound uptake, regulation, redox metabolism and ring-cleavage pathways. In contrast, functions associated with primary cork-polymer degradation were not overrepresented. A conserved vdcBCD cluster was present in the genomes of Streptomyces species comprising this group and embedded in a partially conserved chromosomal neighborhood containing regulatory, oxidative and transport-related genes. Heterologous expression of the B37 vdcBCD cluster in Streptomyces lividans JI66 conferred the ability to decarboxylate p -hydroxybenzoate into phenol and vanillic acid into guaiacol, whereas the empty-vector control S. lividans JI66(pIJ699) showed no detectable decarboxylase activity. These results identify the B37 vdcBCD cluster as a bifunctional aromatic acid decarboxylation module and link this reaction to the formation of phenolic intermediates relevant to yellow-stained cork and cork taint-associated chemistry, including the de novo formation of chlorophenols and chloroanisoles.

Deciphering the Function and Structure of PA1216 as an S‐Adenosyl‐l‐Methionine Binding Protein Using Differential Scanning Fluorimetry and Circular Dichroism

Microbes produce bioactive secondary metabolites as toxins, pigments, or virulence factors. These specialized compounds are produced by nonribosomal peptide synthetases (NRPS), polyketide synthases (PKS), or hybrid NRPS/PKS pathways. The genes encoding NRPS and PKS reside in biosynthetic gene clusters (BGCs), some of which have no identified metabolite associated with them. Characterization of these orphan BGCs could provide insights into potential bioactive compounds that have yet to be discovered. Here, we characterize PA1216, a putative methyltransferase embedded within an NRPS BGC in Pseudomonas aeruginosa strain PAO1. We cloned, expressed, and purified PA1216, and developed an optimized differential scanning fluorimetry assay to measure its thermal stability, demonstrating concentration‐dependent stabilization in the presence of established methyltransferase cofactors and inhibitors. We then adapted this assay for high‐throughput screening of potential PA1216 substrates, identifying destabilizing compounds, including glycyl‐glycine dipeptides, amino esters with aromatic or basic side chains, and N‐Boc‐protected amino acids. In contrast, sodium salts of organic acids stabilized PA1216. Lastly, we employed AlphaFold to construct a predictive model, revealing that PA1216 contains a Rossmann‐like fold and a glycine‐rich loop, typical of class I methyltransferases, and we corroborated these secondary structural elements using circular dichroism spectroscopy. Overall, these studies illuminate PA1216 function and establish a platform for characterizing cryptic gene clusters within secondary metabolic pathways.

Discovery and Comprehensive Characterization of Pseudomonas sp. MUP55: Taxonomy, Massetolide-Mediated Biocontrol, and Regulatory and Antimicrobial Contributions of the pvf Cluster

Pseudomonas sp. MUP55, isolated from rainfall water in Western Australia, was characterized by polyphasic taxonomy and functional assays. Whole-genome and 16S rRNA phylogeny placed Pseudomonas sp. MUP55 in the Pseudomonas fluorescens species group. Massetolide A/D was identified as the leading candidate bioactive compound(s), consistent with its biosynthetic gene cluster, GNPS library matching, and loss of activity in regulatory mutants. The strain showed broad-spectrum antimicrobial activity against bacterial (Escherichia coli and Xanthomonas campestris) and fungal (Fusarium oxysporum and Rhizoctonia solani) plant pathogens. GacA regulates Massetolide production: a P58L mutation abolished synthesis and reduced biocontrol efficacy. Metabolomic and transcriptomic analysis of a ΔpvfC mutant revealed that the pvf cluster regulates specialized metabolism while also contributing to secreted growth-inhibitory activity. The pvf cluster differentially regulates dual siderophore systems and uncouples the co-regulated small RNAs rsmY and rsmZ in the Gac/Rsm cascade. Deletion of pvfC partially reduced the growth-inhibitory activity of Pseudomonas sp. MUP55 supernatants against bacterial pathogens, indicating that pvfC also influences secreted antimicrobial activity beyond its global regulatory role. These findings establish Pseudomonas sp. MUP55 as a taxonomically novel, mechanistically characterized biocontrol agent with potential for sustainable agriculture.

Characterization and genomic analysis of Bacillus halotolerans G3-2: a potential biocontrol agent against apple Alternaria leaf blotch disease.

BACKGROUND Apple Alternaria leaf blotch (ALB) is a devastating disease threatening the apple industry worldwide. Biocontrol offers an effective and environmentally friendly alternative for disease management. RESULTS Bacillus strain G3-2 exhibits strong antagonistic activity against Alternaria alternata (a major causal pathogen of ALB). In dual-culture assays, G3-2 inhibited A. alternata by 88.39%; in detached-leaf inoculation assays, it reduced the lesion area by >88%. 16S rRNA sequencing and phylogenetic analysis identified this strain as Bacillus halotolerans. Oxford Nanopore Technology (ONT) sequencing generated a 4.18-Mb complete genome (43.8% G + C) containing 4149 protein-coding genes, 30 rRNAs and 86 tRNAs. CAZy annotation identified 182 genes encoding carbohydrate-active enzymes (CAZymes), including glycoside hydrolases, glycosyltransferase, and carbohydrate esterases, suggesting potential for glycosylated secondary metabolite production. AntiSMASH analysis detected nine biosynthetic gene clusters, including those for surfactin, fengycin, bacillaene and laterocidine. Plate assays confirmed that G3-2 has the ability to produce protease, cellulase and siderophore. Moreover, it exhibits ~70% inhibition against several other phytopathogenic fungi. CONCLUSIONS These findings demonstrate that G3-2 suppresses A. alternata through antibiosis (lipopeptides and polyketides), nutrient competition (siderophores) and cell-wall degradation (proteases and cellulases). Moreover, our study revealed that it has great potential to be used as a broad-spectrum, environmentally friendly biocontrol agent. © 2026 Society of Chemical Industry.

Genome-wide analysis of the Escherichia coli Keio collection reveals genetic determinants associated with ferulic acid responses.