Genome mining and comparative genome analysis of Pseudomonas fluorescens revealed diverse biosynthetic and metabolic potential

Genomic and pan-genomic analyses of Bacillus subtilis B13 provide insights into biosynthetic potential and genetic traits associated with environmental adaptation

In Silico Identification and Comparative Synteny of Biosynthetic Gene Clusters in Plants.

Evolution, structure and function of the putative biosynthetic gene cluster of the fungal secondary metabolite myriocin, a potent inhibitory sphingolipid.

Myriocin is a fungal secondary metabolite exploited worldwide as a powerful inhibitor of sphingolipid biosynthesis through its structural similarity to sphingosine. We identify the putative myriocin biosynthesis gene cluster (BGC) through de novo sequencing of two producing fungi, Isaria sinclairii and Mycelia sterilia, yielding genomes of 25.2 Mb and 34.2 Mb encoding 27 and 20 secondary metabolite BGCs, respectively. BGCs #5 in I. sinclairii and #18 in M. sterilia both shared and expressed the polyketide synthase (PKS) and alpha oxo-amine synthase (AOS) predicted for myriocin biosynthesis, with 74% and 79% sequence similarity, respectively. Analysis of a 2,236-fungal-genome database suggests the pathway originated in the Sordariomycete ancestor, presenting in two major clades distinguished by PKS gene orientation. The placement of thermophilic M. sterilia suggests myriocin BGC acquisition through horizontal gene transfer, but its origin in I. sinclairii is ambiguous. Heterologously-expressed IsMyrA bound aminomalonate, and a protein-protein docking interface was identified between the acyl carrier protein and IsMyrA. A model of PKS domain function, the roles of the PKS and AOS genes and the synteny of the putative myriocin biosynthetic gene cluster across 34 carrier species of ascomycetes is presented.

Diversity and evolution of the transcriptional regulatory networks of Pseudomonas strains revealed using machine learning

The genus Pseudomonas consists of diverse and ecologically significant species that form close associations with both plants and animals. This genus is widely studied due to the clinically relevant Pseudomonas aeruginosa, model plant pathogen Pseudomonas syringae, and non-pathogenic, industrially relevant Pseudomonas putida. The different metabolic and physiological capabilities of these species are enabled by their unique genetic makeup as well as varying regulatory mechanisms. To study the transcriptional basis for the diversity of the three species, we applied independent component analysis to strain-specific RNA-seq datasets to identify independently modulated gene sets (iModulons) and their condition-specific activity levels. We then mapped iModulons across strains based on their similarity in orthologous gene membership. Through comparison of iModulon gene membership and activities, we find that: (i) iModulons reveal shared and unique regulatory modalities across strains; (ii) unique adaptations in common functions, such as translation and pyoverdine production/uptake, manifest through both differential iModulon gene membership and condition-specific activation states in each strain; (iii) iModulons facilitate comparison of stress responses at the systems level; and (iv) iModulons highlight unique virulence factor enrichment and host-specific adaptations in human and plant pathogens. Altogether, comparing the modularized transcriptomes of the three strains provides unique and comprehensive insights into their differential evolution. Importance Closely related bacterial species often have vastly different metabolic and physiological capabilities, yet the regulatory mechanisms underlying these adaptations remain poorly understood. Here, we compare the transcriptional regulatory networks of three representative Pseudomonas strains through cross-strain iModulon analysis. By comparing both iModulon gene composition and activity across strains, we identify conserved regulatory modules alongside lineage-specific adaptations in functions associated with virulence, translation, iron acquisition, motility, and stress responses. Our results demonstrate that iModulons provide a genome-scale framework for comparing transcriptional regulation across closely related organisms, revealing regulatory innovations that are not apparent from genome comparisons alone. This work establishes a scalable approach for studying the evolution of bacterial transcriptional regulatory networks and the regulatory basis of niche specialization.

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.

Pangenome analysis of Nocardia brasiliensis reveals phylogenetic divergence, high genomic diversity and widespread distribution of biosynthetic gene clusters involved in secondary metabolite biosynthesis.

Actinobacteria are a diverse and heterogeneous group of bacteria with complex taxonomy that produce most of the natural products used in medicine. Although comparative genomic studies of Nocardia species have been reported, comprehensive species-level analyses integrating phylogenomics, pangenome structure, and biosynthetic gene cluster distribution in N. brasiliensis remain limited. In this study, we performed phylogenomic orthology inference, analyzed pangenome composition, and evaluated the potential of Nocardia brasiliensis as a source of secondary metabolites using comparative genomics. Four clinical strains from Mexico and 22 publicly accessible genomes were included. Genomic identification was performed, orthologous genes were identified, core genome and pangenome composition were estimated, and phylogenomic orthology inference was assessed. All genomes were searched for known BGCs, secondary metabolites were predicted, and data on reported biological activity were collected. A pangenome comprising 17,715 clusters was calculated, with the core genome accounting for 22.76 % and the cloud genome for 48.17 %. The trend in the gene accumulation curve indicated that the species had an open pangenome, as the continuous increase in gene clusters with the addition of new genomes suggests a high level of genomic diversity and ongoing gene acquisition within the species, reflecting its capacity for environmental adaptation and evolutionary plasticity. Phylogenomic analysis showed that geographical origin and isolation conditions affect evolutionary divergence within N. brasiliensis. Computational BGC prediction detected PKS, NRPS, NAPAA, terpenes, aminopolycarboxylic acids, hybrids, and other clusters coding for secondary metabolites with antimicrobial activity (ε-Poly-L-lysine, brasiliquinones A-B), antitumor activity (rhizomides A-C, anthramycin), antioxidant activity (isorenieratene), and a fertilizer for calcareous soils ([S, S]-EDDS). The results reveal significant genomic diversity and a wide distribution of biosynthetic clusters within the Nocardia brasiliensis pangenome, demonstrating its genomic plasticity and the variability in metabolic potential across strains.