Search Results (38)

Advances in whole genome sequencing have transformed GenBank into a veritable goldmine of uncharacterized and predicted proteins, many of which still await functional characterization. Notably, natural product biosynthetic pathways are often organized in gene clusters, unlocking thrilling avenues for the discovery of novel metabolites and distinctive enzymatic reactions. In this review, we focus on the versatile ThiF-like adenylyltransferase superfamily (TLATs), a group of enzymes essential for the biosynthesis of a diverse array of ribosomally synthesized and post-translationally modified peptides (RiPPs). Recent researches have revealed that TLATs are widespread in numerous yet uncharacterized RiPP biosynthetic pathways, highlighting significant gaps in our understanding of their extensive catalytic potential. Here, we critically review the latest insights into RiPP gene clusters containing these enzymes, discussing the natural products they generate, their enzymatic functions, catalytic mechanisms, and promising directions for future research. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article

The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5^T and A. mytilicola subsp. aquatica subsp. nov. A-8^T isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7^T isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5^T and A-7^T shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1^T (99.7% and 99.8%, respectively), while strain A-8^T exhibited 99.7% identity with A. media RM^T. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA–DNA hybridization (dDDH; 56.8−65.9%) and average nucleotide identity (ANI; 94.2–95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed. Full article

Bark beetle-associated bacteria from the sub-boreal and boreal forests of northern Canada represent a largely unexplored source of bioactive natural products. This study aims to investigate the chemical potential of bacteria isolated from Dendroctonus ponderosae, Dendroctonus rufipennis, Dendroctonus pseudotsugae, and Ips perturbatus by focusing on nitrogen-containing secondary metabolites. Genomic analyses of the bacterial isolates identified diverse biosynthetic gene clusters (BGCs), including nonribosomal peptides (NRPs), NRPS-PKS hybrids, and ribosomally synthesized and post-translationally modified peptides (RiPPs), many of which exhibit low sequence homology, suggesting potential for novel bioactive compounds. Nitrogen-15 NMR spectroscopy was employed to detect nitrogen-containing functional groups in crude extracts, revealing distinct signals for amides, amines, and nitrogen heterocycles. The combination of BGC predictions and NMR data highlighted the genetic and chemical diversity of these bacteria and underscored the potential for discovering novel nitrogen-rich metabolites. These findings provide a foundation for further exploration of bioactive natural products with pharmaceutical and agrochemical applications and potential to contribute to the understanding of the chemical ecology of bark beetle–microbe interactions in northern ecosystems. Full article

Background/Objectives: Lactic acid bacteria (LAB) produce several diverse metabolites during fermentation that play key roles in enhancing health and food quality. These metabolites include peptides, organic acids, exopolysaccharides, and antimicrobial compounds, which contribute to gut health, immune system modulation, and pathogen inhibition. This study analyzed the intracellular (Met-Int) and extracellular metabolites (Met-Ext-CFS; cell-free supernatant) of Lactiplantibacillus plantarum UTNGt2, a probiotic strain isolated from Theobroma grandiflorum. Methods: The assessment was performed using capillary LC-MS/MS metabolomics with a SWATH-based data-independent acquisition approach to identify molecules associated with antimicrobial activity. Results: The integration of metabolomic data with whole-genome annotation enabled the identification of several key metabolites, including amino acids, nucleotides, organic acids, oligopeptides, terpenes, and flavonoids, many of which were associated with the antimicrobial activity of UTNGt2. Pathway analysis reveals critical processes such as secondary metabolite biosynthesis, nucleotide and galactose metabolism, and cofactor biosynthesis. By integrating RiPP (ribosomally synthesized and post-translationally modified peptide) cluster gene predictions with LC-MS data, this study validates the production of specific RiPPs and uncovers novel bioactive compounds encoded within the UTNGt2 genome. The oligopeptide val-leu-pro-val-pro-gln found in both Met-Int (ESI+) and Met-Ext-CFS (ESI+) may contribute to the strain’s antimicrobial strength. It could also enhance probiotic and fermentation-related functions. Conclusions: While genome-based predictions highlight the strain’s biosynthetic potential, the actual metabolite profile is influenced by factors like transcriptional regulation, post-transcriptional and post-translational modifications, and environmental conditions. These findings emphasize the value of multi-omics approaches in providing a holistic understanding of metabolite production and its role in antimicrobial activity. Full article

Lactobacillus is a key genus of probiotics commonly utilized for the treatment of oral infections The primary aim of our research was to investigate the probiotic potential of the newly isolated Levilactobacillus brevis DPL5 strain from human breast milk, focusing on its ability to combat biofilm-forming pathogens such as Staphylococcus aureus. Employing in vitro approaches, we demonstrate L. brevis DPL5′s ability to endure at pH 3 with survival rates above 30%, and withstand the osmotic stress often found during industrial processes like fermentation and freeze drying, retaining over 90% viability. The lyophilized cell-free supernatant of L. brevis DPL5 had a significant antagonistic effect against biofilm-producing nasal strains of Staphylococcus aureus, and it completely eradicated biofilms at subinhibitory concentrations of 20 mg·mL⁻¹. Higher concentrations of 69 mg·mL⁻¹ were found to have a 99% bactericidal effect, based on the conducted probability analysis, indicating the production of bactericidal bioactive extracellular compounds capable of disrupting the biofilm formation of pathogens like S. aureus. Furthermore, genome-wide sequencing and analysis of L. brevis DPL5 with cutting-edge Nanopore technology has uncovered over 50 genes linked to probiotic activity, supporting its ability to adapt and thrive in the harsh gut environment. The genome also contains multiple biosynthetic gene clusters such as lanthipeptide class IV, Type III polyketide synthase (T3PKS), and ribosomally synthesized, and post-translationally modified peptides (RiPP-like compounds), all of which are associated with antibacterial properties. Our study paves the way for the further exploration of DPL5, setting the stage for innovative, nature-inspired solutions to combat stubborn bacterial infections. Full article

Cancer remains a significant medical challenge, necessitating the discovery of novel therapeutic agents. Ribosomally synthesized and post-translationally modified peptides (RiPPs) from plants have emerged as a promising source of anticancer compounds, offering unique structural diversity and potent biological activity. This review identifies and discusses cytotoxic RiPPs across various plant families, focusing on their absolute chemical structures and reported cytotoxic activities against cancer cell lines. Notably, plant-derived RiPPs such as rubipodanin A and mallotumides A–C demonstrated low nanomolar IC₅₀ values against multiple cancer cell types, highlighting their therapeutic potential. By integrating traditional ethnobotanical knowledge with modern genomic and bioinformatic approaches, this study underscores the importance of plant RiPPs as a resource for developing innovative cancer treatments. These findings pave the way for further exploration of plant RiPPs, emphasizing their role in addressing the ongoing challenges in oncology and enhancing the repertoire of effective anticancer therapies. Full article

Background: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. RiPPs have attracted attention for the ability to generate and screen libraries of these compounds for useful biological activities. To facilitate this screening, it is useful to be able to do so with the leader peptide still present. We assessed the suitability of the microviridin family for these screening experiments by determining their activity with the leader peptide still present. Methods: Modified precursor peptides with the leader present were heterologously expressed in Escherichia coli. Their ability to inhibit elastase was tested with a fluorogenic substrate. HPLC was used to monitor degradation of the modified precursor peptides by elastase. SDS-PAGE was used to determine the ability of immobilized modified precursor peptide to pull down elastase. Results: We found that the fully modified precursor peptide of microviridin B can inhibit the serine protease elastase with a low nanomolar IC₅₀, and that the fully modified precursor with an N-terminal His-tag can mediate interactions between elastase and Ni-NTA resin, all indicating leader peptide removal is not necessary for microviridins to bind their target proteases. Additionally, we found that a bicyclic variant was able to inhibit elastase with the leader peptide still present, although with a roughly 100-fold higher IC₅₀ and being subject to hydrolysis by elastase. Conclusions: These results open a pathway to screening libraries of microviridin variants for improved protease inhibition or other characteristics that can serve as, or as inspirations for, new pharmaceuticals. Full article

Genome mining has emerged as a revolutionary tool for discovering new ribosomally synthesized and post-translationally modified peptides (RiPPs) in various genomes. Recently, these approaches have been used to detect and explore unique environments as sources of RiPP-producing microorganisms, particularly focusing on endophytic microorganisms found in medicinal plants. Some endophytic actinobacteria, especially strains of Streptomyces, are notable examples of peptide producers, as specific biosynthetic clusters encode them. To uncover the genetic potential of these organisms, we analyzed the genome of the endophytic actinobacterium Embleya sp. NF3 using genome mining and bioinformatics tools. Our analysis led to the identification of a putative class I lanthipeptide. We cloned the core biosynthetic genes of this putative lanthipeptide, named embleporicin, and expressed them in vitro using a cell-free protein system (CFPS). The resulting product demonstrated antimicrobial activity against Micrococcus luteus ATCC 9341. This represents the first RiPP reported in the genus Embleya and the first actinobacterial lanthipeptide produced through cell-free technology. Full article

The actinomycete genus Rhodococcus is known for its diverse biosynthetic enzymes, with potential in pollutant degradation, chemical biocatalysis, and natural product exploration. Comparative genomics have analyzed the distribution patterns of non-ribosomal peptide synthetases (NRPSs) in Rhodococcus. The diversity and specificity of its secondary metabolism offer valuable insights for exploring natural products, yet remain understudied. In the present study, we analyzed the distribution patterns of biosynthetic gene clusters (BGCs) in the most comprehensive Rhodococcus genome data to date. The results show that 86.5% of the gene cluster families (GCFs) are only distributed in a specific phylogenomic-clade of Rhodococcus, with the most predominant types of gene clusters being NRPS and ribosomally synthesized and post-translationally modified peptides (RiPPs). In-depth mining of RiPP gene clusters revealed that Rhodococcus encodes many clade-specific novel RiPPs, with thirteen core peptides showing antibacterial potential. High-throughput elicitor screening (HiTES) and non-targeted metabolomics revealed that a marine-derived Rhodococcus strain produces a large number of new aurachin-like compounds when exposed to specific elicitors. The present study highlights the diversity and specificity of secondary biosynthetic potential in Rhodococcus, and provides valuable information for the targeted exploration of novel natural products from Rhodococcus, especially for phylogenomic-clade-specific metabolites. Full article

Borosins are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylated backbones. Although the first mature compound of borosin was reported in 1997, the biosynthetic pathway was elucidated 20 years later. Until this work, borosins have been able to be categorized into 11 types based on the features of their protein structure and core peptides. Type III borosins were reported only in fungi initially. In order to explore the sources and potential of type III borosins, a precise genome mining work of type III borosins was conducted in bacteria and KchMA’s self-methylation activity was validated by biochemical experiment. Furthermore, a commercial protease and AI-assisted rational design was employed to engineer KchMA for the capacity to produce various N-methylated peptides. Our work demonstrates that type III borosins are abundant not only in eukaryotes but also in bacteria and have immense potential as a tool for synthetic biology. Full article

The rapid evolution of drug resistance is one of the greatest health issues of the 21st century. There is an alarming situation to find new therapeutic strategies or candidate drugs to tackle ongoing multi-drug resistance development. The marine environment is one of the prime natural ecosystems on Earth, the majority of which is still unexplored, especially when it comes to the microbes. A wide variety of bioactive compounds have been obtained from a varied range of marine organisms; however, marine bacteria-produced bacteriocins are still undermined. Owing to the distinct environmental stresses that marine bacterial communities encounter, their bioactive compounds frequently undergo distinct adaptations that confer on them a variety of shapes and functions, setting them apart from their terrestrial counterparts. Bacterially produced ribosomally synthesized and posttranslationally modified peptides (RiPPs), known as bacteriocins, are one of the special interests to be considered as an alternative to conventional antibiotics because of their variety in structure and diverse potential biological activities. Additionally, the gut microbiome of marine creatures are a largely unexplored source of new bacteriocins with promising activities. There is a huge possibility of novel bacteriocins from marine bacterial communities that might come out as efficient candidates to fight against antibiotic resistance, especially in light of the growing pressure from antibiotic-resistant diseases and industrial desire for innovative treatments. The present review summarizes known and fully characterized marine bacteriocins, their evolutionary aspects, challenges, and the huge possibilities of unexplored novel bacteriocins from marine bacterial communities present in diverse marine ecosystems. Full article

Lichens have developed numerous adaptations to optimize their survival in various environmental conditions, largely by producing secondary compounds by the fungal partner. They often have antibiotic properties and are involved in protection against intensive UV radiation, pathogens, and herbivores. To contribute to the knowledge of the arsenal of secondary compounds in a crustose lichen species, we sequenced and assembled the genome of Toniniopsis dissimilis, an indicator of old-growth forests, using Oxford Nanopore Technologies (ONT, Oxford, UK) long reads. Our analyses focused on biosynthetic gene clusters (BGCs) and specifically on Type I Polyketide (T1PKS) genes involved in the biosynthesis of polyketides. We used the comparative genomic approach to compare the genome of T. dissimilis with six other members of the family Ramalinaceae and twenty additional lichen genomes from the database. With only six T1PKS genes, a comparatively low number of biosynthetic genes are present in the T. dissimilis genome; from those, two-thirds are putatively involved in melanin biosynthesis. The comparative analyses showed at least three potential pathways of melanin biosynthesis in T. dissimilis, namely via the formation of 1,3,6,8-tetrahydroxynaphthalene, naphthopyrone, or YWA1 putative precursors, which highlights its importance in T. dissimilis. In addition, we report the occurrence of genes encoding ribosomally synthesized and posttranslationally modified peptides (RiPPs) in lichens, with their highest number in T. dissimilis compared to other Ramalinaceae genomes. So far, no function has been assigned to RiPP-like proteins in lichens, which leaves potential for future research on this topic. Full article

Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches. Full article

Natural product (NP)-based pesticides have emerged as a compelling alternative to traditional chemical fungicides, attracting substantial attention within the agrochemical industry as the world is pushing toward sustainable and environmentally friendly approaches to safeguard crops. Microbes, both bacteria and fungi, are a huge source of diverse secondary metabolites with versatile applications across pharmaceuticals, agriculture, and the food industry. Microbial genome mining has been accelerated for pesticide/drug discovery and development in recent years, driven by advancements in genome sequencing, bioinformatics, metabolomics/metabologenomics, and synthetic biology. Here, we isolated and identified Pseudomonas vancouverensis that had shown antifungal activities against crop fungal pathogens Colletotrichum fragariae, Botrytis cinerea, and Phomopsis obscurans in a dual-plate culture and bioautography assay. Further, we sequenced the whole bacterial genome and mined the genome of this bacterium to identify secondary metabolite biosynthetic gene clusters (BGCs) using antiSMASH 7.0, PRISM 4, and BAGEL 4. An in-silico analysis suggests that P. vancouverensis possesses a rich repertoire of BGCs with the potential to produce diverse and novel NPs, including non-ribosomal peptides (NRPs), polyketides (PKs), acyl homoserine lactone, cyclodipeptide, bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). Bovienimide-A, an NRP, and putidacin L1, a lectin-like bacteriocin, were among the previously known predicted metabolites produced by this bacterium, suggesting that the NPs produced by this bacterium could have biological activities and be novel as well. Future studies on the antifungal activity of these compounds will elucidate the full biotechnological potential of P. vancouverensis. Full article