Total and chemoenzymatic synthesis of the lipodepsipeptide rhizomide A

Genomic and metabolomic insights into the modes-of-action of bacterial strains to control the grapevine wood pathogen, Fomitiporia mediterranea

Grapevine trunk diseases (GTDs), particularly Esca, represent a major challenge for viticulture worldwide, leading to substantial economic losses. With no effective control treatments available, developing new methods such as biocontrol is crucial for managing GTDs. Our aim was to select biocontrol bacteria effective against the white-rot fungal pathogen Fomitiporia mediterranea (Fmed) and to investigate their mechanisms of action. A stepwise screening of 58 bacterial strains was conducted in vitro to assess their ability to inhibit Fmed growth through volatile and diffusible metabolites production. The screening was also done on wood sawdust from seven different grapevine cultivars. Out of 58 tested strains, 49 inhibited Fmed growth by over 50 % through their volatile organic compounds, only eight achieving this through their agar-diffusible metabolites. Pseudomonas lactis SV9, Pseudomonas paracarnis S45, and Paenibacillus polymyxa SV13 exhibited a strong efficacy in inhibiting Fmed on wood sawdust in a cultivar-dependent manner. We selected these strains for whole genome analysis and metabolomic profiling via LC-MS/MS for diffusible compounds and SPME GC-MS for volatile compounds. P. polymyxa SV13 inhibited Fmed primarily through diffusible metabolites, producing mainly fusaricidin-type compounds. Conversely, Pseudomonas strains acted mainly via their volatile metabolites, producing mainly the antifungal compound dimethyl disulfide. Genome analysis of the three bacterial strains revealed gene clusters responsible for regulating both direct and indirect mechanisms in biocontrol agents (BCAs). Our findings highlight the importance of comprehensive studies that combine in vitro experiments mimicking field conditions, with detailed investigations into modes of action to improve BCAs efficacy.

"Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature"

The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.

Macrocyclizing-thioesterases in bacterial non-ribosomal peptide biosynthesis

Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties. However, side reactions such as epimerization and oligomerization often pose synthetic challenges. Peptide-cyclizing biocatalysts in the biosynthesis of non-ribosomal peptides (NRPs) have remarkable potentials as chemoenzymatic tools to facilitate more straightforward access to complex macrocycles. This review highlights the biocatalytic potentials of NRP cyclases, especially those of cis-acting thioesterases, the most general cyclizing machinery in NRP biosynthesis. Growing insights into penicillin-binding protein-type thioesterases, a relatively new group of trans-acting thioesterases, are also summarized.

Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov

The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.

Thioesterases as tools for chemoenzymatic synthesis of macrolactones

Macrocycles are a key functional group that can impart unique properties into molecules. Their synthesis has led to the development of many outstanding chemical methodologies and yet still remains challenging. Thioesterase (TE) domains are frequently responsible for macrocyclization in natural product biosynthesis and provide unique strengths for the enzymatic synthesis of macrocycles. In this feature article, we describe our work to characterize the substrate selectivity of TEs and to use these enzymes as biocatalysts. Our efforts have shown that the linear thioester activated substrates are loaded on TEs with limited substrate selectivity to generate acyl-enzyme intermediates. We show that cyclization of the acyl-enzyme intermediates can be highly selective, with competing hydrolysis of the acyl-enzyme intermediates. The mechanisms controlling TE-mediated macrocyclization versus hydrolysis are a significant unsolved problem in TE biochemistry. The potential of TEs as biocatalysts was demonstrated by using them in the chemoenzymatic total synthesis of macrocyclic depsipeptide natural products. This article highlights the strengths and potential of TEs as biocatalysts as well as their limitations, opening exciting research opportunities including TE engineering to optimize these powerful biocatalysts.