Vitamin B3 Triggers Biosynthesis of Secondary Metabolite Dormancy Signals in Streptococcus suis

Remodeling of ribosomally synthesized peptide backbones based on posttranslational modifications

Covering: 2013-2024Benefiting significantly from recent advances in genome mining, ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products have emerged as a source of chemical inspiration to drive the discovery of therapeutic agents and the development of new biological tools for addressing challenges to synthetic approaches. Despite being confined to twenty proteinogenic amino acid building blocks, the structural complexity and diversity of RiPPs that arise from enzymatic posttranslational modifications (PTMs) surpass expectations and are now believed to be comparable to those produced by non-ribosomal peptide synthetases. Here, we highlight the PTM enzymes characterized over the past decade that engage the -(NH-Cα-CO)n- repeating units in transformations, particularly those leading to structural rearrangements by peptide backbone remodeling. Unveiling the catalytic mechanisms of these unusual PTM enzymes deepens the understanding in RiPP biosynthesis and, eventually, will enhance our capability of rational design, development and production of functional peptide agents using synthetic biology strategies.

Iron limitation triggers roseoceramide biosynthesis and membrane remodeling in marine roseobacter

Chemical communication between marine bacteria and their algal hosts drives population dynamics and ultimately determines the fate of major biogeochemical cycles in the ocean. To gain deeper insights into this small molecule exchange, we screened niche-specific metabolites as potential modulators of the secondary metabolome of the roseobacter, Roseovarius tolerans. Metabolomic analysis led to the identification of a group of cryptic lipids that we have termed roseoceramides. The roseoceramides are elicited by iron-binding algal flavonoids, which are produced by macroalgae that Roseovarius species associate with. Investigations into the mechanism of elicitation show that iron limitation in R. tolerans initiates a stress response that results in lowered oxidative phosphorylation, increased import and catabolism of algal exudates, and reconfiguration of lipid ynthesis to prioritize production of roseoceramides over phospholipids, likely to fortify membrane integrity as well as promote a sessile and symbiotic lifestyle. Our findings add new small molecule words and their "meanings" to the algal-bacterial lexicon and have implications for the initiation of these interactions.

Unlocking hidden treasures: the evolution of high-throughput mass spectrometry in screening for cryptic natural products

Covering: 1994 to 2024Historically, microbial natural product discovery has been predominantly guided by biological activity from crude microbial extracts with metabolite characterization proceeding one molecule at a time. Despite decades of bioactivity-guided isolations, genomic evidence now suggests that we have only accessed a small fraction of the total natural product potential from microorganisms and that the products of the vast majority of biosynthetic pathways remain to be identified. Here we describe recent advancements that have enabled high-throughput mass spectrometry and comparative metabolomics, which in turn facilitate high-throughput natural product discovery. These advancement promise to fully unlock the reservoir of microbial natural products.

Discovery of Cryptic Natural Products Using High-Throughput Elicitor Screening on Agar Media

It is now well-established that microbial genomes carry sparingly expressed biosynthetic gene clusters (BGCs) that need to be induced in order to characterize their products. To do so, we herein subjected two well-known producers, Burkholderia plantarii and Burkholderia gladioli, to high-throughput elicitor screening (HiTES), an emerging approach for accessing the products of these "cryptic" BGCs. Both organisms have previously been examined extensively in liquid cultures. We therefore applied HiTES on agar and found several novel natural products that are only produced in this format and not in liquid cultures. Most notably we found two metabolites, termed burkethyl A and B, that contain an unusual m-ethylbenzoyl group and for which we identified the cognate BGC using bioinformatic and genetic studies. Our results indicate that agar-based HiTES is a promising approach for natural product discovery and are in line with the notion that even "drained" strains remain sources of new metabolites as long as alternative approaches are employed.

Genome Mining for New Enzyme Chemistry

A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.

An intramolecular macrocyclase in plant ribosomal peptide biosynthesis

The biosynthetic dogma of ribosomally synthesized and posttranslationally modified peptides (RiPP) involves enzymatic intermolecular modification of core peptide motifs in precursor peptides. The plant-specific BURP-domain protein family, named after their four founding members, includes autocatalytic peptide cyclases involved in the biosynthesis of side-chain-macrocyclic plant RiPPs. Here we show that AhyBURP, a representative of the founding Unknown Seed Protein-type BURP-domain subfamily, catalyzes intramolecular macrocyclizations of its core peptide during the sequential biosynthesis of monocyclic lyciumin I via glycine-tryptophan crosslinking and bicyclic legumenin via glutamine-tyrosine crosslinking. X-ray crystallography of AhyBURP reveals the BURP-domain fold with two type II copper centers derived from a conserved stapled-disulfide and His motif. We show the macrocyclization of lyciumin-C(sp3)-N-bond formation followed by legumenin-C(sp3)-O-bond formation requires dioxygen and radical involvement based on enzyme assays in anoxic conditions and isotopic labeling. Our study expands enzymatic intramolecular modifications beyond catalytic moiety and chromophore biogenesis to RiPP biosynthesis.

Modern Trends in Natural Antibiotic Discovery

Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.