Thiopeptide pyridine synthases catalyze a multistep reaction involving a unique and nonspontaneous intramolecular aza-4 + 2 cycloaddition between two dehydroalanines to forge a trisubstituted ...pyridine core. We discovered that the in vitro activity of pyridine synthases from the thiocillin and thiomuracin pathways are significantly enhanced by general base catalysis and that this broadly expands the enzymes substrate tolerance. Remarkably, TbtD is competent to perform an intermolecular cyclization in addition to its cognate intramolecular reaction, underscoring its versatility as a biocatalyst. These data provide evidence that pyridine synthases use a two-site substrate recognition model to engage and process their substrates.
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Bacteria have evolved the ability to produce a wide range of structurally complex natural products historically called “secondary” metabolites. Although some of these compounds have been identified ...as bacterial communication cues, more frequently natural products are scrutinized for antibiotic activities that are relevant to human health. However, there has been little regard for how these compounds might otherwise impact the physiology of neighboring microbes present in complex communities. Bacillus cereus secretes molecules that activate expression of biofilm genes in Bacillus subtilis . Here, we use imaging mass spectrometry to identify the thiocillins, a group of thiazolyl peptide antibiotics, as biofilm matrix-inducing compounds produced by B. cereus . We found that thiocillin increased the population of matrix-producing B. subtilis cells and that this activity could be abolished by multiple structural alterations. Importantly, a mutation that eliminated thiocillin’s antibiotic activity did not affect its ability to induce biofilm gene expression in B. subtilis. We go on to show that biofilm induction appears to be a general phenomenon of multiple structurally diverse thiazolyl peptides and use this activity to confirm the presence of thiazolyl peptide gene clusters in other bacterial species. Our results indicate that the roles of secondary metabolites initially identified as antibiotics may have more complex effects—acting not only as killing agents, but also as specific modulators of microbial cellular phenotypes.
Significance Thiazolyl peptides are known antibiotics produced by diverse bacterial taxa. It has been believed that antibiotics are deployed by bacteria as weapons, providing them with an evolutionary advantage over other microbes. We show here that these weapons can also act as chemical tools that elicit biofilm production in the model bacterium Bacillus subtilis . Importantly, the biofilm-inducing (and therefore signaling) properties of these compounds are independent of their killing activity. We go on to use this biofilm-inducing activity to identify and confirm the presence of thiazolyl peptide gene clusters in other bacteria. These results indicate that thiazolyl peptides, and potentially other antibiotics, have the ability to alter bacterial behavior in ways important both to the environment and to human health.
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The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple ...genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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The substrate lends a hand Bowers, Albert A
Nature chemical biology,
10/2018, Volume:
14, Issue:
10
Journal Article
Peer reviewed
Duramycin is a small post-translationally modified peptide with antibody-like affinity for phosphatidylethanolamine. As it turns out, the same functionality that is essential for duramycin activity ...helps to catalyze the formation of its conformationally constrained and compact polycyclic architecture.
Thiocillins from Bacillus cereus ATCC 14579 are members of the well-known thiazolyl peptide class of natural product antibiotics, the biosynthesis of which has recently been shown to proceed via ...post-translational modification of ribosomally encoded precursor peptides. It has long been hypothesized that the final step of thiazolyl peptide biosynthesis involves a formal 4 + 2 cycloaddition between two dehydroalanines, a unique transformation that had eluded enzymatic characterization. Here we demonstrate that TclM, a single enzyme from the thiocillin biosynthetic pathway, catalyzes this transformation. To facilitate characterization of this new class of enzyme, we have developed a combined chemical and biological route to the complex peptide substrate, relying on chemical synthesis of a modified C-terminal fragment and coupling to a 38-residue leader peptide by means of native chemical ligation (NCL). This strategy, combined with active enzyme, provides a new chemoenzymatic route to this promising class of antibiotics.
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Visible light catalysis allows the efficient construction of single electron transfer (SET) redox cycles that result in minimal formation of byproducts and proceed under exogenous control of a ...removable light source. The O-glycosylation of thioglycosides via visible light photoredox chemistry is reported. Mechanistic studies show that the reaction is fully light responsive and support a mechanism involving decomposition of an oxidatively generated sulfur radical cation and propagation via reduction of the thiol side product.
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PaaA is a RiPP enzyme that catalyzes the transformation of two glutamic acid residues within a substrate peptide into the bicyclic core of Pantocin A. Here, for the first time, we use mRNA display ...techniques to understand RiPP enzyme–substrate interactions to illuminate PaaA substrate recognition. Additionally, our data revealed insights into the enzymatic timing of glutamic acid modification. The technique developed is quite sensitive and a significant advancement over current RiPP studies and opens the door to enzyme modified mRNA display libraries for natural product-like inhibitor pans.
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Sactipeptides are ribosomally synthesized peptides that contain a characteristic thioether bridge (sactionine bond) that is installed posttranslationally and is absolutely required for their ...antibiotic activity. Sactipeptide biosynthesis requires a unique family of radical SAM enzymes, which contain multiple 4Fe-4S clusters, to form the requisite thioether bridge between a cysteine and the α-carbon of an opposing amino acid through radical-based chemistry. Here we present the structure of the sactionine bond-forming enzyme CteB, from Clostridium thermocellum ATCC 27405, with both SAM and an N-terminal fragment of its peptidyl-substrate at 2.04 Å resolution. CteB has the (β/α)6-TIM barrel fold that is characteristic of radical SAM enzymes, as well as a C-terminal SPASM domain that contains two auxiliary 4Fe-4S clusters. Importantly, one 4Fe-4S cluster in the SPASM domain exhibits an open coordination site in absence of peptide substrate, which is coordinated by a peptidyl-cysteine residue in the bound state. The crystal structure of CteB also reveals an accessory N-terminal domain that has high structural similarity to a recently discovered motif present in several enzymes that act on ribosomally synthesized and post-translationally modified peptides (RiPPs), known as a RiPP precursor peptide recognition element (RRE). This crystal structure is the first of a sactionine bond forming enzyme and sheds light on structures and mechanisms of other members of this class such as AlbA or ThnB.
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Covering: up to 2014
Dithiolopyrrolone (DTP) group antibiotics were first isolated in the early half of the 20th century, but only recently has research been reawakened by insights gained from the ...synthesis and biosynthesis of this structurally intriguing class of molecules. DTPs are characterized by an electronically unique bicyclic structure, which contains a compact disulfide bridge between two ene-thiols. Points of diversity within the compound class occur outside of the bicyclic core, at the two amide nitrogens. Such modifications distinguish three of the most well studied members of the class, holomycin, thiolutin, and aureothricin; the DTP core has also more recently been identified in the marine antibiotic thiomarinol, in which it is linked to a marinolic acid moiety, analog of the FDA-approved topical antibiotic Bactroban® (GlaxoSmithKline). Dithiolopyrrolones exhibit relatively broad-spectrum antibiotic activity against many Gram-positive and Gram-negative bacteria, as well as strains of
Mycobacterium tuberculosis
. Additionally, they have been shown to exhibit potent and selective anti-cancer activity. Despite this promising profile, there is still much unknown about the mechanisms of action for DTPs. Early reports suggested that they inhibit yeast growth at the level of transcription and that this effect is largely responsible for their distinctive microbial static properties; a similar mechanism is supported in bacteria. Elucidation of biosynthetic pathways for holomycin in
Streptomyces clavuligerus
and
Yersinia ruckeri
and thiomarinol in
Alteromonas rava
sp. nov. SANK 73390, have contributed evidence suggesting that multiple mechanisms may be operative in the activity of these compounds. This review will comprehensively cover the history and development of dithiolopyrrolones with particular emphasis on the biosynthesis, synthesis, biological activity and mechanism of action.
Dithiolopyrrolone natural products have unique structures and exhibit a broad-spectrum of antimicrobial and anticancer activities. Isolated in the late 1940s, these molecules have attracted an increasing interest towards their biosynthesis, synthesis and mechanisms of action.
Thiopeptides are structurally complex, bioactive natural products derived from ribosomally synthesized and post-translationally modified peptides. A remarkable set of enzymes were recently revealed ...to catalyze the formation of the core trithiazolylpyridine of thiopeptides via a formal 4 + 2 cycloaddition. These pyridine synthases typically act late in thiopeptide biosynthesis to affect macrocyclization and cleavage of the N-terminal leader peptide, making them potentially useful biocatalysts for preparation of new thiopeptide variants. Herein we investigate the leader peptide requirements for TclM from thiocillin biosynthesis in Bacillus cereus ATCC 14579. Through a series of truncations, we define a minimum recognition sequence (RS) that is necessary and sufficient for TclM activity. This RS can be readily synthesized and ligated to linear thiopeptide cores prepared via solid-phase peptide synthesis (SPPS), giving an efficient and modular route to thiopeptide variants. We exploit this strategy to define C-terminal core peptide requirements and explore the differences in promiscuity of two pyridine synthases, TclM and TbtD, ultimately examining their ability to access new structural variants.
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