Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases

Identification and Characterization of the Biosynthesis of the Hybrid NRPS-NIS Siderophore Nocardichelin

Bacteria cope with the limitation of iron by producing siderophores, small molecules they export that have high affinity for iron. Once complexed, the ferric siderophore is transported into the cell through specialized receptors allowing the iron to be released and used in a variety of biological processes. Many peptide siderophores that use catechol, phenolate, or oxazoline/thiazoline groups to coordinate iron are produced by a family of enzymes called nonribosomal peptide synthetases (NRPSs). Alternately, a smaller family of NRPS-independent siderophores (NISs) is produced by a different biosynthetic strategy. The NIS pathways employ one or more NIS synthetases that combine an amine commonly harboring a hydroxamate with a carboxylate substrate. Discovered in 2007 in an uncharacterized Nocardia species, a siderophore called nocardichelin was identified and chemically characterized that contained features of both NIS and NRPS siderophores. Nocardichelin contains an N-salicyloxazoline moiety, predicted to be built by a modular NRPS, and a dihydroxamate containing N-hydroxy-N-succinylcadaverine and N-hydroxy-N-tetradecenoylcadaverine groups. To explore this potential hybrid NRPS/NIS, we identified a biosynthetic gene cluster in Nocardia carnea containing 13 enzymes and four proteins involved in transport. We have functionally characterized four of the enzymes for their activity and substrate specificity and further solved the structures of two enzymes. We present our discovery and initial characterization of this cluster, describe remaining questions for elucidation of the unusual siderophore, and discuss the potential for use in downstream biocatalytic applications.

An efficient lysate-based approach for biosynthesis of the pyrrolobenzodiazepine natural product tilimycin

Many bacteria use nonribosomal peptide synthetases (NRPSs), a family of multidomain enzymes that produce peptide natural products using an assembly line strategy. One class of such compounds are pyrrolobenzodiazepines, which have DNA alkylating activity. One example is tilimycin, a compound produced by the human gut microbiota that plays a role in epithelial damage during antibiotic-associated dysbiosis. The production of analogs of these natural products may facilitate the discovery of novel bioactive molecules. However, the synthesis of these natural products typically requires significant resources and time to produce in sufficient amounts for microbial and biochemical testing. Biocatalysis offers an environmentally friendly approach, but enzyme yield and stability, particularly with large multidomain enzymes that are often used in natural product pathways, can limit biochemical reactions with purified protein. Here, we demonstrate a cell lysate-based method to synthesize the nonribosomal peptide natural product tilimycin directly from the substrates 3-hydroxyanthranilic acid and L-proline with lysates from E. coli cell lines that express the tilimycin biosynthetic proteins. We present our protocol optimization and scale-up to produce tilimycin in a fast, efficient manner.

NMR chemical shift assignment of the IMLV methyl groups of a di-domain of the Tomaymycin non-ribosomal peptide synthetase

Non-ribosomal peptide synthetases (NRPSs) are macromolecular enzymatic complexes responsible for the biosynthesis of an array of microbial natural products, many of which have important applications for human health. The nature of the NRPS machinery, which has been likened to an assembly line, should be amenable to bio-engineering efforts directed towards efficient synthesis of novel and tailored molecules. However, the success of such endeavours depends on a detailed understanding of the mechanistic principles governing the various steps in the peptide assembly-line. Here, we report the near-complete assignment of the Ile, Met, Leu and Val methyl-groups of the 59-kDa adaptor-condensation di-domain (BN-BC) from the Tomaymycin NRPS. These assignments will provide the foundation for future NMR studies of the complex dynamic behaviour of the condensation domain both in isolation and in the context of the enzymatic cycle, which will themselves form the basis for developing a complete mechanistic description of the central condensation reaction in this prototypical NRPS.

Teicoplanin Nonribosomal Peptide Synthetase Is Unable to Incorporate Alpha-Ketoacid Building Blocks

Glycopeptide antibiotics (GPAs) are a vital class of nonribosomal peptides used as therapies of last resort to treat infections by multidrug-resistant bacteria. These peptide antibiotics are assembled by nonribosomal peptide synthetases (NRPSs), modular megasynthases central to the biosynthesis of a wide range of peptide natural products. The adenylation (A) domains of NRPSs are involved in the selection and activation of the amino acid building blocks forming these peptide natural products, with their subsequent loading onto a neighboring carrier protein for incorporation into the growing peptide chain. This makes A-domains the gatekeepers of specificity in nonribosomal peptide biosynthesis, with further studies needed to reveal how this specificity is enforced at all stages of catalysis. The first building block found in GPAs is diverse and can comprise an amino acid, a ketoacid, or mixtures of both, which suggests that the A-domains responsible for selecting these residues can also incorporate non-amino acid substrates. In this study, we explored the acceptance of such substrates by the initiation module of the teicoplanin NRPS. Our in vitro assays demonstrated that this A-domain possesses an unexpected preference for activating ketoacids over the native amino acid substrate l-Hpg. However, only (d/l)-Hpg and related amino acids were able to be loaded onto the neighboring carrier protein domain during the subsequent thioesterification step. We further characterized the structure of this A-domain from teicoplanin biosynthesis in complex with d-4-hydroxyphenylglycine (d-Hpg), which revealed alterations in the positioning of the substrate carboxylate that help explain the high levels of pyrophosphate release seen with this amino acid. In combination with extensive molecular dynamics simulations, these data suggest that ketoacid incorporation in GPA biosynthesis is likely performed after amino acid incorporation by the NRPS and highlight the importance of considering both activation and carrier protein loading reactions performed by an A-domain when investigating substrate selectivity in nonribosomal peptide biosynthesis.

Structure of a putative terminal amidation domain in natural product biosynthesis

Bacteria are rich sources of pharmaceutically valuable natural products, many crafted by modular polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). PKS and NRPS systems typically contain a thioesterase (TE) to offload a linear or cyclized product from a carrier protein, but alternative chemistry is needed for products with a terminal amide. Several pathways with amidated products also possess an uncharacterized 400-amino acid terminal domain. We present the characterization and structure of this putative terminal amidation domain (TAD). TAD binds NAD with the nicotinamide near an invariant cysteine that is also accessible to an intermediate on a carrier protein, indicating a catalytic role. The TAD structure resembles cyanobacterial acyl-ACP reductase (AAR), which binds NADPH near an analogous catalytic cysteine. Bioinformatic analysis reveals that TADs are broadly distributed across bacterial phyla and often occur at the end of terminal NRPS modules, suggesting many amidated products may yet be discovered.

l-2,3-Diaminopropionate Binding Mode of the SulM Adenylation Domain Limits Engineering Monobactam Analogue Biosynthesis with Larger Substrates

The simple but essential azetidinone core of the β-lactam antibiotics is uniquely N-sulfonated in the monobactam subfamily. This feature confers both target binding specificity to inactivate bacterial cell wall biosynthesis (antibiosis) and structural differentiation to elude destruction by metallo-β-lactamases (MBLs). The recent FDA approval of Emblaveo to treat serious bacterial infections combines an established synthetic monobactam aztreonam and avibactam, which additionally blocks serine β-lactamases, to create a broadly effective antibacterial therapeutic. Here we report experiments to capture the native monobactam biosynthetic steps to the natural product sulfazecin with the aim of accessing new monobactams by reprogramming its biosynthetic machinery. In sulfazecin biosynthesis, the β-lactam ring is formed by a nonribosomal peptide synthetase SulM that incorporates l-2,3-diaminopropionate (Dap), which is then N-sulfonated in trans and efficiently cyclized to the fully elaborated monobactam by an unusual thioesterase (TE) domain. We describe an improved synthesis of (2S,3R)-vinylDap to support rational structure-based engineering experiments to obtain the corresponding (4R)-vinyl sulfazecin. While these experiments were initially based on an AlphaFold model of the adenylation domain that incorporates Dap (SulM A3), we further report high-resolution X-ray crystal structures with both the l-Dap substrate and an accurate analogue of the activated (3R)-methyl-Dap adenylate bound. The ligand-bound structures rationalize the inability of SulA3 to incorporate larger substrates. Comparisons with the structures of other diamino acid-activating adenylation domains identify alternate binding modes that may be more suitable for the production of sulfazecin analogues. The impact of these structures on the further engineering of the SulA3 domain and its relation to monobactam synthesis in the recently structurally characterized SulTE are discussed.

Protein ligation for the assembly and study of nonribosomal peptide synthetase megaenzymes

Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes found in bacteria and fungi, that synthesize a plethora of pharmaceutically relevant compounds. NRPSs consist of repeating sets of functional domains called modules, and each module is responsible for the incorporation of a single amino acid to the growing peptidyl intermediate. The synthetic logic of an NRPS resembles an assembly line, with growing biosynthesis intermediates covalently attached to the prosthetic 4'-phosphopantetheine (ppant) moieties of T (thiolation or transfer) domains for shuttling within and between modules. Therefore, NRPSs must have each T domain phosphopantetheinylated to be functional, and host organisms encode ppant transferases that affix ppant to T domains. Ppant transferases can be promiscuous with respect to the T domain substrate and with respect to chemical modifications of the ppant thiol, which has been a useful characteristic for study of megaenzymes and other systems. However, defined studies of multimodular megaenzymes, where different analogs are required to be affixed to different T domains within the same multimodular protein, are hindered by this promiscuity. Study of NRPS peptide bond formation, for which two T domains simultaneously deliver substrates to the condensation domain, is a prime example where one would want two T domains bearing different acyl/peptidyl groups. Here, we report a strategy where two NRPS modules that are normally part of the same protein are expressed as separate constructs, modified separately with different acyl-ppants, and then ligated together by sortase A of Staphylococcus aureus or asparaginyl endopeptidase 1 of Oldenlandia affinis (OaAEP1). We assessed various reaction conditions to optimize the ligation reactions and maximize the yield of the complex of interest. Finally, we apply this method in large scale and show it allows the complex built by OaAEP1-mediated ligation to be characterized by X-ray crystallography.

The structural basis of substrate selectivity of the acinetobactin biosynthetic adenylation domain, BasE

Siderophores are small molecule natural products that are often produced by enzymes called nonribosomal peptide synthetases that many pathogenic bacteria produce to adapt to low iron conditions. Nonribosomal peptide synthetase bioengineering could lead to the production of siderophore analogs with the potential to interrupt this unique bacterial iron uptake system, endowing the molecules with antimicrobial properties. Acinetobacter baumannii produces the catecholate siderophore acinetobactin to scavenge iron, a nutrient essential for several metabolic processes. Previous studies have reported synthetic analogs of acinetobactin that disrupt iron acquisition by A. baumannii, resulting in inhibition of bacterial growth. To foster a long-term goal of using a chemoenzymatic approach to produce additional analogs, we have targeted the adenylation domain BasE for the incorporation of alternate substrates. Here, we report a structure-guided approach to investigate the substrate selectivity of BasE for non-native aryl substrates. Using targeted mutagenesis in the active site of BasE, we generated mutants that catalyze the activation of alternate substrates with catalytic efficiencies comparable to the WT enzyme with its natural substrate 2,3-dihydroxybenzoic acid. We further solved structures of these mutants bound to the non-native substrates that illustrate an expanded binding pocket that support the improved promiscuity of BasE. Motivated to develop an approach to produce analogs of acinetobactin, including molecules that could block iron uptake or be readily conjugated to antibiotic cargo, our work aims to develop a structure-guided approach for using catecholate siderophore pathways to incorporate alternate substrates.

Identification of Key Amino Acids in the A Domains of Polymyxin Synthetase Responsible for 2,4-Diaminobutyric Acid Adenylation in Paenibacillus polymyxa NBRC3020 Strain

Developing novel nonribosomal peptides (NRPs) requires a comprehensive understanding of the enzymes involved in their biosynthesis, particularly the substrate amino acid recognition mechanisms in the adenylation (A) domain. This study focused on the A domain responsible for adenylating l-2,4-diaminobutyric acid (l-Dab) within the synthetase of polymyxin, an NRP produced by Paenibacillus polymyxa NBRC3020. To date, investigations into recombinant proteins that selectively adenylate l-Dab─exploring substrate specificity and enzymatic activity parameters─have been limited to reports on A domains found in enzymes synthesizing l-Dab homopolymers (pldA from S. celluloflavus USE31 and pddA from S. hindustanus NBRC15115), which remain exceedingly rare. The polymyxin synthetase in NBRC3020 contains five A domains specific to l-Dab, distributed across five distinct modules (modules 1, 3, 4, 5, 8, and 9). In this study, we successfully obtained soluble A domain proteins from modules 1, 5, 8, and 9 by preparing module-specific recombinant proteins. These proteins were expressed in E. coli BAP-1, purified via Ni-affinity chromatography, and demonstrated high specificity for l-Dab. Through sequence homology analysis, three-dimensional structural modeling, docking simulations to estimate substrate-binding sites, and functional validation using alanine mutants, we identified Glu281 and Asp344 as critical residues for recognizing the side chain amino group of l-Dab, and Asp238 as essential for recognizing its main chain amino group in the A domain. Notably, these key residues were conserved not only across the A domains in modules 1, 5, 8, and 9 of P. polymyxa NBRC3020 but also in those of the P. polymyxa PKB1 strain, as confirmed by sequence homology analysis. Interestingly, in pldA and pddA, the key residues involved in recognizing the side-chain amino group of l-Dab, which are conserved among polymyxin synthetases of NBRC3020 and PKB1 strain, were not observed. This suggests a potentially different mechanism for l-Dab recognition.

In-Situ Purification of Non-Ribosomal Peptide Synthetases Assembly Line for Structural and Biochemical Studies

Nonribosomal peptide synthetases (NRPS) are essential for the biosynthesis of therapeutically valuable molecules, including antibiotics, immunosuppressants, and anticancer agents. The assembly-line mechanism of NRPS offers significant potential for engineering novel natural products through reprogramming. However, the challenging purification of NRPS proteins has impeded the investigation of their assembly and catalytic mechanisms. In this study, we employed homologous recombination to insert a purification tag at the C-terminus of the NRPS gene within the chromosome. This genetic modification enabled efficient purification of NRPS proteins from the tagged mutant strain using a one-step affinity chromatography approach. Additionally, we discovered that MbtH-like proteins (MLPs) form stable complexes with all pyoverdine (PVD) NRPS subunits, allowing for the purification of the entire NRPS assembly line via tagged MLP. Negative stain electron microscopy analysis revealed that the purified PVD NRPS proteins exist as dynamically linear monomers. Our in-situ tag-based purification method enhances NRPS research in both biochemical and structural biology, providing a robust platform for further investigations into NRPS mechanisms and applications.

Structures and mechanism of condensation in non-ribosomal peptide synthesis

Non-ribosomal peptide synthetases (NRPSs) are megaenzymes responsible for the biosynthesis of many clinically important natural products, from early modern medicines (penicillin, bacitracin) to current blockbuster drugs (cubicin, vancomycin) and newly approved therapeutics (rezafungin)1,2. The key chemical step in these biosyntheses is amide bond formation between aminoacyl building blocks, catalysed by the condensation (C) domain3. There has been much debate over the mechanism of this reaction3-12. NRPS condensation has been difficult to fully characterize because it is one of many successive reactions in the NRPS synthetic cycle and because the canonical substrates are each attached transiently as thioesters to mobile carrier domains, which are often both contained in the same very flexible protein as the C domain. Here we have produced a dimodular NRPS protein in two parts, modified each with appropriate non-hydrolysable substrate analogues13,14, assembled the two parts with protein ligation15, and solved the structures of the substrate- and product-bound states. The structures show the precise orientation of the megaenzyme preparing the nucleophilic attack of its key chemical step, and enable biochemical assays and quantum mechanical simulations to precisely interrogate the reaction. These data suggest that NRPS C domains use a concerted reaction mechanism, whereby the active-site histidine likely functions not as a general base, but as a crucial stabilizing hydrogen bond acceptor for the developing ammonium.

Application of Cas9-Based Gene Editing to Engineering of Nonribosomal Peptide Synthetases

Engineering of nonribosomal peptide synthetases (NRPSs) could transform the production of bioactive natural product derivatives. A number of recent reports have described the engineering of NRPSs without marked reductions in yield. Comparative analysis of evolutionarily related NRPSs can provide insights regarding permissive fusion sites for engineering where recombination may occur during evolutionary processes. Studies involving engineering of NRPSs using these recombination sites showed that they have great potential. Moreover, we highlight recent advances in engineering of NRPSs using CRISPR-associated protein 9 (Cas9)-based gene editing technology. The use of Cas9 facilitates the editing of even larger biosynthetic gene clusters (BGCs) close to or over 100 kb in size by precisely targeting and digesting DNA sequences at specific sites. This technology combined with growing understanding of potential fusion sites from large-scale informatics analyses will accelerate the scalable exploration of engineered NRPS assembly lines to obtain bioactive natural product derivatives in high yields.

Cyclic natural product oligomers: diversity and (bio)synthesis of macrocycles

Cyclic compounds are generally preferred over linear compounds for functional studies due to their enhanced bioavailability, stability towards metabolic degradation, and selective receptor binding. This has led to a need for effective cyclization strategies for compound synthesis and hence increased interest in macrocyclization mediated by thioesterase (TE) domains, which naturally boost the chemical diversity and bioactivities of cyclic natural products. Many non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) derived natural products are assembled to form cyclodimeric compounds, with these molecules possessing diverse structures and biological activities. There is significant interest in identifying the biosynthetic pathways that produce such molecules given the challenge that cyclodimerization represents from a biosynthetic perspective. In the last decade, many groups have pursued the characterization of TE domains and have provided new insights into this biocatalytic machinery: however, the enzymes involved in formation of cyclodimeric compounds have proven far more elusive. In this review we focus on natural products that involve macrocyclization in their biosynthesis and chemical synthesis, with an emphasis on the function and biosynthetic investigation on the special family of TE domains responsible for forming cyclodimeric natural products. We also introduce additional macrocyclization catalysts, including butelase and the CT-mediated cyclization of peptides, alongside the formation of cyclodipeptides mediated by cyclodipeptide synthases (CDPS) and single-module NRPSs. Due to the interdisciplinary nature of biosynthetic research, we anticipate that this review will prove valuable to synthetic chemists, drug discovery groups, enzymologists, and the biosynthetic community in general, and inspire further efforts to identify and exploit these biocatalysts for the formation of novel bioactive molecules.

Expanding the Substrate Selectivity of the Fimsbactin Biosynthetic Adenylation Domain, FbsH

Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.

Discovery, functional characterization, and structural studies of the NRPS-independent siderophore synthetases

To adapt to low-iron environments, many bacteria produce siderophores, low molecular weight iron chelators that are secreted into the environment where they bind ferric iron. The production of siderophore uptake systems then allows retrieval of the iron-complexed siderophore into the cell, where the metal ion can be used for structural and catalytic roles in many proteins. While many siderophores are produced by the activity of a family of large modular nonribosomal peptide synthetase (NRPS) enzymes, a second class of siderophores are produced by an alternate pathway. These so-called NRPS-independent siderophores (NIS) are biosynthesized through a shared catalytic step that is performed by an NIS synthetase. These enzymes catalyze the formation of an amide linkage between a carboxylate and an amine or, more rarely, form an ester with a hydroxyl substrate. Here we describe the discovery and biochemical studies of diverse NIS synthetases from different siderophore pathways to provide insight into their substrate specificity and catalytic mechanism. The structures of a small number of family members are additionally described that correlates the functional work with the enzyme structure. While the field has come a long way since it was described as a "long-overlooked" family in 2009, there remains much to discover in this large and important enzyme family.

Computation-driven redesign of an NRPS-like carboxylic acid reductase improves activity and selectivity

Engineering nonribosomal peptide synthetases (NRPSs) has been a "holy grail" in synthetic biology due to their modular nature and limited understanding of catalytic mechanisms. Here, we reported a computational redesign of the "gate-keeper" adenylation domain of the model NRPS-like enzyme carboxylic acid reductases (CARs) by using approximate mechanism-based geometric criteria and the Rosetta energy score. Notably, MabCAR3 mutants ACA-1 and ACA-4 displayed a remarkable improvement in catalytic efficiency (kcat/KM) for 6-aminocaproic acid, up to 101-fold. Furthermore, G418K exhibited an 86-fold enhancement in substrate specificity for adipic acid compared to 6-aminocaproic acid. Our work provides not only promising biocatalysts for nylon monomer biosynthesis but also a strategy for efficient NRPSs engineering.

Activity and Biocatalytic Potential of an Indolylamide Generating Thioesterase

The chemical synthesis of N-acyl indoles is hindered by the poor nucleophilicity of indolic nitrogen, necessitating the use of strongly basic reaction conditions that encumber elaboration of highly functionalized scaffolds. Herein, we describe the total chemoenzymatic synthesis of the bulbiferamide natural products by the biochemical activity reconstitution of a nonribosomal peptide synthetase assembly line-derived (NRPS-derived) thioesterase that neatly installs the macrocyclizing indolylamide. The enzyme represents a starting point for biocatalytic access to macrocyclic indolylamide peptides and natural products.

Structure, Function and Engineering of the Nonribosomal Peptide Synthetase Condensation Domain

The nonribosomal peptide synthetase (NRPS) is a highly precise molecular assembly machinery for synthesizing structurally diverse peptides, which have broad medicinal applications. Withinthe NRPS, the condensation (C) domain is a core catalytic domain responsible for the formation of amide bonds between individual monomer residues during peptide elongation. This review summarizes various aspects of the C domain, including its structural characteristics, catalytic mechanisms, substrate specificity, substrate gating function, and auxiliary functions. Moreover, through case analyses of the NRPS engineering targeting the C domains, the vast potential of the C domain in the combinatorial biosynthesis of peptide natural product derivatives is demonstrated.

Altering glycopeptide antibiotic biosynthesis through mutasynthesis allows incorporation of fluorinated phenylglycine residues

Glycopeptide antibiotics (GPAs) are peptide natural products used as last resort treatments for antibiotic resistant bacterial infections. They are produced by the sequential activities of a linear nonribosomal peptide synthetase (NRPS), which assembles the heptapeptide core of GPAs, and cytochrome P450 (Oxy) enzymes, which perform a cascade of cyclisation reactions. The GPAs contain proteinogenic and nonproteinogenic amino acids, including phenylglycine residues such as 4-hydroxyphenylglycine (Hpg). The ability to incorporate non-proteinogenic amino acids in such peptides is a distinctive feature of the modular architecture of NRPSs, with each module selecting and incorporating a desired amino acid. Here, we have exploited this ability to produce and characterise GPA derivatives containing fluorinated phenylglycine (F-Phg) residues through a combination of mutasynthesis, biochemical, structural and bioactivity assays. Our data indicate that the incorporation of F-Phg residues is limited by poor acceptance by the NRPS machinery, and that the phenol moiety normally present on Hpg residues is essential to ensure both acceptance by the NRPS and the sequential cyclisation activity of Oxy enzymes. The principles learnt here may prove useful for the future production of GPA derivatives with more favourable properties through mixed feeding mutasynthesis approaches.

The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain

Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation, and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain of SulM, which catalyzes an unusual β-lactam-forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the monobactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The position of variant lid helices results in an active site pocket that is quite constrained, a feature that is likely necessary to orient the substrate properly for β-lactam formation. Modeling of a sulfazecin tripeptide into the active site identifies a plausible binding mode identifying potential interactions for the sulfamate and the peptide backbone with Arg2849 and Asn2819, respectively. The overall structure is similar to the β-lactone-forming thioesterase domain that is responsible for similar ring closure in the production of obafluorin. We further use these insights to enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.

Expanding the substrate selectivity of the fimsbactin biosynthetic adenylation domain, FbsH

Nonribosomal peptide synthetases (NRPSs) produce diverse natural products including siderophores, chelating agents that many pathogenic bacteria produce to survive in low iron conditions. Engineering NRPSs to produce diverse siderophore analogs could lead to the generation of novel antibiotics and imaging agents that take advantage of this unique iron uptake system in bacteria. The highly pathogenic and antibiotic-resistant bacteria Acinetobacter baumannii produces fimsbactin, an unusual branched siderophore with iron-binding catechol groups bound to a serine or threonine side chain. To explore the substrate promiscuity of the assembly line enzymes, we report a structure-guided investigation of the stand-alone aryl adenylation enzyme FbsH. We report on structures bound to its native substrate 2,3-dihydroxybenzoic acid (DHB) as well as an inhibitor that mimics the adenylate intermediate. We produced enzyme variants with an expanded binding pocket that are more tolerant for analogs containing a DHB C4 modification. Wild-type and mutant enzymes were then used in an in vitro reconstitution analysis to assess the production of analogs of the final product as well as several early-stage intermediates. This analysis shows that some altered substrates progress down the fimsbactin assembly line to the downstream domains. However, analogs from alternate building blocks are produced at lower levels, indicating that selectivity exists in the downstream catalytic domains. These findings expand the substrate scope of producing condensation products between serine and aryl acids and identify the bottlenecks for chemoenzymatic production of fimsbactin analogs.

Structural, biochemical and bioinformatic analyses of nonribosomal peptide synthetase adenylation domains

Covering: 1997 to July 2023The adenylation reaction has been a subject of scientific intrigue since it was first recognized as essential to many biological processes, including the homeostasis and pathogenicity of some bacteria and the activation of amino acids for protein synthesis in mammals. Several foundational studies on adenylation (A) domains have facilitated an improved understanding of their molecular structures and biochemical properties, in particular work on nonribosomal peptide synthetases (NRPSs). In NRPS pathways, A domains activate their respective acyl substrates for incorporation into a growing peptidyl chain, and many nonribosomal peptides are bioactive. From a natural product drug discovery perspective, improving existing bioinformatics platforms to predict unique NRPS products more accurately from genomic data is desirable. Here, we summarize characterization efforts of A domains primarily from NRPS pathways from July 1997 up to July 2023, covering protein structure elucidation, in vitro assay development, and in silico tools for improved predictions.

Natural Products That Contain Higher Homologated Amino Acids

This review focuses on discussing natural products (NPs) that contain higher homologated amino acids (homoAAs) in the structure as well as the proposed and characterized biosynthesis of these non-proteinogenic amino acids. Homologation of amino acids includes the insertion of a methylene group into its side chain. It is not a very common modification found in NP biosynthesis as approximately 450 homoAA-containing NPs have been isolated from four bacterial phyla (Cyanobacteria, Actinomycetota, Myxococcota, and Pseudomonadota), two fungal phyla (Ascomycota and Basidiomycota), and one animal phylum (Porifera), except for a few examples. Amino acids that are found to be homologated and incorporated in the NP structures include the following ten amino acids: alanine, arginine, cysteine, isoleucine, glutamic acid, leucine, phenylalanine, proline, serine, and tyrosine, where isoleucine, leucine, phenylalanine, and tyrosine share the comparable enzymatic pathway. Other amino acids have their individual homologation pathway (arginine, proline, and glutamic acid for bacteria), likely utilize the primary metabolic pathway (alanine and glutamic acid for fungi), or have not been reported (cysteine and serine). Despite its possible high potential in the drug discovery field, the biosynthesis of homologated amino acids has a large room to explore for future combinatorial biosynthesis and metabolic engineering purpose.

The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain

Nonribosomal peptide synthetases (NRPSs) are responsible for the production of important biologically active peptides. The large, multidomain NRPSs operate through an assembly line strategy in which the growing peptide is tethered to carrier domains that deliver the intermediates to neighboring catalytic domains. While most NRPS domains catalyze standard chemistry of amino acid activation, peptide bond formation and product release, some canonical NRPS catalytic domains promote unexpected chemistry. The paradigm monobactam antibiotic sulfazecin is produced through the activity of a terminal thioesterase domain that catalyzes an unusual β-lactam forming reaction in which the nitrogen of the C-terminal N-sulfo-2,3-diaminopropionate residue attacks its thioester tether to release the β-lactam product. We have determined the structure of the thioesterase domain as both a free-standing domain and a didomain complex with the upstream holo peptidyl-carrier domain. The structure illustrates a constrained active site that orients the substrate properly for β-lactam formation. In this regard, the structure is similar to the β-lactone forming thioesterase domain responsible for the production of obafluorin. Analysis of the structure identifies features that are responsible for this four-membered ring closure and enable bioinformatic analysis to identify additional, uncharacterized β-lactam-forming biosynthetic gene clusters by genome mining.

Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains

Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two different conformations in the NRPS catalytic cycle. Our data reveal that the dynamic interaction between the C and the A domains in these modules is mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation are prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insights into the catalytic mechanism of NRPSs and their engineering strategy for synthetic peptides with different structures and properties.

Controlling Substrate- and Stereospecificity of Condensation Domains in Nonribosomal Peptide Synthetases

Nonribosomal peptide synthetases (NRPSs) are sophisticated molecular machines that biosynthesize peptide drugs. In attempts to generate new bioactive compounds, some parts of NRPSs have been successfully manipulated, but especially the influence of condensation (C-)domains on substrate specificity remains enigmatic and poorly controlled. To understand the influence of C-domains on substrate preference, we extensively evaluated the peptide formation of C-domain mutants in a bimodular NRPS system. Thus, we identified three key mutations that govern the preference for stereoconfiguration and side-chain identity. These mutations show similar effects in three different C-domains (GrsB1, TycB1, and SrfAC) when di- or pentapeptides are synthesized in vitro or in vivo. Strikingly, mutation E386L allows the stereopreference to be switched from d- to l-configured donor substrates. Our findings provide valuable insights into how cryptic specificity filters in C-domains can be re-engineered to clear roadblocks for NRPS engineering and enable the production of novel bioactive compounds.

Recent progress in the reprogramming of nonribosomal peptide synthetases

Nonribosomal peptide synthetases (NRPSs) biosynthesize nonribosomal peptide (NRP) natural products, which belong to the most promising resources for drug discovery and development because of their wide range of therapeutic applications. The results of genetic, biochemical, and bioinformatics analyses have enhanced our understanding of the mechanisms of the NRPS machinery. A major goal in NRP biosynthesis is to reprogram the NRPS machinery to enable the biosynthetic production of designed peptides. Reprogramming strategies for the NRPS machinery have progressed considerably in recent years, thereby increasing the yields and generating modified peptides. Here, the recent progress in NRPS reprogramming and its application in peptide synthesis are described.

Engineered and total biosynthesis of fungal specialized metabolites

Filamentous fungi produce a very wide range of complex and often bioactive metabolites, demonstrating their inherent ability as hosts of complex biosynthetic pathways. Recent advances in molecular sciences related to fungi have afforded the development of new tools that allow the rational total biosynthesis of highly complex specialized metabolites in a single process. Increasingly, these pathways can also be engineered to produce new metabolites. Engineering can be at the level of gene deletion, gene addition, formation of mixed pathways, engineering of scaffold synthases and engineering of tailoring enzymes. Combination of these approaches with hosts that can metabolize low-value waste streams opens the prospect of one-step syntheses from garbage.

Module-Based Polyketide Synthase Engineering for de Novo Polyketide Biosynthesis

Polyketide retrobiosynthesis, where the biosynthetic pathway of a given polyketide can be reversibly engineered due to the colinearity of the polyketide synthase (PKS) structure and function, has the potential to produce millions of organic molecules. Mixing and matching modules from natural PKSs is one of the routes to produce many of these molecules. Evolutionary analysis of PKSs suggests that traditionally used module boundaries may not lead to the most productive hybrid PKSs and that new boundaries around and within the ketosynthase domain may be more active when constructing hybrid PKSs. As this is still a nascent area of research, the generality of these design principles based on existing engineering efforts remains inconclusive. Recent advances in structural modeling and synthetic biology present an opportunity to accelerate PKS engineering by re-evaluating insights gained from previous engineering efforts with cutting edge tools.

Structural and functional insights into δ-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii

Cationic homo-polyamino acid (CHPA) peptides containing isopeptide bonds of diamino acids have been identified from Actinomycetes strains. However, none has been reported from other bacteria. Here, we report a δ-poly-L-ornithine synthetase from Acinetobacter baumannii, which we name PosA. Surprisingly, structural analysis of the adenylation domain and biochemical assay shows L-ornithine as the substrate for PosA. The product from the enzymatic reaction was purified and identified as poly-L-ornithine composed of 7-12 amino acid units. Chemical labeling of the polymer confirmed the isopeptide linkage of δ-poly-L-ornithine. We examine the biological activity of chemically synthesized 12-mer δ-poly-L-ornithine, illustrating that the polymer may act as an anti-fungal agent. Structures of the isolated adenylation domain from PosA are presented with several diamino acids and biochemical assays identify important substrate binding residues. Structurally-guided genome-mining led to the identification of homologs with different substrate binding residues that could activate additional substrates. A homolog from Bdellovibrionales sp. shows modest activity with L-arginine but not with any diamino acids observed to be substrates for previously examined CHPA synthetases. Our study indicates the possibility that additional CHPAs may be produced by various microbes, supporting the further exploration of uncharacterized natural products.

Biomimetic engineering of nonribosomal peptide synthesis

Nonribosomal peptides (NRPs) have gained attention due to their diverse biological activities and potential applications in medicine and agriculture. The natural diversity of NRPs is a result of evolutionary processes that have occurred over millions of years. Recent studies have shed light on the mechanisms by which nonribosomal peptide synthetases (NRPSs) evolve, including gene duplication, recombination, and horizontal transfer. Mimicking natural evolution could be a useful strategy for engineering NRPSs to produce novel compounds with desired properties. Furthermore, the emergence of antibiotic-resistant bacteria has highlighted the urgent need for new drugs, and NRPs represent a promising avenue for drug discovery. This review discusses the engineering potential of NRPSs in light of their evolutionary history.