1
|
Ishida K, Litomska A, Dunbar KL, Hertweck C. An Enzymatic Prodrug-like Route to Thio and Selenoamides. Angew Chem Int Ed Engl 2024:e202404243. [PMID: 38747847 DOI: 10.1002/anie.202404243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Indexed: 06/28/2024]
Abstract
6-Thioguanine (6TG) is a clinically used antitumor agent that was rationally designed as a DNA-targeting antimetabolite, but it also occurs naturally. 6TG is a critical virulence factor produced by Erwinia amylovorans, a notorious plant pathogen that causes fire blight of pome fruit trees. The biosynthesis of the rare thioamide metabolite involves an adenylating enzyme (YcfA) and a sulfur-mobilizing enzyme (YcfC), but the mechanism of sulfur transfer and putative intermediates have remained elusive. Through dissection and in vitro reconstitution of the thionation process using diverse substrates, we uncover an intermediate, prodrug-like thio-conjugate and elucidate the precise enzyme functions. YcfA not only adenylates GMP but also transfers the mercapto group of l-cysteine to the activated carbonyl. A designated C-S lyase (YcfC) then cleaves the resulting S-adduct to yield the thioamide. This pathway is distinct from canonical tRNA sulfur modifications and known enzymatic peptide thionations. By exploring a wide range of substrate surrogates, we exploited the tolerance of the enzyme pair to produce even a seleno analog. This study provides valuable insight into a previously unexplored area of bacterial thioamide formation and lays the groundwork for synthetic biology approaches to produce thioamide antimetabolites.
Collapse
Affiliation(s)
- Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| |
Collapse
|
2
|
Shende VV, Bauman KD, Moore BS. The shikimate pathway: gateway to metabolic diversity. Nat Prod Rep 2024; 41:604-648. [PMID: 38170905 PMCID: PMC11043010 DOI: 10.1039/d3np00037k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.
Collapse
Affiliation(s)
- Vikram V Shende
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Katherine D Bauman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
3
|
Steele AD, Kiefer AF, Shen B. The many facets of sulfur incorporation in natural product biosynthesis. Curr Opin Chem Biol 2023; 76:102366. [PMID: 37451204 PMCID: PMC10527158 DOI: 10.1016/j.cbpa.2023.102366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Sulfur-containing natural products (S-containing NPs) exhibit diverse chemical structures and biosynthetic machineries. Unraveling the intricate chemistry of S-incorporation requires innovative and multidisciplinary approaches. In this review, we surveyed the landscape of S-containing NP biosynthetic machineries, classified the S-incorporation chemistry into four distinct classes, and highlighted each of the four classes with representative examples from recent studies. All highlighted chemistry has been correlated to the genes encoding the biosynthetic machineries of the S-containing NPs, which open new opportunities to discover S-containing NPs through genome mining. These examples should inspire the community to explore uncharted territories in NP research, promoting further advancements in both novel S-containing NP discovery and S-incorporation chemistry.
Collapse
Affiliation(s)
- Andrew D Steele
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States
| | - Alexander F Kiefer
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States
| | - Ben Shen
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Natural Products Discovery Center, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL 33458, United States; Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, Jupiter, FL 33458, United States.
| |
Collapse
|
4
|
Amino acid (acyl carrier protein) ligase-associated biosynthetic gene clusters reveal unexplored biosynthetic potential. Mol Genet Genomics 2023; 298:49-65. [PMID: 36271918 DOI: 10.1007/s00438-022-01962-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023]
Abstract
This study aimed to evaluate the postulated cellular function of a novel family of amino acid (acyl carrier protein) ligases (AALs) in natural product biosynthesis. Here, we analyzed the manually curated, putative, aal-associated natural product biosynthetic gene clusters (NP BGCs) using two computational platforms for NP prediction, antiSMASH-BiG-SCAPE-CORASON and DeepBGC. The detected BGCs included a diversity of type I polyketide/nonribosomal peptide (PKS/NRPS) hybrid BGCs, exemplified by the guadinomine BGC, which suggested a dedicated function of AALs in the biosynthesis of rare (2S)-aminomalonyl-ACP extension units. Besides modular PKS/NRPSs and NRPSs, AAL-associated BGCs were predicted to assemble arylpolyenes, ladderane lipids, phosphonates, aminoglycosides, β-lactones, and thioamides of both nonribosomal and ribosomal origins. Additionally, we revealed a frequent association of AALs with putative, seldom observed transglutaminase-like and BtrH-like transferases of the cysteine protease superfamily, which may form larger families of ACP-dependent amide bond catalysts used in NP synthesis. Our results disclosed an exceptional chemical novelty and biosynthetic potential of the AAL-associated BGCs in NP biosynthesis. The presented in silico evidence supports the initial hypothesis and provides an important foundation for future experimental studies aimed at discovering novel pharmaceutically relevant active compounds.
Collapse
|
5
|
Zhang D, Wang J, Qiao Y, Lin B, Deng Z, Kong L, You D. Genome Mining and Metabolic Profiling Reveal Cytotoxic Cyclodipeptides in Streptomyces hygrospinosus var. Beijingensis. Antibiotics (Basel) 2022; 11:1463. [PMID: 36358118 PMCID: PMC9686873 DOI: 10.3390/antibiotics11111463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 08/27/2023] Open
Abstract
Two new cyclodipeptide (CDP) derivatives (1-2) and another seven known cyclodipeptides (3-9) were isolated from Streptomyces 26D9-414 by the genome mining approach combined with genetic dereplication and the "one strain many compounds" (OSMAC) strategy. The structures of the new CDPs were established on the basis of 1D- and 2D-NMR and comparative electronic circular dichroism (ECD) spectra analysis. The biosynthetic gene clusters (BGCs) for these CDPs were identified through antiSMASH analysis. The relevance between this cdp cluster and the identified nine CDPs was established by genetic interruption manipulation. The newly discovered natural compound 2 displayed comparable cytotoxicity against MDA-MB-231 and SW480 with that of cisplatin, a widely used chemotherapeutic agent for the treatment of various cancers.
Collapse
Affiliation(s)
| | | | | | | | | | - Lingxin Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
6
|
Chatterjee S, Hausinger RP. Sulfur incorporation into biomolecules: recent advances. Crit Rev Biochem Mol Biol 2022; 57:461-476. [PMID: 36403141 PMCID: PMC10192010 DOI: 10.1080/10409238.2022.2141678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022]
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.
Collapse
Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
7
|
Ackenhusen SE, Wang Y, Chun SW, Narayan ARH. Understanding and Circumventing the Requirement for Native Thioester Substrates for α-Oxoamine Synthase Reactions. ACS Chem Biol 2022; 17:2389-2395. [PMID: 35972789 PMCID: PMC10082970 DOI: 10.1021/acschembio.2c00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Many enzyme classes require thioester electrophiles such as acyl-carrier proteins and acyl-coenzyme A substrates. For in vitro applications, these substrates can render these chemical transformations impractical. To address this challenge, we have investigated the mechanism of coenzyme A in gating catalysis of one α-oxoamine synthase, SxtA AOS. Through investigating the reactivity of SxtA AOS and corresponding enzyme variants against a panel of substrates and coenzyme A mimics, we determined that activity is gated through the binding of the pantetheine arm and a phosphate group that hydrogen bonds to residue Lys154 that is predicted by an AlphaFold2 model to be located in a tunnel leading to the active site. To provide an economical solution for preparative-scale reactions, in situ transthioesterification was used with pantetheine and simple thioester substrate precursors, resulting in productive reactions. These findings outline a strategy for employing ACP- and CoA-dependent enzymes that are inaccessible through other means without the need for cost-prohibitive coenzyme A or carrier protein-activated substrates.
Collapse
|
8
|
Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022; 61:e202206168. [PMID: 35852818 PMCID: PMC9545259 DOI: 10.1002/anie.202206168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/04/2022]
Abstract
Understanding antibiotic resistance mechanisms is central to the development of anti‐infective therapies and genomics‐based drug discovery. Yet, many knowledge gaps remain regarding the resistance strategies employed against novel types of antibiotics from less‐explored producers such as anaerobic bacteria, among them the Clostridia. Through the use of genome editing and functional assays, we found that CtaZ confers self‐resistance against the copper chelator and gyrase inhibitor closthioamide (CTA) in Ruminiclostridium cellulolyticum. Bioinformatics, biochemical analyses, and X‐ray crystallography revealed CtaZ as a founding member of a new group of GyrI‐like proteins. CtaZ is unique in binding a polythioamide scaffold in a ligand‐optimized hydrophobic pocket, thereby confining CTA. By genome mining using CtaZ as a handle, we discovered previously overlooked homologs encoded by diverse members of the phylum Firmicutes, including many pathogens. In addition to characterizing both a new role for a GyrI‐like domain in self‐resistance and unprecedented thioamide binding, this work aids in uncovering related drug‐resistance mechanisms.
Collapse
Affiliation(s)
- Finn Gude
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Evelyn M. Molloy
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Therese Horch
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Maria Dell
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Kyle L. Dunbar
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Jana Krabbe
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
| | - Michael Groll
- Center for Protein AssembliesTechnical University of MunichErnst-Otto-Fischer-Straße 885747GarchingGermany
| | - Christian Hertweck
- Research Unit Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteAdolf-Reichwein-Straße 2307745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| |
Collapse
|
9
|
Gude F, Molloy EM, Horch T, Dell M, Dunbar KL, Krabbe J, Groll M, Hertweck C. A Specialized Polythioamide‐Binding Protein Confers Antibiotic Self‐Resistance in Anaerobic Bacteria. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Finn Gude
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Evelyn M. Molloy
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Therese Horch
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Maria Dell
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Kyle L. Dunbar
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Jana Krabbe
- Leibniz-Institut fur Naturstoff-Forschung und Infektionsbiologie eV Hans-Knoll-Institut Biomolecular Chemistry GERMANY
| | - Michael Groll
- TU München: Technische Universitat Munchen Center for Protein Assemblies GERMANY
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI Department of Biomolecular Chemistry Beutenbergstr. 11a 07745 Jena GERMANY
| |
Collapse
|
10
|
McLaughlin MI, Yu Y, van der Donk WA. Substrate Recognition by the Peptidyl-( S)-2-mercaptoglycine Synthase TglHI during 3-Thiaglutamate Biosynthesis. ACS Chem Biol 2022; 17:930-940. [PMID: 35362960 PMCID: PMC9016710 DOI: 10.1021/acschembio.2c00087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
3-Thiaglutamate is a recently identified amino acid analog originating from cysteine. During its biosynthesis, cysteinyl-tRNA is first enzymatically appended to the C-terminus of TglA, a 50-residue ribosomally translated peptide scaffold. After hydrolytic removal of the tRNA, this cysteine residue undergoes modification on the scaffold before eventual proteolysis of the nascent 3-thiaglutamyl residue to release 3-thiaglutamate and regenerate TglA. One of the modifications of TglACys requires a complex of two polypeptides, TglH and TglI, which uses nonheme iron and O2 to catalyze the removal of the peptidyl-cysteine β-methylene group, oxidation of this Cβ atom to formate, and reattachment of the thiol group to the α carbon. Herein, we use in vitro transcription-coupled translation and expressed protein ligation to characterize the role of the TglA scaffold in TglHI recognition and determine the specificity of TglHI with respect to the C-terminal residues of its substrate TglACys. The results of these experiments establish a synthetically accessible TglACys fragment sufficient for modification by TglHI and identify the l-selenocysteine analog of TglACys, TglASec, as an inhibitor of TglHI. These insights as well as a predicted structure and native mass spectrometry data set the stage for deeper mechanistic investigation of the complex TglHI-catalyzed reaction.
Collapse
Affiliation(s)
- Martin I. McLaughlin
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yue Yu
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
11
|
Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
Collapse
Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
| |
Collapse
|
12
|
Dell M, Dunbar KL, Hertweck C. Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature. Nat Prod Rep 2021; 39:453-459. [PMID: 34586117 DOI: 10.1039/d1np00019e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.
Collapse
Affiliation(s)
- Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| |
Collapse
|
13
|
Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
Collapse
Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| |
Collapse
|
14
|
Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
Collapse
Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
| |
Collapse
|
15
|
He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
Collapse
Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
16
|
Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt H, Hertweck C. Enzyme‐Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Veit G. Hänsch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Hans‐Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
| |
Collapse
|
17
|
Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt HD, Hertweck C. Enzyme-Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021; 60:10670-10679. [PMID: 33625794 PMCID: PMC8251862 DOI: 10.1002/anie.202016378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Clostridia coordinate many important processes such as toxin production, infection, and survival by density‐dependent communication (quorum sensing) using autoinducing peptides (AIPs). Although clostridial AIPs have been proposed to be (thio)lactone‐containing peptides, their true structures remain elusive. Here, we report the genome‐guided discovery of an AIP that controls endospore formation in Ruminiclostridium cellulolyticum. Through a combination of chemical synthesis and chemical complementation assays with a mutant strain, we reveal that the genuine chemical mediator is a homodetic cyclopeptide (cAIP). Kinetic analyses indicate that the mature cAIP is produced via a cryptic thiolactone intermediate that undergoes a rapid S→N acyl shift, in a manner similar to intramolecular native chemical ligation (NCL). Finally, by implementing a chemical probe in a targeted screen, we show that this novel enzyme‐primed, intramolecular NCL is a widespread feature of clostridial AIP biosynthesis.
Collapse
Affiliation(s)
- Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Veit G Hänsch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| |
Collapse
|
18
|
Dunbar KL, Dell M, Molloy EM, Büttner H, Kumpfmüller J, Hertweck C. An Unexpected Split-Merge Pathway in the Assembly of the Symmetric Nonribosomal Peptide Antibiotic Closthioamide. Angew Chem Int Ed Engl 2021; 60:4104-4109. [PMID: 33119936 PMCID: PMC7898593 DOI: 10.1002/anie.202011741] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/12/2020] [Indexed: 12/19/2022]
Abstract
Closthioamide (CTA) is a symmetric nonribosomal peptide (NRP) comprised of two diaminopropane-linked polythioamidated monomers. CTA is biosynthesized by Ruminiclostridium cellulolyticum via an atypical NRP synthetase (NRPS)-independent biosynthetic pathway. Although the logic for monomer assembly was recently elucidated, the strategy for the biosynthesis and incorporation of the diamine linker remained a mystery. By means of genome editing, synthesis, and in vitro biochemical assays, we demonstrate that the final steps in CTA maturation proceed through a surprising split-merge pathway involving the dual use of a thiotemplated intermediate. This pathway includes the first examples of an aldo-keto reductase catalyzing the reductive release of a thiotemplated product, and of a transthioamidating transglutaminase. In addition to clarifying the remaining steps in CTA assembly, our data shed light on largely unexplored pathways for NRPS-independent peptide biosynthesis.
Collapse
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Maria Dell
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Evelyn M. Molloy
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Hannah Büttner
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Jana Kumpfmüller
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
| | - Christian Hertweck
- Dept. of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology, HKIBeutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| |
Collapse
|
19
|
Dunbar KL, Dell M, Molloy EM, Büttner H, Kumpfmüller J, Hertweck C. An Unexpected Split‐Merge Pathway in the Assembly of the Symmetric Nonribosomal Peptide Antibiotic Closthioamide. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Hannah Büttner
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
| |
Collapse
|
20
|
Abstract
Microbial natural products, particularly those produced by filamentous Actinobacteria, underpin the majority of clinically used antibiotics. Unfortunately, only a few new antibiotic classes have been discovered since the 1970s, which has exacerbated fears of a postapocalyptic world in which antibiotics have lost their utility. Excitingly, the genome sequencing revolution painted an entirely new picture, one in which an average strain of filamentous Actinobacteria harbors 20 to 50 natural product biosynthetic pathways but expresses very few of these under laboratory conditions. Microbial natural products, particularly those produced by filamentous Actinobacteria, underpin the majority of clinically used antibiotics. Unfortunately, only a few new antibiotic classes have been discovered since the 1970s, which has exacerbated fears of a postapocalyptic world in which antibiotics have lost their utility. Excitingly, the genome sequencing revolution painted an entirely new picture, one in which an average strain of filamentous Actinobacteria harbors 20 to 50 natural product biosynthetic pathways but expresses very few of these under laboratory conditions. Development of methodology to access this “hidden” biochemical diversity has the potential to usher in a second Golden Era of antibiotic discovery. The proliferation of genomic data has led to inconsistent use of “cryptic” and “silent” when referring to biosynthetic gene clusters identified by bioinformatic analysis. In this Perspective, we discuss this issue and propose to formalize the use of this terminology.
Collapse
|
21
|
Kenshole E, Herisse M, Michael M, Pidot SJ. Natural product discovery through microbial genome mining. Curr Opin Chem Biol 2020; 60:47-54. [PMID: 32853968 DOI: 10.1016/j.cbpa.2020.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
The advent of the genomic era has opened up enormous possibilities for the discovery of new natural products. Also known as specialized metabolites, these compounds produced by bacteria, fungi, and plants have long been sought for their bioactive properties. Innovations in both DNA sequencing technologies and bioinformatics now allow the wealth of sequence data to be mined at both the genome and metagenome levels for new specialized metabolites. However, a key problem that remains is rapidly and efficiently linking these identified genes to their corresponding compounds. Within this review, we provide specific examples of studies that have used the power of genomic or metagenomic data to overcome these problems and identify new small molecules and their biosynthetic pathways.
Collapse
Affiliation(s)
- Emma Kenshole
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Marion Herisse
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Michael Michael
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000
| | - Sacha J Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia, 3000.
| |
Collapse
|