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Müller S, DeLeon O, Atkinson SN, Saravia F, Kellogg S, Shank EA, Kirby JR. Thiocillin contributes to the ecological fitness of Bacillus cereus ATCC 14579 during interspecies interactions with Myxococcus xanthus. Front Microbiol 2023; 14:1295262. [PMID: 38075900 PMCID: PMC10704990 DOI: 10.3389/fmicb.2023.1295262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/09/2023] [Indexed: 02/12/2024] Open
Abstract
The soil-dwelling delta-proteobacterium Myxococcus xanthus is a model organism to study predation and competition. M. xanthus preys on a broad range of bacteria mediated by lytic enzymes, exopolysaccharides, Type-IV pilus-based motility, and specialized metabolites. Competition between M. xanthus and prey bacterial strains with various specialized metabolite profiles indicates a range of fitness, suggesting that specialized metabolites contribute to prey survival. To expand our understanding of how specialized metabolites affect predator-prey dynamics, we assessed interspecies interactions between M. xanthus and two strains of Bacillus cereus. While strain ATCC 14579 resisted predation, strain T was found to be highly sensitive to M. xanthus predation. The interaction between B. cereus ATCC 14579 and M. xanthus appears to be competitive, resulting in population loss for both predator and prey. Genome analysis revealed that ATCC 14579 belongs to a clade that possesses the biosynthetic gene cluster for production of thiocillins, whereas B. cereus strain T lacks those genes. Further, purified thiocillin protects B. cereus strains unable to produce this specialized metabolite, strengthening the finding that thiocillin protects against predation and contributes to the ecological fitness of B. cereus ATCC 14579. Lastly, strains that produce thiocillin appear to confer some level of protection to their own antibiotic by encoding an additional copy of the L11 ribosomal protein, a known target for thiopeptides. This work highlights the importance of specialized metabolites affecting predator-prey dynamics in soil microenvironments.
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Affiliation(s)
- Susanne Müller
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Orlando DeLeon
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Samantha N. Atkinson
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Fatima Saravia
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Stephanie Kellogg
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worchester, MA, United States
| | - John R. Kirby
- Department of Microbiology & Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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2
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Do T, Link AJ. Protein Engineering in Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Biochemistry 2023; 62:201-209. [PMID: 35006671 PMCID: PMC9454058 DOI: 10.1021/acs.biochem.1c00714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) make up a rapidly growing superfamily of natural products. RiPPs exhibit an extraordinary range of structures, but they all begin as gene-encoded precursor peptides that are linear chains of amino acids produced by ribosomes. Given the gene-encoded nature of RiPP precursor peptides, the toolbox of protein engineering can be directly applied to these precursors. This Perspective will discuss examples of site-directed mutagenesis, noncanonical amino acid mutagenesis, and the construction and screening of combinatorial libraries as applied to RiPPs. These studies have led to important insights into the biosynthesis and bioactivity of RiPPs and the reengineering of RiPPs for entirely new functions.
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Affiliation(s)
- Truc Do
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
| | - A. James Link
- Department of Chemical and Biological Engineering, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Chemistry, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
- Department of Molecular Biology, 207 Hoyt Laboratory Princeton University, Princeton, NJ 08544 USA
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3
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Baliarda A, Winkler M, Tournier L, Tinsley CR, Aymerich S. Dynamic interspecies interactions and robustness in a four-species model biofilm. Microbiologyopen 2021; 10:e1254. [PMID: 34964290 PMCID: PMC8650569 DOI: 10.1002/mbo3.1254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/18/2022] Open
Abstract
Interspecific interactions within biofilms determine relative species abundance, growth dynamics, community resilience, and success or failure of invasion by an extraneous organism. However, deciphering interspecific interactions and assessing their contribution to biofilm properties and function remain a challenge. Here, we describe the constitution of a model biofilm composed of four bacterial species belonging to four different genera (Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus), derived from a biofilm isolated from an industrial milk pasteurization unit. We demonstrate that the growth dynamics and equilibrium composition of this biofilm are highly reproducible. Based on its equilibrium composition, we show that the establishment of this four-species biofilm is highly robust against initial, transient perturbations but less so towards continuous perturbations. By comparing biofilms formed from different numbers and combinations of the constituent species and by fitting a growth model to the experimental data, we reveal a network of dynamic, positive, and negative interactions that determine the final composition of the biofilm. Furthermore, we reveal that the molecular determinant of one negative interaction is the thiocillin I synthesized by the B. cereus strain, and demonstrate its importance for species distribution and its impact on robustness by mutational analysis of the biofilm ecosystem.
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Affiliation(s)
- Aurélie Baliarda
- INRAE, AgroParisTech, Micalis InstituteUniversité Paris‐SaclayJouy‐en‐JosasFrance
| | - Michèle Winkler
- INRAE, AgroParisTech, Micalis InstituteUniversité Paris‐SaclayJouy‐en‐JosasFrance
| | | | - Colin R. Tinsley
- INRAE, AgroParisTech, Micalis InstituteUniversité Paris‐SaclayJouy‐en‐JosasFrance
| | - Stéphane Aymerich
- INRAE, AgroParisTech, Micalis InstituteUniversité Paris‐SaclayJouy‐en‐JosasFrance
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4
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Bird KE, Xander C, Murcia S, Schmalstig AA, Wang X, Emanuele MJ, Braunstein M, Bowers AA. Thiopeptides Induce Proteasome-Independent Activation of Cellular Mitophagy. ACS Chem Biol 2020; 15:2164-2174. [PMID: 32589399 PMCID: PMC7442609 DOI: 10.1021/acschembio.0c00364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Thiopeptide antibiotics are emerging clinical candidates that exhibit potent antibacterial activity against a variety of intracellular pathogens, including Mycobacterium tuberculosis (Mtb). Many thiopeptides directly inhibit bacterial growth by disrupting protein synthesis. However, recent work has shown that one thiopeptide, thiostrepton (TSR), can also induce autophagy in infected macrophages, which has the potential to be exploited for host-directed therapies against intracellular pathogens, such as Mtb. To better define the therapeutic potential of this class of antibiotics, we studied the host-directed effects of a suite of natural thiopeptides that spans five structurally diverse thiopeptide classes, as well as several analogs. We discovered that thiopeptides as a class induce selective autophagic removal of mitochondria, known as mitophagy. This activity is independent of other biological activities, such as proteasome inhibition or antibiotic activity. We also find that many thiopeptides exhibit potent activity against intracellular Mtb in macrophage infection models. However, the thiopeptide-induced mitophagy occurs outside of pathogen-containing autophagosomes and does not appear to contribute to thiopeptide control of intracellular Mtb. These results expand basic understanding of thiopeptide biology and provide key guidance for the development of new thiopeptide antibiotics and host-directed therapeutics.
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Affiliation(s)
- Kelly E. Bird
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christian Xander
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sebastian Murcia
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alan A. Schmalstig
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xianxi Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael J. Emanuele
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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5
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Bogart JW, Kramer NJ, Turlik A, Bleich RM, Catlin DS, Schroeder FC, Nair SK, Williamson RT, Houk KN, Bowers AA. Interception of the Bycroft-Gowland Intermediate in the Enzymatic Macrocyclization of Thiopeptides. J Am Chem Soc 2020; 142:13170-13179. [PMID: 32609512 DOI: 10.1021/jacs.0c05639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thiopeptides are a broad class of macrocyclic, heavily modified peptide natural products that are unified by the presence of a substituted, nitrogen-containing heterocycle core. Early work indicated that this core might be fashioned from two dehydroalanines by an enzyme-catalyzed aza-[4 + 2] cycloaddition to give a cyclic-hemiaminal intermediate. This common intermediate could then follow a reductive path toward a dehydropiperidine, as in the thiopeptide thiostrepton, or an aromatization path to yield the pyridine groups observed in many other thiopeptides. Although several of the enzymes proposed to perform this cycloaddition have been reconstituted, only pyridine products have been isolated and any hemiaminal intermediates have yet to be observed. Here, we identify the conditions and substrates that decouple the cycloaddition from subsequent steps and allow interception and characterization of this long hypothesized intermediate. Transition state modeling indicates that the key amide-iminol tautomerization is the major hurdle in an otherwise energetically favorable cycloaddition. An anionic model suggests that deprotonation and polarization of this amide bond by TbtD removes this barrier and provides a sufficient driving force for facile (stepwise) cycloaddition. This work provides evidence for a mechanistic link between disparate cyclases in thiopeptide biosynthesis.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nicholas J Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Rachel M Bleich
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel S Catlin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Ithaca, New York 14853, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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6
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Resilient living materials built by printing bacterial spores. Nat Chem Biol 2019; 16:126-133. [PMID: 31792444 DOI: 10.1038/s41589-019-0412-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 10/22/2019] [Indexed: 02/01/2023]
Abstract
Materials can be made multifunctional by embedding them with living cells that perform sensing, synthesis, energy production, and physical movement. A challenge is that the conditions needed for living cells are not conducive to materials processing and require continuous water and nutrients. Here, we present a three dimensional (3D) printer that can mix material and cell streams to build 3D objects. Bacillus subtilis spores were printed within the material and germinated on its exterior surface, including spontaneously in new cracks. The material was resilient to extreme stresses, including desiccation, solvents, osmolarity, pH, ultraviolet light, and γ-radiation. Genetic engineering enabled the bacteria to respond to stimuli or produce chemicals on demand. As a demonstration, we printed custom-shaped hydrogels containing bacteria that can sense or kill Staphylococcus aureus, a causative agent of infections. This work demonstrates materials endued with living functions that can be used in applications that require storage or exposure to environmental stresses.
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7
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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8
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Natural thiopeptides as a privileged scaffold for drug discovery and therapeutic development. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02361-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Yñigez-Gutierrez AE, Bachmann BO. Fixing the Unfixable: The Art of Optimizing Natural Products for Human Medicine. J Med Chem 2019; 62:8412-8428. [PMID: 31026161 DOI: 10.1021/acs.jmedchem.9b00246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecules isolated from natural sources including bacteria, fungi, and plants are a long-standing source of therapeutics that continue to add to our medicinal arsenal today. Despite their potency and prominence in the clinic, complex natural products often exhibit a number of liabilities that hinder their development as therapeutics, which may be partially responsible for the current trend away from natural product discovery, research, and development. However, advances in synthetic biology and organic synthesis have inspired a new generation of natural product chemists to tackle powerful undeveloped scaffolds. In this Perspective, we will present case studies demonstrating the historical and current focus on making targeted, but significant, changes to natural product scaffolds via biosynthetic gene cluster manipulation, total synthesis, semisynthesis, or a combination of these methods, with a focus on increasing activity, decreasing toxicity, or improving chemical and pharmacological properties.
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Affiliation(s)
| | - Brian O Bachmann
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
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10
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Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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11
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Characterization of Nocardithiocin Derivatives Produced by Amino Acid Substitution of Precursor Peptide notG. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09836-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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Soor HS, Appavoo SD, Yudin AK. Heterocycles: Versatile control elements in bioactive macrocycles. Bioorg Med Chem 2018; 26:2774-2779. [DOI: 10.1016/j.bmc.2017.10.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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13
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Zheng Q, Fang H, Liu W. Post-translational modifications involved in the biosynthesis of thiopeptide antibiotics. Org Biomol Chem 2018; 15:3376-3390. [PMID: 28358161 DOI: 10.1039/c7ob00466d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins. Since the biosynthetic gene clusters of thiopeptides were first discovered in 2009, several research studies regarding the biochemistry and enzymology of thiopeptide biosyntheses have been reported, indicating that their characteristic framework is constructed via a cascade of common PTMs and that additional specific PTMs diversify the molecules. In this review, we primarily summarize recent advances in understanding the biosynthesis of thiopeptide antibiotics and propose some potential applications based on our insights into the biosynthetic logic and machinery.
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Affiliation(s)
- Qingfei Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
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14
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Lin Z, He Q, Liu W. Bio-inspired engineering of thiopeptide antibiotics advances the expansion of molecular diversity and utility. Curr Opin Biotechnol 2017; 48:210-219. [PMID: 28672170 DOI: 10.1016/j.copbio.2017.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 02/08/2023]
Abstract
Thiopeptide antibiotics, which are a class of sulfur-rich and highly modified peptide natural products, exhibit a wide variety of important biological properties. These antibiotics are ribosomally synthesized and arise from post-translational modifications, exemplifying a process through which nature develops the structural complexity from Ser/Thr and Cys-rich precursor peptides. Following a brief review of the knowledge gained from nature in terms of the formation of a common thiopeptide scaffold and its specialization to individual members, we highlight the significance of bio-inspired engineering, which has greatly expanded the molecular diversity and utility of thiopeptide antibiotics regarding the search for clinically useful agents, investigation into new mechanisms of action and access to typically 'inaccessible' biosynthetic processes over the past two years.
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Affiliation(s)
- Zhi Lin
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qingli He
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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15
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Xu YX, Shen CJ, Ma JQ, Chen W, Mao J, Zhou YY, Chen L. Quantitative Succinyl-Proteome Profiling of Camellia sinensis cv. 'Anji Baicha' During Periodic Albinism. Sci Rep 2017; 7:1873. [PMID: 28500349 PMCID: PMC5431936 DOI: 10.1038/s41598-017-02128-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 04/06/2017] [Indexed: 12/31/2022] Open
Abstract
Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. ‘Anji Baicha’ is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in ‘Anji Baicha’ has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in ‘Anji Baicha’, representing the first extensive data on the lysine succinylome in the tea plant. Eleven conserved succinylation motifs were enriched among the identified succinylated peptides. The protein-protein interaction maps were visualized using Cytoscape software. Comparison across three typical developmental stages of ‘Anji Baicha’ revealed that proteins exhibiting differential succinylation levels were primarily involved in photosynthesis, carbon fixation, biosynthesis of amino acids and porphyrin and chlorophyll metabolism, suggesting that these succinylated proteins are involved in ‘Anji Baicha’ leaf colour variability. These results not only deepen our understanding of the mechanism underlying ‘Anji Baicha’ albinism and the regulatory role of succinylation in the tea plant but also provide new insight into molecular breeding for leaf colour variety.
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Affiliation(s)
- Yan-Xia Xu
- Tea Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Chen-Jia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Jian-Qiang Ma
- Tea Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Wei Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Juan Mao
- Tea Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Yan-Yan Zhou
- Jingjie PTM Biolab (Hangzhou) Co., Ltd., Hangzhou, 310018, China
| | - Liang Chen
- Tea Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China.
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16
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Elucidating and engineering thiopeptide biosynthesis. World J Microbiol Biotechnol 2017; 33:119. [DOI: 10.1007/s11274-017-2283-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/03/2017] [Indexed: 01/15/2023]
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17
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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18
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Reconstitution and Minimization of a Micrococcin Biosynthetic Pathway in Bacillus subtilis. J Bacteriol 2016; 198:2431-8. [PMID: 27381911 DOI: 10.1128/jb.00396-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 06/24/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Thiopeptides represent one of several families of highly modified peptide antibiotics that hold great promise for natural product engineering. These macrocyclic peptides are produced by a combination of ribosomal synthesis and extensive posttranslational modification by dedicated processing enzymes. We previously identified a compact, plasmid-borne gene cluster for the biosynthesis of micrococcin P1 (MP1), an archetypal thiopeptide antibiotic. In an effort to genetically dissect this pathway, we have reconstituted it in Bacillus subtilis Successful MP1 production required promoter engineering and the reassembly of essential biosynthetic genes in a modular plasmid. The resulting system allows for rapid pathway manipulation, including protein tagging and gene deletion. We find that 8 processing proteins are sufficient for the production of MP1 and that the tailoring enzyme TclS catalyzes a C-terminal reduction step that distinguishes MP1 from its sister compound micrococcin P2. IMPORTANCE The emergence of antibiotic resistance is one of the most urgent human health concerns of our day. A crucial component in an integrated strategy for countering antibiotic resistance is the ability to engineer pathways for the biosynthesis of natural and derivatized antimicrobial compounds. In this study, the model organism B. subtilis was employed to reconstitute and genetically modularize a 9-gene system for the biosynthesis of micrococcin, the founding member of a growing family of thiopeptide antibiotics.
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Chen M, Liu J, Duan P, Li M, Liu W. Biosynthesis and molecular engineering of templated natural products. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww045] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Abstract
Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.
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Affiliation(s)
- Ming Chen
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyu Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panpan Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mulin Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Huzhou Center of Bio-Synthetic Innovation, Huzhou 313000, China
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20
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Lin Z, Chen D, Liu W. Biosynthesis-based artificial evolution of microbial natural products. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
Thiopeptides are a subclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs) with complex molecular architectures and an array of biological activities, including potent antimicrobial activity. Here we report the generation of thiopeptides containing noncanonical amino acids (ncAAs) by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs into a thiocillin producer strain of Bacillus cereus .We demonstrate that thiopeptide variants containing ncAAs with bioorthogonal chemical reactivity can be further postbiosynthetically modified with biophysical probes, including fluorophores and photo-cross-linkers. This work allows the site-specific incorporation of ncAAs into thiopeptides to increase their structural diversity and probe their biological activity; similar approaches can likely be applied to other classes of RiPPs.
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Zhang F, Li C, Kelly WL. Thiostrepton Variants Containing a Contracted Quinaldic Acid Macrocycle Result from Mutagenesis of the Second Residue. ACS Chem Biol 2016; 11:415-24. [PMID: 26630475 DOI: 10.1021/acschembio.5b00731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The thiopeptides are a family of ribosomally synthesized and post-translationally modified peptide metabolites, and the vast majority of thiopeptides characterized to date possess one highly modified macrocycle. A few members, including thiostrepton A, harbor a second macrocycle that incorporates a quinaldic acid moiety and the four N-terminal residues of the peptide. The antibacterial properties of thiostrepton A are well established, and its recently discovered ability to inhibit the proteasome has additional implications for the development of antimalarial and anticancer therapeutics. We have conducted the saturation mutagenesis of Ala2 in the precursor peptide, TsrA, to examine which variants can be transformed into a mature thiostrepton analogue. Although the thiostrepton biosynthetic system is somewhat restrictive toward substitutions at the second residue, eight thiostrepton Ala2 analogues were isolated. The TsrA Ala2Ile and Ala2Val variants were largely channeled through an alternate processing pathway wherein the first residue of the core peptide, Ile1, is removed, and the resulting thiostrepton analogues bear quinaldic acid macrocycles abridged by one residue. This is the first report revealing that quinaldic acid loop size is amenable to alteration during the course of thiostrepton biosynthesis. Both the antibacterial and proteasome inhibitory properties of the thiostrepton Ala2 analogues were examined. While the identity of the residue at the second position of the core peptide influences thiostrepton biosynthesis, our report suggests it may not be crucial for antibacterial and proteasome inhibitory properties of the full-length variants. In contrast, the contracted quinaldic acid loop can, to differing degrees, affect both types of biological activity.
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Affiliation(s)
- Feifei Zhang
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Chaoxuan Li
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Wendy L. Kelly
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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Maricic N, Anderson ES, Opipari AE, Yu EA, Dawid S. Characterization of a Multipeptide Lantibiotic Locus in Streptococcus pneumoniae. mBio 2016; 7:e01656-15. [PMID: 26814178 PMCID: PMC4742701 DOI: 10.1128/mbio.01656-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/28/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Bacterial communities are established through a combination of cooperative and antagonistic interactions between the inhabitants. Competitive interactions often involve the production of antimicrobial substances, including bacteriocins, which are small antimicrobial peptides that target other community members. Despite the nearly ubiquitous presence of bacteriocin-encoding loci, inhibitory activity has been attributed to only a small fraction of gene clusters. In this study, we characterized a novel locus (the pld locus) in the pathogen Streptococcus pneumoniae that drives the production of a bacteriocin called pneumolancidin, which has broad antimicrobial activity. The locus encodes an unusual tandem array of four inhibitory peptides, three of which are absolutely required for antibacterial activity. The three peptide sequences are similar but appear to play distinct roles in regulation and inhibition. A modification enzyme typically found in loci encoding a class of highly modified bacteriocins called lantibiotics was required for inhibitory activity. The production of pneumolancidin is controlled by a two-component regulatory system that is activated by the accumulation of modified peptides. The locus is located on a mobile element that has been found in many pneumococcal lineages, although not all elements carry the pld genes. Intriguingly, a minimal region containing only the genes required for pneumolancidin immunity was found in several Streptococcus mitis strains. The pneumolancidin-producing strain can inhibit nearly all pneumococci tested to date and provided a competitive advantage in vivo. These peptides not only represent a unique strategy for bacterial competition but also are an important resource to guide the development of new antimicrobials. IMPORTANCE Successful colonization of a polymicrobial host surface is a prerequisite for the subsequent development of disease for many bacterial pathogens. Bacterial factors that directly inhibit the growth of neighbors may provide an advantage during colonization if the inhibition of competitors outweighs the energy for production. In this work, we found that production of a potent antimicrobial called pneumolancidin conferred a competitive advantage to the pathogen Streptococcus pneumoniae. S. pneumoniae secreting pneumolancidin inhibits a wide array of Gram-positive organisms, including all but one tested pneumococcal strain. The pneumolancidin genetic locus is of particular interest because it encodes three similar modified peptides (lantibiotics), each of which has a distinct role in the function of the locus. Lantibiotics represent a relatively untapped resource for the development of clinically useful antibiotics which are desperately needed. The broad inhibitory activity of pneumolancidin makes it an ideal candidate for further characterization and development.
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Affiliation(s)
- Natalie Maricic
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Erica S Anderson
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - AnneMarie E Opipari
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily A Yu
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Suzanne Dawid
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
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24
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Wang S, Zheng X, Pan Q, Chen Y. Mutagenesis of precursor peptide for the generation of nosiheptide analogues. RSC Adv 2016. [DOI: 10.1039/c6ra20302g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Thr3 in the core peptide of NosM could be mutated to generate nosiheptide analogues retaining antimicrobial activities.
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Affiliation(s)
- Shuzhen Wang
- State Key Laboratory of Natural Medicines
- Laboratory of Chemical Biology
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Xulu Zheng
- State Key Laboratory of Natural Medicines
- Laboratory of Chemical Biology
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Qi Pan
- State Key Laboratory of Natural Medicines
- Laboratory of Chemical Biology
- China Pharmaceutical University
- Nanjing
- People's Republic of China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines
- Laboratory of Chemical Biology
- China Pharmaceutical University
- Nanjing
- People's Republic of China
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25
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Zhang F, Kelly WL. Saturation mutagenesis of TsrA Ala4 unveils a highly mutable residue of thiostrepton A. ACS Chem Biol 2015; 10:998-1009. [PMID: 25572285 DOI: 10.1021/cb5007745] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thiopeptides are post-translationally processed macrocyclic peptide metabolites, characterized by extensive backbone and side chain modifications that include a six-membered nitrogeneous ring, thiazol(in)e/oxazol(in)e rings, and dehydrated amino acid residues. Thiostrepton A, one of the more structurally complex and well-studied thiopeptides, contains a second macrocycle bearing a quinaldic acid moiety. Antibacterial, antimalarial, and anticancer properties have been described for thiostrepton A and other thiopeptides, although the molecular details for binding the cellular target in each case are not fully elaborated. We previously demonstrated that a mutation of the TsrA core peptide, Ala4Gly, supported the successful production of the corresponding thiostrepton variant. To more thoroughly probe the thiostrepton biosynthetic machinery's tolerance toward structural variation at the fourth position of the TsrA core peptide, we report here the saturation mutagenesis of this residue using a fosmid-dependent biosynthetic engineering method and the isolation of 16 thiostrepton analogues. Several types of side chain substitutions at the fourth position of TsrA, including those that introduce polar or branched hydrophobic residues are accepted, albeit with varied preferences. In contrast, proline and amino acid residues inherently charged at physiological pH are not well-tolerated at the queried site by the thiostrepton biosynthetic system. These newly generated thiostrepton analogues were assessed for their antibacterial activities and abilities to inhibit the proteolytic functions of the eukaryotic 20S proteasome. We demonstrate that the identity of the fourth amino acid residue in the thiostrepton scaffold is not critical for either ribosome or proteasome inhibition.
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Affiliation(s)
- Feifei Zhang
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Wendy L. Kelly
- School of Chemistry and Biochemistry
and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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26
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Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis. Proc Natl Acad Sci U S A 2015; 112:3086-91. [PMID: 25713360 DOI: 10.1073/pnas.1414272112] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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27
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Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, Fischbach MA. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell 2014; 158:1402-1414. [PMID: 25215495 DOI: 10.1016/j.cell.2014.08.032] [Citation(s) in RCA: 450] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 05/30/2014] [Accepted: 08/20/2014] [Indexed: 11/28/2022]
Abstract
In complex biological systems, small molecules often mediate microbe-microbe and microbe-host interactions. Using a systematic approach, we identified 3,118 small-molecule biosynthetic gene clusters (BGCs) in genomes of human-associated bacteria and studied their representation in 752 metagenomic samples from the NIH Human Microbiome Project. Remarkably, we discovered that BGCs for a class of antibiotics in clinical trials, thiopeptides, are widely distributed in genomes and metagenomes of the human microbiota. We purified and solved the structure of a thiopeptide antibiotic, lactocillin, from a prominent member of the vaginal microbiota. We demonstrate that lactocillin has potent antibacterial activity against a range of Gram-positive vaginal pathogens, and we show that lactocillin and other thiopeptide BGCs are expressed in vivo by analyzing human metatranscriptomic sequencing data. Our findings illustrate the widespread distribution of small-molecule-encoding BGCs in the human microbiome, and they demonstrate the bacterial production of drug-like molecules in humans. PAPERCLIP:
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Affiliation(s)
- Mohamed S Donia
- Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Peter Cimermancic
- Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christopher J Schulze
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - John Martin
- The Genome Institute, Department of Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Makedonka Mitreva
- The Genome Institute, Department of Medicine and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Roger G Linington
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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28
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Characterization of a novel plasmid-borne thiopeptide gene cluster in Staphylococcus epidermidis strain 115. J Bacteriol 2014; 196:4344-50. [PMID: 25313391 DOI: 10.1128/jb.02243-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiopeptides are small (12- to 17-amino-acid), heavily modified peptides of bacterial origin. This antibiotic family, with more than 100 known members, is characterized by the presence of sulfur-containing heterocyclic rings and dehydrated residues within a macrocyclic peptide structure. Thiopeptides, including micrococcin P1, have garnered significant attention in recent years for their potent antimicrobial activity against bacteria, fungi, and even protozoa. Micrococcin P1 is known to target the ribosome; however, like those of other thiopeptides, its biosynthesis and mechanisms of self-immunity are poorly characterized. We have discovered an isolate of Staphylococcus epidermidis harboring the genes for thiopeptide production and self-protection on a 24-kb plasmid. Here we report the characterization of this plasmid, identify the antimicrobial peptide that it encodes, and provide evidence of a target replacement-mediated mechanism of self-immunity.
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29
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Just-Baringo X, Albericio F, Álvarez M. Engineering von Thiopeptiden: ein multidisziplinärer Weg zu neuen Wirkstoffen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307288] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Just-Baringo X, Albericio F, Álvarez M. Thiopeptide engineering: a multidisciplinary effort towards future drugs. Angew Chem Int Ed Engl 2014; 53:6602-16. [PMID: 24861213 DOI: 10.1002/anie.201307288] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Indexed: 11/12/2022]
Abstract
The recent development of thiopeptide analogues of antibiotics has allowed some of the limitations inherent to these naturally occurring substances to be overcome. Chemical synthesis, semisynthetic derivatization, and engineering of the biosynthetic pathway have independently led to complementary modifications of various thiopeptides. Some of the new substances have displayed improved profiles, not only as antibiotics, but also as antiplasmodial and anticancer drugs. The design of novel molecules based on the thiopeptide scaffold appears to be the only strategy to exploit the high potential they have shown in vitro. Herein we present the most relevant achievements in the production of thiopeptide analogues and also discuss the way the different approaches might be combined in a multidisciplinary strategy to produce more sophisticated structures.
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Affiliation(s)
- Xavier Just-Baringo
- Institute for Research in Biomedicine, Barcelona Science Park, University of Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain) http://www.pcb.ub.edu/fama/htm/home.htm; CIBER-BBN, Networking Centre on Bioengineering Biomaterials and Nanomedicine, 08028 Barcelona (Spain)
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31
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Guo H, Wang J, Li Y, Yu Y, Zheng Q, Wu J, Liu W. Insight into bicyclic thiopeptide biosynthesis benefited from development of a uniform approach for molecular engineering and production improvement. Chem Sci 2014. [DOI: 10.1039/c3sc52015c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Olsen CA. An update on lysine deacylases targeting the expanding "acylome". ChemMedChem 2013; 9:434-7. [PMID: 24375937 DOI: 10.1002/cmdc.201300421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 11/12/2022]
Abstract
Lysine ε-amino acetylation has long been recognized as an epigenetically relevant post-translational modification of multiple residues in histone proteins. However, it has become clear that lysine acetylation is not restricted to histones, and therefore, it may be involved in the regulation of a wide variety of proteins, some of which have been identified and studied in detail. More recently, post-translational modifications of lysine side chains by additional acyl groups have also been identified, and some of these appear to be regulated by histone deacetylases (HDACs) and/or sirtuins. In this Concept, new developments are discussed with emphasis on the enzymes that have been shown to catalyze the cleavage of these novel marks, including new assays and inhibitors. Ultimately, a deeper understand of these mechanisms should facilitate the development of ligands with therapeutic potential.
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Affiliation(s)
- Christian A Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, 2800 (Denmark).
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33
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SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol Cell 2013; 50:919-30. [PMID: 23806337 DOI: 10.1016/j.molcel.2013.06.001] [Citation(s) in RCA: 672] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/19/2013] [Accepted: 06/04/2013] [Indexed: 12/31/2022]
Abstract
Protein function is regulated by diverse posttranslational modifications. The mitochondrial sirtuin SIRT5 removes malonyl and succinyl moieties from target lysines. The spectrum of protein substrates subject to these modifications is unknown. We report systematic profiling of the mammalian succinylome, identifying 2,565 succinylation sites on 779 proteins. Most of these do not overlap with acetylation sites, suggesting differential regulation of succinylation and acetylation. Our analysis reveals potential impacts of lysine succinylation on enzymes involved in mitochondrial metabolism; e.g., amino acid degradation, the tricarboxylic acid cycle (TCA) cycle, and fatty acid metabolism. Lysine succinylation is also present on cytosolic and nuclear proteins; indeed, we show that a substantial fraction of SIRT5 is extramitochondrial. SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase. Our data reveal widespread roles for lysine succinylation in regulating metabolism and potentially other cellular functions.
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Capturing Linear Intermediates and C-Terminal Variants during Maturation of the Thiopeptide GE2270. ACTA ACUST UNITED AC 2013; 20:1067-77. [DOI: 10.1016/j.chembiol.2013.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022]
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35
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Wang S, Zhou S, Liu W. Opportunities and challenges from current investigations into the biosynthetic logic of nosiheptide-represented thiopeptide antibiotics. Curr Opin Chem Biol 2013; 17:626-34. [PMID: 23838388 DOI: 10.1016/j.cbpa.2013.06.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/04/2013] [Accepted: 06/17/2013] [Indexed: 11/16/2022]
Abstract
Nosiheptide is an archetypal thiopeptide antibiotic, possessing a characteristic macrocyclic core that contains a 6-membered heterocycle central to multiple azol(in)es and dehydroamino acids. The discovery of the ribosomal origin of thiopeptides revealed a unifying theme, showing that the structural complexity arises from post-translational modifications (PTMs) of precursor peptides. Thiopeptide framework formation proceeds via cyclodehydration/dehydrogenation (for azol(in)es), dehydration (for dehydroamino acids), and cycloaddition (for the central heterocycle domain). This common process has not been reproduced in vitro, partly due to the poorly understood logic of thiopeptide biosynthetic pathways. Utilizing nosiheptide biosynthesis as a model system, we herein consider how nature coordinates a number of highly interwined, common and specific PTMs to accomplish the complexity of ribosomally synthesized and post-translationally modified peptides.
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Affiliation(s)
- Shoufeng Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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36
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Young TS, Dorrestein PC, Walsh CT. Codon randomization for rapid exploration of chemical space in thiopeptide antibiotic variants. ACTA ACUST UNITED AC 2013; 19:1600-10. [PMID: 23261603 DOI: 10.1016/j.chembiol.2012.10.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/03/2012] [Accepted: 10/08/2012] [Indexed: 01/22/2023]
Abstract
Thiopeptide antibiotics exhibit a profound level of chemical diversity that is installed through cascades of posttranslational modifications on ribosomal peptides. Here, we present a technique to rapidly explore the chemical space of the thiopeptide GE37468 through codon randomization, yielding insights into thiopeptide maturation as well as structure and activity relationships. In this incarnation of the methodology, we randomized seven residues of the prepeptide-coding region, enabling the generation of 133 potential thiopeptide variants. Variant libraries were subsequently queried in two ways. First, high-throughput MALDI-TOF mass spectrometry was applied to colony-level expressions to sample mutants that permitted full maturation of the antibiotic. Second, the activity of producing mutants was detected in an antibiotic overlay assay. In total, 29 of the 133 variants produced mature compound, 12 of which retained antibiotic activity and 1 that had improved activity.
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Affiliation(s)
- Travis S Young
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Armenise 608, Boston, MA 02115, USA
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37
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Yang X, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: new insights into the role of leader and core peptides during biosynthesis. Chemistry 2013; 19:7662-77. [PMID: 23666908 DOI: 10.1002/chem.201300401] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Indexed: 11/08/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural products with a high degree of structural diversity and a wide variety of bioactivities. Understanding the biosynthetic machinery of these RiPPs will benefit the discovery and development of new molecules with potential pharmaceutical applications. In this Concept article, we discuss the features of the biosynthetic pathways to different RiPP classes, and propose mechanisms regarding recognition of the precursor peptide by the post-translational modification enzymes. We propose that the leader peptides function as allosteric regulators that bind the active form of the biosynthetic enzymes in a conformational selection process. We also speculate how enzymes that generate polycyclic products of defined topologies may have been selected for during evolution.
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Affiliation(s)
- Xiao Yang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Illinois 61801, USA
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The posttranslational modification cascade to the thiopeptide berninamycin generates linear forms and altered macrocyclic scaffolds. Proc Natl Acad Sci U S A 2013; 110:8483-8. [PMID: 23650400 DOI: 10.1073/pnas.1307111110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Berninamycin is a member of the pyridine-containing thiopeptide class of antibiotics that undergoes massive posttranslational modifications from ribosomally generated preproteins. Berninamycin has a 2-oxazolyl-3-thiazolyl-pyridine core embedded in a 35-atom macrocycle rather than typical trithiazolylpyridine cores embedded in 26-atom and 29-atom peptide macrocycles. We describe the cloning of an 11-gene berninamycin cluster from Streptomyces bernensis UC 5144, its heterologous expression in Streptomyces lividans TK24 and Streptomyces venezuelae ATCC 10712, and detection of variant and incompletely processed scaffolds. Posttranslational maturation in S. lividans of both the wild-type berninamycin prepeptide (BerA) and also a T3A mutant generates macrocyclic compounds as well as linear variants, which have failed to form the pyridine and the macrocycle. Expression of the gene cluster in S. venezuelae generates a variant of the 35-atom skeleton of berninamycin, containing a methyloxazoline in the place of a methyloxazole within the macrocyclic framework.
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Arnison PG, Bibb MJ, Bierbaum G, Bowers AA, Bugni TS, Bulaj G, Camarero JA, Campopiano DJ, Challis GL, Clardy J, Cotter PD, Craik DJ, Dawson M, Dittmann E, Donadio S, Dorrestein PC, Entian KD, Fischbach MA, Garavelli JS, Göransson U, Gruber CW, Haft DH, Hemscheidt TK, Hertweck C, Hill C, Horswill AR, Jaspars M, Kelly WL, Klinman JP, Kuipers OP, Link AJ, Liu W, Marahiel MA, Mitchell DA, Moll GN, Moore BS, Müller R, Nair SK, Nes IF, Norris GE, Olivera BM, Onaka H, Patchett ML, Piel J, Reaney MJT, Rebuffat S, Ross RP, Sahl HG, Schmidt EW, Selsted ME, Severinov K, Shen B, Sivonen K, Smith L, Stein T, Süssmuth RD, Tagg JR, Tang GL, Truman AW, Vederas JC, Walsh CT, Walton JD, Wenzel SC, Willey JM, van der Donk WA. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat Prod Rep 2013; 30:108-60. [PMID: 23165928 DOI: 10.1039/c2np20085f] [Citation(s) in RCA: 1423] [Impact Index Per Article: 129.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review presents recommended nomenclature for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), a rapidly growing class of natural products. The current knowledge regarding the biosynthesis of the >20 distinct compound classes is also reviewed, and commonalities are discussed.
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Affiliation(s)
- Paul G Arnison
- Prairie Plant Systems Inc, Botanical Alternatives Inc, Suite 176, 8B-3110 8th Street E, Saskatoon, SK, S7H 0W2, Canada
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40
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Zhang Q, Liu W. Biosynthesis of thiopeptide antibiotics and their pathway engineering. Nat Prod Rep 2013; 30:218-26. [DOI: 10.1039/c2np20107k] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Bowers AA, Acker MG, Young TS, Walsh CT. Generation of thiocillin ring size variants by prepeptide gene replacement and in vivo processing by Bacillus cereus. J Am Chem Soc 2012; 134:10313-6. [PMID: 22686940 DOI: 10.1021/ja302820x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thiocillins from Bacillus cereus ATCC 14579 are natural products from the broader class of thiazolyl peptides. Their biosynthesis proceeds via extensive post-translational modification of a ribosomally encoded precursor peptide. This post-translational tailoring involves a key step formal cycloaddition between two distal serine residues. In the wild-type structure, this cycloaddition forms a major macrocycle circumscribed by 26-atoms (shortest path). Results presented herein demonstrate the promiscuity of this last step by means of a set of "competition" experiments. Cyclization proceeds in many cases to provide altered ring sizes, giving access to several variant rings sizes that have not previously been observed in nature.
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Affiliation(s)
- Albert A Bowers
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, USA
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42
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Lin H, Su X, He B. Protein lysine acylation and cysteine succination by intermediates of energy metabolism. ACS Chem Biol 2012; 7:947-60. [PMID: 22571489 DOI: 10.1021/cb3001793] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In the past few years, several new protein post-translational modifications that use intermediates in metabolism have been discovered. These include various acyl lysine modifications (formylation, propionylation, butyrylation, crotonylation, malonylation, succinylation, myristoylation) and cysteine succination. Here, we review the discovery and the current understanding of these modifications. Several of these modifications are regulated by the deacylases, sirtuins, which use nicotinamide adenine dinucleotide (NAD), an important metabolic small molecule. Interestingly, several of these modifications in turn regulate the activity of metabolic enzymes. These new modifications reveal interesting connections between metabolism and protein post-translational modifications and raise many questions for future investigations.
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Affiliation(s)
- Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United
States
| | - Xiaoyang Su
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United
States
| | - Bin He
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United
States
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Thompson AD, Makley LN, McMenimen K, Gestwicki JE. The three cornerstones of chemical biology: innovative probes, new discoveries, and enabling tools. ACS Chem Biol 2012; 7:791-6. [PMID: 22594530 DOI: 10.1021/cb3001827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea D. Thompson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leah N. Makley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kathryn McMenimen
- Department of Chemistry, Mt. Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Jason E. Gestwicki
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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Insights into Quinaldic Acid Moiety Formation in Thiostrepton Biosynthesis Facilitating Fluorinated Thiopeptide Generation. ACTA ACUST UNITED AC 2012; 19:443-8. [DOI: 10.1016/j.chembiol.2012.02.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/01/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
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Walsh CT, Malcolmson SJ, Young TS. Three ring posttranslational circuses: insertion of oxazoles, thiazoles, and pyridines into protein-derived frameworks. ACS Chem Biol 2012; 7:429-42. [PMID: 22206579 DOI: 10.1021/cb200518n] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitrogen heterocycles are the key functional and structural elements in both RNA and DNA, in half a dozen of the most important coenzymes, and in many synthetic drug scaffolds. On the other hand, only 3 of 20 proteinogenic amino acids have nitrogen heterocycles: proline, histidine, and tryptophan. This inventory can be augmented in microbial proteins by posttranslational modifications downstream of leader peptide regions that convert up to 10 serine, threonine, and cysteine residues, side chains and peptide backbones, into oxazoles, thiazoles, and pyridine rings. Subsequent proteolysis releases these heterocyclic scaffolds in both linear and macrocyclic frameworks as bioactive small molecules.
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Affiliation(s)
- Christopher T. Walsh
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven J. Malcolmson
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Travis S. Young
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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Bowers AA. Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20068f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural product gene clusters are increasingly being used to compliment biochemical methods for production of cyclic peptide libraries.
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Affiliation(s)
- Albert A. Bowers
- Purdue University
- Dept. of Medicinal Chemistry and Molecular Pharmacology
- West Lafayette
- USA
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48
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Li C, Zhang F, Kelly WL. Mutagenesis of the thiostrepton precursor peptide at Thr7 impacts both biosynthesis and function. Chem Commun (Camb) 2011; 48:558-60. [PMID: 22068975 DOI: 10.1039/c1cc14281j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The seventh residue of thiostrepton is predicted to be critical for antibacterial activity. Substitution of Thr7 in the thiostrepton precursor peptide disrupts both biological activity and the successful biosynthesis of analogs.
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Affiliation(s)
- Chaoxuan Li
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
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Identification of the thiazolyl peptide GE37468 gene cluster from Streptomyces ATCC 55365 and heterologous expression in Streptomyces lividans. Proc Natl Acad Sci U S A 2011; 108:13053-8. [PMID: 21788474 DOI: 10.1073/pnas.1110435108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thiazolyl peptides are bacterial secondary metabolites that potently inhibit protein synthesis in Gram-positive bacteria and malarial parasites. Recently, our laboratory and others reported that this class of trithiazolyl pyridine-containing natural products is derived from ribosomally synthesized preproteins that undergo a cascade of posttranslational modifications to produce architecturally complex macrocyclic scaffolds. Here, we report the gene cluster responsible for production of the elongation factor Tu (EF-Tu)-targeting 29-member thiazolyl peptide GE37468 from Streptomyces ATCC 55365 and its heterologous expression in the model host Streptomyces lividans. GE37468 harbors an unusual β-methyl-δ-hydroxy-proline residue that may increase conformational rigidity of the macrocycle and impart reduced entropic costs of target binding. Isotope feeding and gene knockout were employed in the engineered S. lividans strain to identify the P450 monooxygenase GetJ as the enzyme involved in posttranslational transformation of isoleucine 8 to β-methyl-δ-hydroxy-proline through a predicted tandem double hydroxylation/cyclization mechanism. Loss of Ile8 oxygenative cyclization or mutation of Ile8 to alanine via preprotein gene replacement resulted in a 4-fold and 2-fold drop in antibiotic activity, respectively. This report of genetic manipulation of a 29-member thiazolyl peptide sets the stage for further genetic examination of structure activity relationships in the EF-Tu targeting class of thiazolyl peptides.
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Melby JO, Nard NJ, Mitchell DA. Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. Curr Opin Chem Biol 2011; 15:369-78. [PMID: 21429787 PMCID: PMC3947797 DOI: 10.1016/j.cbpa.2011.02.027] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/10/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
With billions of years of evolution under its belt, Nature has been expanding and optimizing its biosynthetic capabilities. Chemically complex secondary metabolites continue to challenge and inspire today's most talented synthetic chemists. A brief glance at these natural products, especially the substantial structural variation within a class of compounds, clearly demonstrates that Nature has long played the role of medicinal chemist. The recent explosion in genome sequencing has expanded our appreciation of natural product space and the vastness of uncharted territory that remains. One small corner of natural product chemical space is occupied by the recently dubbed thiazole/oxazole-modified microcins (TOMMs), which are ribosomally produced peptides with posttranslationally installed heterocycles derived from cysteine, serine and threonine residues. As with other classes of natural products, the genetic capacity to synthesize TOMMs has been widely disseminated among bacteria. Over the evolutionary timescale, Nature has tested countless random mutations and selected for gain of function in TOMM biosynthetic gene clusters, yielding several privileged molecular scaffolds. Today, this burgeoning class of natural products encompasses a structurally and functionally diverse set of molecules (i.e. microcin B17, cyanobactins, and thiopeptides). TOMMs presumably provide their producers with an ecological advantage. This advantage can include chemical weapons wielded in the battle for nutrients, disease-promoting virulence factors, or compounds presumably beneficial for symbiosis. Despite this plethora of functions, many TOMMs await experimental interrogation. This review will focus on the biosynthesis and natural combinatorial diversity of the TOMM family.
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Affiliation(s)
- Joel O Melby
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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