1
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YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Nat Chem Biol 2023; 19:111-119. [PMID: 36280794 DOI: 10.1038/s41589-022-01141-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022]
Abstract
YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.
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2
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Collin F, Maxwell A. The Microbial Toxin Microcin B17: Prospects for the Development of New Antibacterial Agents. J Mol Biol 2019; 431:3400-3426. [PMID: 31181289 PMCID: PMC6722960 DOI: 10.1016/j.jmb.2019.05.050] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 01/03/2023]
Abstract
Microcin B17 (MccB17) is an antibacterial peptide produced by strains of Escherichia coli harboring the plasmid-borne mccB17 operon. MccB17 possesses many notable features. It is able to stabilize the transient DNA gyrase-DNA cleavage complex, a very efficient mode of action shared with the highly successful fluoroquinolone drugs. MccB17 stabilizes this complex by a distinct mechanism making it potentially valuable in the fight against bacterial antibiotic resistance. MccB17 was the first compound discovered from the thiazole/oxazole-modified microcins family and the linear azole-containing peptides; these ribosomal peptides are post-translationally modified to convert serine and cysteine residues into oxazole and thiazole rings. These chemical moieties are found in many other bioactive compounds like the vitamin thiamine, the anti-cancer drug bleomycin, the antibacterial sulfathiazole and the antiviral nitazoxanide. Therefore, the biosynthetic machinery that produces these azole rings is noteworthy as a general method to create bioactive compounds. Our knowledge of MccB17 now extends to many aspects of antibacterial-bacteria interactions: production, transport, interaction with its target, and resistance mechanisms; this knowledge has wide potential applicability. After a long time with limited progress on MccB17, recent publications have addressed critical aspects of MccB17 biosynthesis as well as an explosion in the discovery of new related compounds in the thiazole/oxazole-modified microcins/linear azole-containing peptides family. It is therefore timely to summarize the evidence gathered over more than 40 years about this still enigmatic molecule and place it in the wider context of antibacterials.
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Affiliation(s)
- Frederic Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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3
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Ghilarov D, Stevenson CEM, Travin DY, Piskunova J, Serebryakova M, Maxwell A, Lawson DM, Severinov K. Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison. Mol Cell 2019; 73:749-762.e5. [PMID: 30661981 PMCID: PMC6395948 DOI: 10.1016/j.molcel.2018.11.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/24/2018] [Accepted: 11/27/2018] [Indexed: 11/29/2022]
Abstract
The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B4C2D2 complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products. Azole synthetase McbBCD is co-crystallized with its product, microcin B17 Crystal structure of McbBCD reveals an octameric assembly of B4C2D2 Two McbB subunits within each asymmetric unit interact to recognize a peptide Formation of each azole ring requires shuttling of peptide between two active centers
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Affiliation(s)
- Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland
| | | | - Dmitrii Y Travin
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julia Piskunova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia
| | - Marina Serebryakova
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, NR4 7UH Norwich, UK.
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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4
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Travin DY, Metelev M, Serebryakova M, Komarova ES, Osterman IA, Ghilarov D, Severinov K. Biosynthesis of Translation Inhibitor Klebsazolicin Proceeds through Heterocyclization and N-Terminal Amidine Formation Catalyzed by a Single YcaO Enzyme. J Am Chem Soc 2018; 140:5625-5633. [PMID: 29601195 DOI: 10.1021/jacs.8b02277] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Klebsazolicin (KLB) is a recently discovered Klebsiella pneumonia peptide antibiotic targeting the exit tunnel of bacterial ribosome. KLB contains an N-terminal amidine ring and four azole heterocycles installed into a ribosomally synthesized precursor by dedicated maturation machinery. Using an in vitro system for KLB production, we show that the YcaO-domain KlpD maturation enzyme is a bifunctional cyclodehydratase required for the formation of both the core heterocycles and the N-terminal amidine ring. We further demonstrate that the amidine ring is formed concomitantly with proteolytic cleavage of azole-containing pro-KLB by a cellular protease TldD/E. Members of the YcaO family are diverse enzymes known to activate peptide carbonyls during natural product biosynthesis leading to the formation of azoline, macroamidine, and thioamide moieties. The ability of KlpD to simultaneously perform two distinct types of modifications is unprecedented for known YcaO proteins. The versatility of KlpD opens up possibilities for rational introduction of modifications into various peptide backbones.
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Affiliation(s)
- Dmitrii Y Travin
- Department of Bioengineering and Bioinformatics , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Mikhail Metelev
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia
| | - Marina Serebryakova
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , 119992 , Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology , Lomonosov Moscow State University , Moscow , 119992 , Russia.,Center for Translational Biomedicine , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia
| | - Dmitry Ghilarov
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology , Skolkovo Institute of Science and Technology , Skolkovo , 143025 , Russia.,Institute of Gene Biology of the Russian Academy of Sciences , Moscow , 119334 , Russia.,Waksman Institute for Microbiology , Rutgers, The State University of New Jersey , Piscataway , New Jersey 08854 , United States
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5
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Ghilarov D, Serebryakova M, Stevenson CEM, Hearnshaw SJ, Volkov DS, Maxwell A, Lawson DM, Severinov K. The Origins of Specificity in the Microcin-Processing Protease TldD/E. Structure 2017; 25:1549-1561.e5. [PMID: 28943336 PMCID: PMC5810440 DOI: 10.1016/j.str.2017.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/21/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022]
Abstract
TldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli TldD and TldE interact to form a heterodimeric metalloprotease. TldD/E cleaves the N-terminal leader sequence from the modified MccB17 precursor peptide, to yield mature antibiotic, while it has no effect on the unmodified peptide. Both proteins are essential for the activity; however, only the TldD subunit forms a novel metal-containing active site within the hollow core of the heterodimer. Peptide substrates are bound in a sequence-independent manner through β sheet interactions with TldD and are likely cleaved via a thermolysin-type mechanism. We suggest that TldD/E acts as a “molecular pencil sharpener”: unfolded polypeptides are fed through a narrow channel into the active site and processively truncated through the cleavage of short peptides from the N-terminal end. E. coli proteins TldD and TldE form a heterodimeric metalloprotease Binding of peptides within the active-site cleft is not sequence-specific Specificity is controlled through the access of substrates via a narrow channel Peptides enter the channel N-terminus first and are processively digested
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Affiliation(s)
- Dmitry Ghilarov
- Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Marina Serebryakova
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Stephen J Hearnshaw
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dmitry S Volkov
- Lomonosov Moscow State University, Department of Chemistry, Analytical Chemistry Division, 119991 Moscow, Russia
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Konstantin Severinov
- Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Bionano Institute, Peter the Great Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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6
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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: 138] [Impact Index Per Article: 19.7] [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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7
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Osterman IA, Komarova ES, Shiryaev DI, Korniltsev IA, Khven IM, Lukyanov DA, Tashlitsky VN, Serebryakova MV, Efremenkova OV, Ivanenkov YA, Bogdanov AA, Sergiev PV, Dontsova OA. Sorting Out Antibiotics' Mechanisms of Action: a Double Fluorescent Protein Reporter for High-Throughput Screening of Ribosome and DNA Biosynthesis Inhibitors. Antimicrob Agents Chemother 2016; 60:7481-7489. [PMID: 27736765 PMCID: PMC5119032 DOI: 10.1128/aac.02117-16] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
In order to accelerate drug discovery, a simple, reliable, and cost-effective system for high-throughput identification of a potential antibiotic mechanism of action is required. To facilitate such screening of new antibiotics, we created a double-reporter system for not only antimicrobial activity detection but also simultaneous sorting of potential antimicrobials into those that cause ribosome stalling and those that induce the SOS response due to DNA damage. In this reporter system, the red fluorescent protein gene rfp was placed under the control of the SOS-inducible sulA promoter. The gene of the far-red fluorescent protein, katushka2S, was inserted downstream of the tryptophan attenuator in which two tryptophan codons were replaced by alanine codons, with simultaneous replacement of the complementary part of the attenuator to preserve the ability to form secondary structures that influence transcription termination. This genetically modified attenuator makes possible Katushka2S expression only upon exposure to ribosome-stalling compounds. The application of red and far-red fluorescent proteins provides a high signal-to-background ratio without any need of enzymatic substrates for detection of the reporter activity. This reporter was shown to be efficient in high-throughput screening of both synthetic and natural chemicals.
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Affiliation(s)
- Ilya A Osterman
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Ekaterina S Komarova
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry I Shiryaev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Ilya A Korniltsev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Irina M Khven
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russia
| | - Dmitry A Lukyanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Vadim N Tashlitsky
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Marina V Serebryakova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Olga V Efremenkova
- G. F. Gauze Institute for Search for New Antibiotics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Yan A Ivanenkov
- Moscow Institute of Physics and Technology (State University), Moscow Region, Russia
| | - Alexey A Bogdanov
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Petr V Sergiev
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga A Dontsova
- Lomonosov Moscow State University, Department of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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8
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Sardar D, Pierce E, McIntosh JA, Schmidt EW. Recognition sequences and substrate evolution in cyanobactin biosynthesis. ACS Synth Biol 2015; 4:167-76. [PMID: 24625112 PMCID: PMC4384831 DOI: 10.1021/sb500019b] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
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Ribosomally
synthesized and posttranslationally modified peptide
(RiPP) natural products are of broad interest because of their intrinsic
bioactivities and potential for synthetic biology. The RiPP cyanobactin
pathways pat and tru have been experimentally
shown to be extremely tolerant of mutations. In nature, the pathways
exhibit “substrate evolution”, where enzymes remain
constant while the substrates of those enzymes are hypervariable and
readily evolvable. Here, we sought to determine the mechanism behind
this promiscuity. Analysis of a series of different enzyme–substrate
combinations from five different cyanobactin gene clusters, in addition
to engineered substrates, led us to define short discrete recognition
elements within substrates that are responsible for directing enzymes.
We show that these recognition sequences (RSs) are portable and can
be interchanged to control which functional groups are added to the
final natural product. In addition to the previously assigned N- and
C-terminal proteolysis RSs, here we assign the RS for heterocyclization
modification. We show that substrate elements can be swapped in vivo leading to successful production of natural products
in E. coli. The exchangeability of these elements
holds promise in synthetic biology approaches to tailor peptide products in vivo and in vitro.
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Affiliation(s)
- Debosmita Sardar
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Elizabeth Pierce
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - John A. McIntosh
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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9
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Metelev MV, Ghilarov DA. Structure, function, and biosynthesis of thiazole/oxazole-modified microcins. Mol Biol 2014. [DOI: 10.1134/s0026893314010105] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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The C-terminal part of microcin B is crucial for DNA gyrase inhibition and antibiotic uptake by sensitive cells. J Bacteriol 2014; 196:1759-67. [PMID: 24563033 DOI: 10.1128/jb.00015-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin B (McB) is a ribosomally synthesized antibacterial peptide. It contains up to nine oxazole and thiazole heterocycles that are introduced posttranslationally and are required for activity. McB inhibits the DNA gyrase, a validated drug target. Previous structure-activity analyses indicated that two fused heterocycles located in the central part of McB are important for antibacterial action and gyrase inhibition. Here, we used site-specific mutagenesis of the McB precursor gene to assess the functional significance of the C-terminal part of McB that is located past the second fused heterocycle and contains two single heterocycles as well as an unmodified four-amino-acid C-terminal tail. We found that removal of unmodified C-terminal amino acids of McB, while having no effect on fused heterocycles, has a very strong negative effect on activity in vivo and in vitro. In fact, even nonconservative point substitutions in the last McB amino acid have a very strong effect by simultaneously decreasing uptake and ability to inhibit the gyrase. The results highlight the importance of unmodified McB amino acids for function and open the way for creation of recombinant McB derivatives with an altered or expanded spectrum of antibacterial action.
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11
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Structure of microcin B-like compounds produced by Pseudomonas syringae and species specificity of their antibacterial action. J Bacteriol 2013; 195:4129-37. [PMID: 23852863 DOI: 10.1128/jb.00665-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli microcin B (Ec-McB) is a posttranslationally modified antibacterial peptide containing multiple oxazole and thiazole heterocycles and targeting the DNA gyrase. We have found operons homologous to the Ec-McB biosynthesis-immunity operon mcb in recently sequenced genomes of several pathovars of the plant pathogen Pseudomonas syringae, and we produced two variants of P. syringae microcin B (Ps-McB) in E. coli by heterologous expression. Like Ec-McB, both versions of Ps-McB target the DNA gyrase, but unlike Ec-McB, they are active against various species of the Pseudomonas genus, including human pathogen P. aeruginosa. Through analysis of Ec-McB/Ps-McB chimeras, we demonstrate that three centrally located unmodified amino acids of Ps-McB are sufficient to determine activity against Pseudomonas, likely by allowing specific recognition by a transport system that remains to be identified. The results open the way for construction of McB-based antibacterial molecules with extended spectra of biological activity.
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12
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Dunbar KL, Mitchell DA. Revealing nature's synthetic potential through the study of ribosomal natural product biosynthesis. ACS Chem Biol 2013; 8:473-87. [PMID: 23286465 DOI: 10.1021/cb3005325] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized posttranslationally modified peptides (RiPPs) are a rapidly growing class of natural products with diverse structures and activities. In recent years, a great deal of progress has been made in elucidating the biosynthesis of various RiPP family members. As with the study of nonribosomal peptide and polyketide biosynthetic enzymes, these investigations have led to the discovery of entirely new biological chemistry. With each unique enzyme investigated, a more complex picture of Nature's synthetic potential is revealed. This Review focuses on recent reports (since 2008) that have changed the way that we think about ribosomal natural product biosynthesis and the enzymology of complex bond-forming reactions.
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Affiliation(s)
- Kyle L. Dunbar
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United
States
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13
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Dunbar KL, Melby JO, Mitchell DA. YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations. Nat Chem Biol 2012; 8:569-75. [PMID: 22522320 PMCID: PMC3428213 DOI: 10.1038/nchembio.944] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/15/2012] [Indexed: 11/09/2022]
Abstract
Thiazole/oxazole-modified microcins (TOMMs) encompass a recently defined class of ribosomally synthesized natural products with a diverse set of biological activities. Although TOMM biosynthesis has been investigated for over a decade, the mechanism of heterocycle formation by the synthetase enzymes remains poorly understood. Using substrate analogs and isotopic labeling, we demonstrate that ATP is used to directly phosphorylate the peptide amide backbone during TOMM heterocycle formation. Moreover, we present what is to our knowledge the first experimental evidence that the D-protein component of the heterocycle-forming synthetase (YcaO/domain of unknown function 181 family member), formerly annotated as a docking protein involved in complex formation and regulation, is able to perform the ATP-dependent cyclodehydration reaction in the absence of the other TOMM biosynthetic proteins. Together, these data reveal the role of ATP in the biosynthesis of azole and azoline heterocycles in ribosomal natural products and prompt a reclassification of the enzymes involved in their installation.
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Affiliation(s)
- Kyle L Dunbar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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