1
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Wang M, Wu M, Han M, Niu X, Fan A, Zhu S, Tong Y. Mining the Biosynthetic Landscape of Lactic Acid Bacteria Unearths a New Family of RiPPs Assembled by a Novel Type of ThiF-like Adenylyltransferases. ACS OMEGA 2024; 9:30891-30903. [PMID: 39035879 PMCID: PMC11256085 DOI: 10.1021/acsomega.4c03760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are chemically diverse natural products of ribosomal origin. These peptides, which frequently act as signals or antimicrobials, are biosynthesized by conserved enzymatic machinery, making genome mining a powerful strategy for unearthing previously uncharacterized members of their class. Herein, we investigate the untapped biosynthetic potential of Lactobacillales (i.e., lactic acid bacteria), an order of Gram-positive bacteria closely associated with human life, including pathogenic species and industrially relevant fermenters of dairy products. Through genome mining methods, we systematically explored the distribution and diversity of ThiF-like adenylyltransferase-utilizing RiPP systems in lactic acid bacteria and identified a number of unprecedented biosynthetic gene clusters. In one of these clusters, we found a previously undescribed group of macrocyclic imide biosynthetic pathways containing multiple transporters that may be involved in a potential quorum sensing (QS) system. Through in vitro assays, we determined that one such adenylyltransferase specifically catalyzes the intracyclization of its precursor peptide through macrocyclic imide formation. Incubating the enzyme with various primary amines revealed that it could effectively amidate the C-terminus of the precursor peptide. This new transformation adds to the growing list of Nature's peptide macrocyclization strategies and expands the impressive catalytic repertoire of the adenylyltransferase family. The diverse RiPP systems identified herein represent a vast, unexploited landscape for the discovery of a novel class of natural products and QS systems.
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Affiliation(s)
- Mengjiao Wang
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, People’s Republic of China
| | - Mengyue Wu
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People’s
Republic of China
| | - Meng Han
- MOE
Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Xiaogang Niu
- Beijing
Nuclear Magnetic Resonance Center, College of Chemistry and Molecular
Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Aili Fan
- State
Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People’s
Republic of China
| | - Shaozhou Zhu
- National
Institutes for Food and Drug Control, Beijing 102629, People’s Republic of China
| | - Yigang Tong
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, People’s Republic of China
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2
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Shi C, Patel VA, Mitchell DA, Zhao H. Enterolyin S, a Polythiazole-containing Hemolytic Peptide from Enterococcus caccae. Chembiochem 2024; 25:e202400212. [PMID: 38648232 PMCID: PMC11186716 DOI: 10.1002/cbic.202400212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
The β-hemolytic factor streptolysin S (SLS) is an important linear azol(in)e-containing peptide (LAP) that contributes significantly to the virulence of Streptococcus pyogenes. Despite its discovery 85 years ago, SLS has evaded structural characterizing owing to its notoriously problematic physicochemical properties. Here, we report the discovery and characterization of a structurally analogous hemolytic peptide from Enterococcus caccae, termed enterolysin S (ELS). Through heterologous expression, site-directed mutagenesis, chemoselective modification, and high-resolution mass spectrometry, we found that ELS contains an intriguing contiguous octathiazole moiety. The discovery of ELS expands our knowledge of hemolytic LAPs by adding a new member to this virulence-promoting family of modified peptides.
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Affiliation(s)
- Chengyou Shi
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Varshal A Patel
- Department of Biochemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois, Urbana Champaign, Urbana, IL, 61801, USA
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3
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Calvopina-Chavez DG, Bursey DM, Tseng YJ, Patil LM, Bewley KD, Bennallack PR, McPhie JM, Wagstaff KB, Daley A, Miller SM, Moody JD, Price JC, Griffitts JS. Micrococcin cysteine-to-thiazole conversion through transient interactions between a scaffolding protein and two modification enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563616. [PMID: 37961320 PMCID: PMC10634744 DOI: 10.1101/2023.10.23.563616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a broad group of compounds mediating microbial competition in nature. Azole/azoline heterocycle formation in the peptide backbone is a key step in the biosynthesis of many RiPPs. Heterocycle formation in RiPP precursors is often carried out by a scaffold protein, an ATP-dependent cyclodehydratase, and an FMN-dependent dehydrogenase. It has generally been assumed that the orchestration of these modifications is carried out by a stable complex including the scaffold, cyclodehydratase and dehydrogenase. The antimicrobial RiPP micrococcin begins as a precursor peptide (TclE) with a 35-amino acid N-terminal leader and a 14-amino acid C-terminal core containing six Cys residues that are converted to thiazoles. The putative scaffold protein (TclI) presumably presents the TclE substrate to a cyclodehydratase (TclJ) and a dehydrogenase (TclN) to accomplish the two-step installation of the six thiazoles. In this study, we identify a minimal TclE leader region required for thiazole formation, we demonstrate complex formation between TclI, TclJ and TclN, and further define regions of these proteins required for complex formation. Our results point to a mechanism of thiazole installation in which TclI associates with the two enzymes in a mutually exclusive fashion, such that each enzyme competes for access to the peptide substrate in a dynamic equilibrium, thus ensuring complete modification of each Cys residue in the TclE core.
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Affiliation(s)
| | - Devan M Bursey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
| | - Yi-Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Leena M Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Kathryn D Bewley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
- Currently at: Genentech Inc, San Francisco, CA 94080
| | - Philip R Bennallack
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
- Currently at: Werfen North America, Bedford, MA 01730
| | - Josh M McPhie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Kimberly B Wagstaff
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Anisha Daley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Susan M Miller
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602
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4
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Mahanta N, PH K, KS S, Das S, G. D. Recent Advancements in Bottromycin Biosynthesis. Synlett 2022. [DOI: 10.1055/s-0042-1751373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractBottromycin is a structurally complex cyclic peptidic compound isolated from Streptomyces bottropensis and related organisms and belongs to the RiPP family of natural products (ribosomally synthesized and post-translationally modified peptides). It exhibits potent antibacterial properties against gram-positive pathogens (including drug resistant strains such as MRSA, MIC 1 μg/mL and VRE, MIC 0.5 μg/mL) and mycoplasma. Bottromycin blocks the binding of the aminoacyl-tRNA to the A-site on the 50S ribosome and hence inhibits protein synthesis. Bottromycins contain structurally diverse post-translational modifications (PTMs) on a small peptide (GPVVVFDC) including a unique macrocyclic amidine, rare β-methylation, terminal thiazole heterocycle, oxidative decarboxylation, and Asp epimerization, among others. It exhibits a precursor peptide organization with a C-terminal follower peptide and a N-terminal core peptide. There are several new studies reported recently which gave detailed insights into the bottromycin biosynthesis pathway. This Account highlights the current advancements in understanding the biosynthetic pathway of bottromycin focusing mainly on the biochemically and structurally characterized enzymes and intricate details of the peptide–protein biophysical interactions. These studies have provided a strong foundation for conducting combinatorial biosynthesis and synthetic biological studies to create novel bottromycin variants for therapeutic applications.1 Introduction2 Biosynthetic Pathway for Bottromycin3 Enzymology of Bottromycin Biosynthesis3.1 Cleavage of Methionine (BotP)3.2 Radical SAM Methyltransferases (BotRMT1, BotRMT2, BotRMT3)3.3 ATP-Dependent YcaO Enzymes3.3.1 Thiazoline Formation by BotC3.3.2 Macrolactamidine Formation by BotCD3.4 Follower Peptide Hydrolysis (BotAH)3.5 Aspartate Epimerization (BotH)3.6 Oxidative Decarboxylation (BotCYP)3.7 O-Methyltransferase (BotOMT)4 Heterologous Bottromycin Production and Analogue Preparation5 Summary and Outlook
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5
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Song I, Kim Y, Yu J, Go SY, Lee HG, Song WJ, Kim S. Molecular mechanism underlying substrate recognition of the peptide macrocyclase PsnB. Nat Chem Biol 2021; 17:1123-1131. [PMID: 34475564 DOI: 10.1038/s41589-021-00855-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023]
Abstract
Graspetides, also known as ω-ester-containing peptides (OEPs), are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) bearing side chain-to-side chain macrolactone or macrolactam linkages. Here, we present the molecular details of precursor peptide recognition by the macrocyclase enzyme PsnB in the biosynthesis of plesiocin, a group 2 graspetide. Biochemical analysis revealed that, in contrast to other RiPPs, the core region of the plesiocin precursor peptide noticeably enhanced the enzyme-precursor interaction via the conserved glutamate residues. We obtained four crystal structures of symmetric or asymmetric PsnB dimers, including those with a bound core peptide and a nucleotide, and suggest that the highly conserved Arg213 at the enzyme active site specifically recognizes a ring-forming acidic residue before phosphorylation. Collectively, this study provides insights into the mechanism underlying substrate recognition in graspetide biosynthesis and lays a foundation for engineering new variants.
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Affiliation(s)
- Inseok Song
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Younghyeon Kim
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Jaeseung Yu
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Su Yong Go
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hong Geun Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Woon Ju Song
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, Seoul, South Korea.
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6
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Pei ZF, Yang MJ, Zhang K, Jian XH, Tang GL. Heterologous characterization of mechercharmycin A biosynthesis reveals alternative insights into post-translational modifications for RiPPs. Cell Chem Biol 2021; 29:650-659.e5. [PMID: 34474009 DOI: 10.1016/j.chembiol.2021.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/12/2021] [Accepted: 08/12/2021] [Indexed: 11/03/2022]
Abstract
Mechercharmycin A (MCM-A) is a marine natural product belonging to a family of polyazole cyclopeptides with remarkable bioactivities and unique structures. Identification, heterologous expression, and genetic characterizations of the MCM biosynthetic gene cluster in Bacillus subtilis revealed that it is a ribosomally synthesized and post-translationally modified peptide (RiPP) possessing complex with distinctive modifications. Based on this heterologous expression system, two MCM analogs with comparable antitumor activity are generated by engineering the biosynthetic pathway. Combinatorial co-production of a precursor peptide with different modifying enzymes in Escherichia coli identifies a different timing of modifications, showing that a tRNAGlu-dependent highly regioselective dehydration is the first modification step, followed by polyazole formation through heterocyclization and dehydrogenation in an N- to C-terminal direction. Therefore, a rational biosynthetic pathway of MCMs is proposed, which unveils a subfamily of azol(in)e-containing RiPPs and sets the stage for further investigations of the enzymatic mechanism and synthetic biology.
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Affiliation(s)
- Zeng-Fei Pei
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Min-Jie Yang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Kai Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiao-Hong Jian
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China.
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7
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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8
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Du Y, Qiu Y, Meng X, Feng J, Tao J, Liu W. A Heterotrimeric Dehydrogenase Complex Functions with 2 Distinct YcaO Proteins to Install 5 Azole Heterocycles into 35-Membered Sulfomycin Thiopeptides. J Am Chem Soc 2020; 142:8454-8463. [DOI: 10.1021/jacs.0c02329] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yanping Qiu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiang Meng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Junyin Feng
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
| | - Jiang Tao
- Department of General Dentistry, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhizaoju Road, Shanghai 200011, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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9
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Song H, Rao C, Deng Z, Yu Y, Naismith JH. The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Haigang Song
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University 185 East Lake Road Wuhan 430071 P. R. China
- Division of Structural BiologyWellcome Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN UK
- The Research Complex at Harwell Harwell Campus OX11 0FA UK
- The Rosalind Franklin Institute Harwell Campus OX11 0FA UK
| | - Cong Rao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University 185 East Lake Road Wuhan 430071 P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University 185 East Lake Road Wuhan 430071 P. R. China
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University 185 East Lake Road Wuhan 430071 P. R. China
| | - James H. Naismith
- Division of Structural BiologyWellcome Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN UK
- The Research Complex at Harwell Harwell Campus OX11 0FA UK
- The Rosalind Franklin Institute Harwell Campus OX11 0FA UK
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10
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Travin DY, Bikmetov D, Severinov K. Translation-Targeting RiPPs and Where to Find Them. Front Genet 2020; 11:226. [PMID: 32296456 PMCID: PMC7136475 DOI: 10.3389/fgene.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
Prokaryotic translation is among the major targets of diverse natural products with antibacterial activity including several classes of clinically relevant antibiotics. In this review, we summarize the information about the structure, biosynthesis, and modes of action of translation inhibiting ribosomally synthesized and post-translationally modified peptides (RiPPs). Azol(in)e-containing RiPPs are known to target translation, and several new compounds inhibiting the ribosome have been characterized recently. We performed a systematic search for biosynthetic gene clusters (BGCs) of azol(in)e-containing RiPPs. This search uncovered several groups of clusters that likely direct the synthesis of novel compounds, some of which may be targeting the ribosome.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Bikmetov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, Piscataway, NJ, United States
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11
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Song H, Rao C, Deng Z, Yu Y, Naismith JH. The Biosynthesis of the Benzoxazole in Nataxazole Proceeds via an Unstable Ester and has Synthetic Utility. Angew Chem Int Ed Engl 2020; 59:6054-6061. [PMID: 31903677 PMCID: PMC7204872 DOI: 10.1002/anie.201915685] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/25/2022]
Abstract
Heterocycles, a class of molecules that includes oxazoles, constitute one of the most common building blocks in current pharmaceuticals and are common in medicinally important natural products. The antitumor natural product nataxazole is a model for a large class of benzoxazole‐containing molecules that are made by a pathway that is not characterized. We report structural, biochemical, and chemical evidence that benzoxazole biosynthesis proceeds through an ester generated by an ATP‐dependent adenylating enzyme. The ester rearranges via a tetrahedral hemiorthoamide to yield an amide, which is a shunt product and not, as previously thought, an intermediate in the pathway. A second zinc‐dependent enzyme catalyzes the formation of hemiorthoamide from the ester but, by shuttling protons, the enzyme eliminates water, a reverse hydrolysis reaction, to yield the benzoxazole and avoids the amide. These insights have allowed us to harness the pathway to synthesize a series of novel halogenated benzoxazoles.
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Affiliation(s)
- Haigang Song
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University185 East Lake RoadWuhan430071P. R. China
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOX11 0FAUK
| | - Cong Rao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University185 East Lake RoadWuhan430071P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University185 East Lake RoadWuhan430071P. R. China
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education)School of Pharmaceutical SciencesWuhan University185 East Lake RoadWuhan430071P. R. China
| | - James H. Naismith
- Division of Structural BiologyWellcome Centre for Human GeneticsRoosevelt DriveOxfordOX3 7BNUK
- The Research Complex at HarwellHarwell CampusOX11 0FAUK
- The Rosalind Franklin InstituteHarwell CampusOX11 0FAUK
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12
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Kato Y, Kuroda T, Huang Y, Ohta R, Goto Y, Suga H. Chemoenzymatic Posttranslational Modification Reactions for the Synthesis of Ψ[CH 2NH]‐Containing Peptides. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201910894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yasuharu Kato
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
| | - Tomohiro Kuroda
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
| | - Yichao Huang
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
| | - Risa Ohta
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
| | - Yuki Goto
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
- JST-PRESTO The University of Tokyo Bunkyo Tokyo 113-0033 Japan
| | - Hiroaki Suga
- Department of Chemistry Graduate School of Science The University of Tokyo Bunkyo Tokyo 113-0033 Japan
- JST-CREST The University of Tokyo Bunkyo Tokyo 113-0033 Japan
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13
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Kato Y, Kuroda T, Huang Y, Ohta R, Goto Y, Suga H. Chemoenzymatic Posttranslational Modification Reactions for the Synthesis of Ψ[CH 2 NH]-Containing Peptides. Angew Chem Int Ed Engl 2019; 59:684-688. [PMID: 31622000 DOI: 10.1002/anie.201910894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/13/2019] [Indexed: 11/08/2022]
Abstract
The Ψ[CH2 NH] reduced amide bond is a peptide isostere widely used in the development of bioactive pseudopeptides. Reported here is a method of chemoenzymatic posttranslational modification for the synthesis of Ψ[CH2 NH]-containing peptides converted from ribosomally expressed peptides. The posttranslational conversion composed of an enzymatic cyclodehydration and facile two-step chemical reduction achieves deoxygenation of a specific amide bond present in a nonprotected peptide in water. This method generates the Ψ[CH2 NH] bond in peptides and is applicable to various peptide sequences, potentially enabling the preparation of a library of Ψ[CH2 NH]-containing peptides.
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Affiliation(s)
- Yasuharu Kato
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Tomohiro Kuroda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Risa Ohta
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.,JST-PRESTO, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.,JST-CREST, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
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14
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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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15
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Dong SH, Liu A, Mahanta N, Mitchell DA, Nair SK. Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS CENTRAL SCIENCE 2019; 5:842-851. [PMID: 31139720 PMCID: PMC6535971 DOI: 10.1021/acscentsci.9b00124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/16/2023]
Abstract
YcaO enzymes are known to catalyze the ATP-dependent formation of azoline heterocycles, thioamides, and (macro)lactamidines on peptide substrates. These enzymes are found in multiple biosynthetic pathways, including those for several different classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, there are major knowledge gaps in the mechanistic and structural underpinnings that govern each of the known YcaO-mediated modifications. Here, we present the first structure of any YcaO enzyme bound to its peptide substrate in the active site, specifically that from Methanocaldococcus jannaschii which is involved in the thioamidation of the α-subunit of methyl-coenzyme M reductase (McrA). The structural data are leveraged to identify and test the residues involved in substrate binding and catalysis by site-directed mutagenesis. We also show that thioamide-forming YcaOs can carry out the cyclodehydration of a related peptide substrate, which underscores the mechanistic conservation across the YcaO family and allows for the extrapolation of mechanistic details to azoline-forming YcaOs involved in RiPP biosynthesis. A bioinformatic survey of all YcaOs highlights the diverse sequence space in azoline-forming YcaOs and suggests their early divergence from a common ancestor. The data presented within provide a detailed molecular framework for understanding this family of enzymes, which reconcile several decades of prior data on RiPP cyclodehydratases. These studies also provide the foundational knowledge to impact our mechanistic understanding of additional RiPP biosynthetic classes.
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Affiliation(s)
- Shi-Hui Dong
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Andi Liu
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Nilkamal Mahanta
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Satish K. Nair
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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16
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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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17
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Sikandar A, Koehnke J. The role of protein–protein interactions in the biosynthesis of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2019; 36:1576-1588. [DOI: 10.1039/c8np00064f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review covers the role of protein–protein complexes in the biosynthesis of selected ribosomally synthesized and post-translationally modified peptide (RiPP) classes.
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Affiliation(s)
- Asfandyar Sikandar
- Workgroup Structural Biology of Biosynthetic Enzymes
- Helmholtz Institute for Pharmaceutical Research Saarland
- Helmholtz Centre for Infection Research
- Saarland University
- 66123 Saarbrücken
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes
- Helmholtz Institute for Pharmaceutical Research Saarland
- Helmholtz Centre for Infection Research
- Saarland University
- 66123 Saarbrücken
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18
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Goto Y, Suga H. Engineering of RiPP pathways for the production of artificial peptides bearing various non-proteinogenic structures. Curr Opin Chem Biol 2018; 46:82-90. [DOI: 10.1016/j.cbpa.2018.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 11/15/2022]
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19
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Vishwanatha TM, Kurpiewska K, Kalinowska-Tłuścik J, Dömling A. Cysteine Isocyanide in Multicomponent Reaction: Synthesis of Peptido-Mimetic 1,3-Azoles. J Org Chem 2017; 82:9585-9594. [PMID: 28817272 PMCID: PMC5603900 DOI: 10.1021/acs.joc.7b01615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An alternative approach toward the
simple and robust synthesis
of highly substituted peptidic thiazole derivatives using Ugi-multicomponent
reaction (U-MCR) is described. Thus, we introduced the enantiopure
(R)-2-methyl-2-isocyano-3-(tritylthio)propanoate
as a novel class of isocyanide in MCR. This bifunctional isocyanide
was found to undergo mild cyclodehydration to afford thiazole containing
peptidomimetics in a short synthetic sequence. Several examples of
bis-heterocyclic rings were also synthesized through the proper choice
of the aldehyde component in the U-4CR. The method opens a wide range
of applications toward the synthesis of nonribosomal natural products
and other bioactive compounds.
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Affiliation(s)
- Thimmalapura M Vishwanatha
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Katarzyna Kurpiewska
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Justyna Kalinowska-Tłuścik
- Jagiellonian University , Department of Crystal Chemistry and Crystal Physics, Ingardena 3, 30-060 Krakow, Poland
| | - Alexander Dömling
- University of Groningen , Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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20
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 354] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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21
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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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22
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Staś M, Bujak M, Broda MA, Siodłak D. Conformational preferences and synthesis of isomers Z and E of oxazole-dehydrophenylalanine. Biopolymers 2017; 106:283-94. [PMID: 27061820 DOI: 10.1002/bip.22852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/17/2022]
Abstract
Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation β2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation β, but the conformation β2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Maciej Bujak
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, Opole, 45-052, Poland
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23
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Czekster CM, Ge Y, Naismith JH. Mechanisms of cyanobactin biosynthesis. Curr Opin Chem Biol 2016; 35:80-88. [PMID: 27639115 DOI: 10.1016/j.cbpa.2016.08.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 01/22/2023]
Abstract
Cyanobactins are a diverse collection of natural products that originate from short peptides made on a ribosome. The amino acids are modified in a series of transformations catalyzed by multiple enzymes. The patellamide pathway is the most well studied and characterized example. Here we review the structures and mechanisms of the enzymes that cleave peptide bonds, macrocyclise peptides, heterocyclise cysteine (as well as threonine and serine) residues, oxidize five-membered heterocycles and attach prenyl groups. Some enzymes operate by novel mechanisms which is of interest and in addition the enzymes uncouple recognition from catalysis. The normally tight relationship between these factors hinders biotechnology. The cyanobactin pathway may be particularly suitable for exploitation, with progress observed with in vivo and in vitro approaches.
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Affiliation(s)
- Clarissa Melo Czekster
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST Scotland, UK
| | - Ying Ge
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST Scotland, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST Scotland, UK
- State Key Laboratory of Biotherapy, Sichuan University, China
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24
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Montalbán-López M, van Heel AJ, Kuipers OP. Employing the promiscuity of lantibiotic biosynthetic machineries to produce novel antimicrobials. FEMS Microbiol Rev 2016; 41:5-18. [PMID: 27591436 DOI: 10.1093/femsre/fuw034] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/07/2016] [Accepted: 07/28/2016] [Indexed: 12/30/2022] Open
Abstract
As the number of new antibiotics that reach the market is decreasing and the demand for them is rising, alternative sources of novel antimicrobials are needed. Lantibiotics are potent peptide antimicrobials that are ribosomally synthesized and stabilized by post-translationally introduced lanthionine rings. Their ribosomal synthesis and enzymatic modifications provide excellent opportunities to design and engineer a large variety of novel antimicrobial compounds. The research conducted in this area demonstrates that the modularity present in both the peptidic rings as well as in the combination of promiscuous modification enzymes can be exploited to further increase the diversity of lantibiotics. Various approaches, where the modifying enzymes and corresponding leader peptides are decoupled from their natural core peptide and integrated in designed plug-and-play production systems, enable the production of modified peptides that are either derived from vast genomic data or designed using functional parts from a wide diversity of core peptides. These approaches constitute a powerful discovery platform to develop novel antimicrobials with high therapeutic potential.
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Affiliation(s)
- Manuel Montalbán-López
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Auke J van Heel
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
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25
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Deane CD, Burkhart BJ, Blair PM, Tietz JI, Lin A, Mitchell DA. In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products. ACS Chem Biol 2016; 11:2232-43. [PMID: 27248686 PMCID: PMC4992447 DOI: 10.1021/acschembio.6b00369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that exhibits extraordinarily narrow-spectrum antibacterial activity toward the causative agent of anthrax, Bacillus anthracis. During PZN biosynthesis, a cyclodehydratase catalyzes cyclization of cysteine, serine, and threonine residues in the PZN precursor peptide (BamA) to azolines. Subsequently, a dehydrogenase oxidizes most of these azolines to thiazoles and (methyl)oxazoles. The final biosynthetic steps consist of leader peptide removal and dimethylation of the nascent N-terminus. Using a heterologously expressed and purified heterocycle synthetase, the BamA peptide was processed in vitro concordant with the pattern of post-translational modification found in the naturally occurring compound. Using a suite of BamA-derived peptides, including amino acid substitutions as well as contracted and expanded substrate variants, the substrate tolerance of the heterocycle synthetase was elucidated in vitro, and the residues crucial for leader peptide binding were identified. Despite increased promiscuity compared to what was previously observed during heterologous production in E. coli, the synthetase retained exquisite selectivity in cyclization of unnatural peptides only at positions which correspond to those cyclized in the natural product. A cleavage site was subsequently introduced to facilitate leader peptide removal, yielding mature PZN variants after enzymatic or chemical dimethylation. In addition, we report the isolation and characterization of two novel PZN-like natural products that were predicted from genome sequences but whose production had not yet been observed.
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Affiliation(s)
- Caitlin D. Deane
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brandon J. Burkhart
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patricia M. Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan I. Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alice Lin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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26
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Crone WJK, Vior NM, Santos-Aberturas J, Schmitz LG, Leeper FJ, Truman AW. Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics. Angew Chem Int Ed Engl 2016; 55:9639-43. [PMID: 27374993 PMCID: PMC5103208 DOI: 10.1002/anie.201604304] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Indexed: 11/06/2022]
Abstract
Bottromycin A2 is a structurally unique ribosomally synthesized and post-translationally modified peptide (RiPP) that possesses potent antibacterial activity towards multidrug-resistant bacteria. The structural novelty of bottromycin stems from its unprecedented macrocyclic amidine and rare β-methylated amino acid residues. The N-terminus of a precursor peptide (BtmD) is converted into bottromycin A2 by tailoring enzymes encoded in the btm gene cluster. However, little was known about key transformations in this pathway, including the unprecedented macrocyclization. To understand the pathway in detail, an untargeted metabolomic approach that harnesses mass spectral networking was used to assess the metabolomes of a series of pathway mutants. This analysis has yielded key information on the function of a variety of previously uncharacterized biosynthetic enzymes, including a YcaO domain protein and a partner protein that together catalyze the macrocyclization.
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Affiliation(s)
- William J K Crone
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | | | - Lukas G Schmitz
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Finian J Leeper
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
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27
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Crone WJK, Vior NM, Santos-Aberturas J, Schmitz LG, Leeper FJ, Truman AW. Dissecting Bottromycin Biosynthesis Using Comparative Untargeted Metabolomics. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- William J. K. Crone
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Natalia M. Vior
- Department of Molecular Microbiology; John Innes Centre; Colney Lane Norwich NR4 7UH UK
| | | | - Lukas G. Schmitz
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Finian J. Leeper
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Andrew W. Truman
- Department of Molecular Microbiology; John Innes Centre; Colney Lane Norwich NR4 7UH UK
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28
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Truman AW. Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides. Beilstein J Org Chem 2016; 12:1250-68. [PMID: 27559376 PMCID: PMC4979651 DOI: 10.3762/bjoc.12.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 12/15/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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29
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Triflic Anhydride-Mediated Beckmann Rearrangement Reaction of β-Oximyl Amides: Access to 5-Iminooxazolines. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1085-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Chalyk BA, Kandaurova IY, Hrebeniuk KV, Manoilenko OV, Kulik IB, Iminov RT, Kubyshkin V, Tverdokhlebov AV, Ablialimov OK, Mykhailiuk PK. A base promoted multigram synthesis of aminoisoxazoles: valuable building blocks for drug discovery and peptidomimetics. RSC Adv 2016. [DOI: 10.1039/c6ra02365g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An easy access to a large panel of aminoisoxazoles starting from commonly available amino acids.
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Affiliation(s)
| | | | | | | | - Irene B. Kulik
- Institute of Bioorganic Chemistry & Petrochemistry
- NAS of Ukraine
- Kyiv 02660
- Ukraine
| | | | | | | | | | - Pavel K. Mykhailiuk
- Enamine Ltd
- 01103 Kyiv
- Ukraine
- Department of Chemistry
- Taras Shevchenko National University of Kyiv
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31
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Hudson GA, Zhang Z, Tietz JI, Mitchell DA, van der Donk WA. In Vitro Biosynthesis of the Core Scaffold of the Thiopeptide Thiomuracin. J Am Chem Soc 2015; 137:16012-5. [PMID: 26675417 PMCID: PMC4819586 DOI: 10.1021/jacs.5b10194] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Thiopeptides are potent antibiotics
that inhibit protein synthesis.
They are made by a remarkable post-translational modification process
that transforms a linear peptide into a polycyclic structure. We present
here the in vitro biosynthesis of the core scaffold of thiomuracin
catalyzed by six proteins. We show that cyclodehydration precedes
dehydration, and that dehydration is catalyzed by two proteins in
a tRNAGlu-dependent manner. The enzyme that generates the
pyridine core from two dehydroalanines ejects the leader peptide
as a C-terminal carboxamide. Mutagenesis studies of the enzyme TbtD
identified important residues for a formal [4+2] cycloaddition process.
The core structure of thiomuracin exhibits similar antimicrobial
activity to other known congeners, illustrating that in vitro biosynthesis
is a viable route to potent antibiotics that can be explored for the
rapid and renewable generation of analogues.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhengan Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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32
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Koehnke J, Mann G, Bent AF, Ludewig H, Shirran S, Botting C, Lebl T, Houssen W, Jaspars M, Naismith JH. Structural analysis of leader peptide binding enables leader-free cyanobactin processing. Nat Chem Biol 2015; 11:558-563. [PMID: 26098679 PMCID: PMC4512242 DOI: 10.1038/nchembio.1841] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/07/2015] [Indexed: 02/05/2023]
Abstract
Regioselective modification of amino acids within the context of a peptide is common to a number of biosynthetic pathways and many such products have potential as therapeutics. The ATP dependent enzyme LynD heterocyclizes multiple cysteine residues to thiazolines within a peptide substrate. The enzyme requires the substrate to have conserved N-terminal leader for full activity. Catalysis is almost insensitive to immediately flanking residues in the substrate suggesting recognition occurs distant from the active site. Nucleotide and peptide substrate co-complex structures of LynD reveal the substrate leader peptide binds to and extends the β-sheet of a conserved domain of LynD, whilst catalysis is accomplished in another conserved domain. The spatial segregation of catalysis from recognition combines seemingly contradictory properties of regioselectivity and promiscuity; it appears to be a conserved strategy in other peptide modifying enzymes. A variant of LynD that efficiently processes substrates without a leader peptide has been engineered.
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Affiliation(s)
- Jesko Koehnke
- BSRC, University of St Andrews, St Andrews, KY16 9RH
| | - Greg Mann
- BSRC, University of St Andrews, St Andrews, KY16 9RH
| | - Andrew F Bent
- BSRC, University of St Andrews, St Andrews, KY16 9RH
| | | | - Sally Shirran
- BSRC, University of St Andrews, St Andrews, KY16 9RH
| | | | - Tomas Lebl
- BSRC, University of St Andrews, St Andrews, KY16 9RH
| | - Wael Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE.,Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, UK.,Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, Mansoura 35116, Egypt
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE
| | - James H Naismith
- BSRC, University of St Andrews, St Andrews, KY16 9RH.,State Key Laboratory of Biotherapy and Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, China
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33
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Dunbar KL, Tietz JI, Cox CL, Burkhart BJ, Mitchell DA. Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products. J Am Chem Soc 2015; 137:7672-7. [PMID: 26024319 DOI: 10.1021/jacs.5b04682] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Thiazole/oxazole-modified microcins (TOMMs) are a class of post-translationally modified peptide natural products bearing azole and azoline heterocycles. The first step in heterocycle formation is carried out by a two component cyclodehydratase comprised of an E1 ubiquitin-activating and a YcaO superfamily member. Recent studies have demonstrated that the YcaO domain is responsible for cyclodehydration, while the TOMM E1 homologue is responsible for peptide recognition during azoline formation. Although all characterized TOMM biosynthetic clusters contain this canonical TOMM E1 homologue (C domain), we also identified a second, highly divergent E1 superfamily member, annotated as an Ocin-ThiF-like protein (F protein), associated with more than 300 TOMM biosynthetic clusters. Here we describe the in vitro reconstitution of a novel TOMM cyclodehydratase from such a cluster and demonstrate that this auxiliary protein is required for cyclodehydration. Using a combination of biophysical techniques, we demonstrate that the F protein, rather than the C domain, is responsible for engaging the peptide substrate. The C domain instead appears to serve as a scaffolding protein, bringing the catalytic YcaO domain and the peptide binding Ocin-ThiF-like protein into proximity. Our findings provide an updated biosynthetic framework that provides a foundation for the characterization and reconstitution of approximately 25% of bioinformatically identifiable TOMM synthetases.
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Affiliation(s)
- Kyle L Dunbar
- †Department of Chemistry, ‡Institute for Genomic Biology, §Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan I Tietz
- †Department of Chemistry, ‡Institute for Genomic Biology, §Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Courtney L Cox
- †Department of Chemistry, ‡Institute for Genomic Biology, §Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brandon J Burkhart
- †Department of Chemistry, ‡Institute for Genomic Biology, §Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- †Department of Chemistry, ‡Institute for Genomic Biology, §Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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34
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Maxson T, Deane CD, Molloy EM, Cox CL, Markley AL, Lee SW, Mitchell DA. HIV protease inhibitors block streptolysin S production. ACS Chem Biol 2015; 10:1217-26. [PMID: 25668590 DOI: 10.1021/cb500843r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Streptolysin S (SLS) is a post-translationally modified peptide cytolysin that is produced by the human pathogen Streptococcus pyogenes. SLS belongs to a large family of azole-containing natural products that are biosynthesized via an evolutionarily conserved pathway. SLS is an important virulence factor during S. pyogenes infections, but despite an extensive history of study, further investigations are needed to clarify several steps of its biosynthesis. To this end, chemical inhibitors of SLS biosynthesis would be valuable tools to interrogate the various maturation steps of both SLS and biosynthetically related natural products. Such chemical inhibitors could also potentially serve as antivirulence therapeutics, which in theory may alleviate the spread of antibiotic resistance. In this work, we demonstrate that FDA-approved HIV protease inhibitors, especially nelfinavir, block a key proteolytic processing step during SLS production. This inhibition was demonstrated in live S. pyogenes cells and through in vitro protease inhibition assays. A panel of 57 nelfinavir analogs was synthesized, leading to a series of compounds with improved anti-SLS activity while illuminating structure-activity relationships. Nelfinavir was also found to inhibit the maturation of other azole-containing natural products, namely those involved in listeriolysin S, clostridiolysin S, and plantazolicin production. The use of nelfinavir analogs as inhibitors of SLS production has allowed us to begin examining the proteolysis event in SLS maturation and will aid in further investigations of the biosynthesis of SLS and related natural products.
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Affiliation(s)
- Tucker Maxson
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Caitlin D. Deane
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Evelyn M. Molloy
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Courtney L. Cox
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Department
of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Andrew L. Markley
- Department
of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States
| | - Shaun W. Lee
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Department
of Microbiology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
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35
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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
![]()
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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36
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Abstract
α,β-Dehydroamino acids are naturally occurring non-coded amino acids, found primarily in peptides. The review focuses on the type of α,β-dehydroamino acids, the structure of dehydropeptides, the source of their origin and bioactivity. Dehydropeptides are isolated primarily from bacteria and less often from fungi, marine invertebrates or even higher plants. They reveal mainly antibiotic, antifungal, antitumour, and phytotoxic activity. More than 60 different structures were classified, which often cover broad families of peptides. 37 different structural units containing the α,β-dehydroamino acid residues were shown including various side chains, Z and E isomers, and main modifications: methylation of peptide bond as well as the introduction of ester group and heterocycle ring. The collected data show the relation between the structure and bioactivity. This allows the activity of compounds, which were not studied in this field, but which belong to a larger peptide family to be predicted. A few examples show that the type of the geometrical isomer of the α,β-dehydroamino acid residue can be important or even crucial for biological activity.
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Affiliation(s)
- Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska, 48 45-052, Opole, Poland,
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37
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Koehnke J, Bent AF, Houssen WE, Mann G, Jaspars M, Naismith JH. The structural biology of patellamide biosynthesis. Curr Opin Struct Biol 2014; 29:112-121. [PMID: 25460274 DOI: 10.1016/j.sbi.2014.10.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 10/22/2014] [Accepted: 10/29/2014] [Indexed: 11/27/2022]
Abstract
The biosynthetic pathways for patellamide and related natural products have recently been studied by structural biology. These pathways produce molecules that have a complex framework and exhibit a diverse array of activity due to the variability of the amino acids that are found in them. As these molecules are difficult to synthesize chemically, exploitation of their properties has been modest. The patellamide pathway involves amino acid heterocyclization, peptide cleavage, peptide macrocyclization, heterocycle oxidation and epimerization; closely related products are also prenylated. Enzyme activities have been identified for all these transformations except epimerization, which may be spontaneous. This review highlights the recent structural and mechanistic work on amino acid heterocyclization, peptide cleavage and peptide macrocyclization. This work should help in using the enzymes to produce novel analogs of the natural products enabling an exploitation of their properties.
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Affiliation(s)
- Jesko Koehnke
- BSRC, North Haugh, The University, St Andrews, KY16 9ST
| | - Andrew F Bent
- BSRC, North Haugh, The University, St Andrews, KY16 9ST
| | - Wael E Houssen
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE.,Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD
| | - Greg Mann
- BSRC, North Haugh, The University, St Andrews, KY16 9ST
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen, AB24 3UE
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38
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Dunbar KL, Chekan JR, Cox CL, Burkhart BJ, Nair SK, Mitchell DA. Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Nat Chem Biol 2014; 10:823-9. [PMID: 25129028 PMCID: PMC4167974 DOI: 10.1038/nchembio.1608] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/19/2014] [Indexed: 11/24/2022]
Abstract
Despite intensive research, the cyclodehydratase responsible for azoline biogenesis in thiazole/oxazole-modified microcin (TOMM) natural products remains enigmatic. The collaboration of two proteins, C and D, is required for cyclodehydration. The C protein is homologous to E1 ubiquitin-activating enzymes, whereas the D protein is within the YcaO superfamily. Recent studies have demonstrated that TOMM YcaOs phosphorylate amide carbonyl oxygens to facilitate azoline formation. Here we report the X-ray crystal structure of an uncharacterized YcaO from Escherichia coli (Ec-YcaO). Ec-YcaO harbors an unprecedented fold and ATP-binding motif. This motif is conserved among TOMM YcaOs and is required for cyclodehydration. Furthermore, we demonstrate that the C protein regulates substrate binding and catalysis and that the proline-rich C terminus of the D protein is involved in C protein recognition and catalysis. This study identifies the YcaO active site and paves the way for the characterization of the numerous YcaO domains not associated with TOMM biosynthesis.
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Affiliation(s)
- Kyle L. Dunbar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan R. Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Courtney L. Cox
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brandon J. Burkhart
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Satish K. Nair
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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39
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Cox CL, Tietz JI, Sokolowski K, Melby JO, Doroghazi JR, Mitchell DA. Nucleophilic 1,4-additions for natural product discovery. ACS Chem Biol 2014; 9:2014-22. [PMID: 24937678 PMCID: PMC4168802 DOI: 10.1021/cb500324n] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Natural
products remain an important source of drug candidates,
but the difficulties inherent to traditional isolation, coupled with
unacceptably high rates of compound rediscovery, limit the pace of
natural product detection. Here we describe a reactivity-based screening
method to rapidly identify exported bacterial metabolites that contain
dehydrated amino acids (i.e., carbonyl- or imine-activated
alkenes), a common motif in several classes of natural products. Our
strategy entails the use of a commercially available thiol, dithiothreitol,
for the covalent labeling of activated alkenes by nucleophilic 1,4-addition.
Modification is easily discerned by comparing mass spectra of reacted
and unreacted cell surface extracts. When combined with bioinformatic
analysis of putative natural product gene clusters, targeted screening
and isolation can be performed on a prioritized list of strains. Moreover,
known compounds are easily dereplicated, effectively eliminating superfluous
isolation and characterization. As a proof of principle, this labeling
method was used to identify known natural products belonging to the
thiopeptide, lanthipeptide, and linaridin classes. Further, upon screening
a panel of only 23 actinomycetes, we discovered and characterized
a novel thiopeptide antibiotic, cyclothiazomycin C.
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Affiliation(s)
- Courtney L. Cox
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan I. Tietz
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Karol Sokolowski
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joel O. Melby
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - James R. Doroghazi
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, ‡Institute for Genomic
Biology, and §Department of
Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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40
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Goto Y, Ito Y, Kato Y, Tsunoda S, Suga H. One-pot synthesis of azoline-containing peptides in a cell-free translation system integrated with a posttranslational cyclodehydratase. ACTA ACUST UNITED AC 2014; 21:766-74. [PMID: 24856821 DOI: 10.1016/j.chembiol.2014.04.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
Azoline moieties in the backbones of peptidic natural products are important structural motifs that contribute to diverse bioactivities. Some azoline-containing peptides (Az-peptides) are produced from ribosomally synthesized precursor peptides, in which cysteine, serine, and threonine residues are converted to their corresponding azolines by posttranslational modification through a cyclodehydratase. We have devised an in vitro biosynthesis system of Az-peptides, referred to as the FIT-PatD (flexible in vitro translation) system, by the integration of a cell-free translation system with the posttranslational cyclodehydratase PatD. This system enabled the "one-pot" synthesis of a wide variety of Az-peptide derivatives expressed from synthetic DNA templates. The FIT-PatD system also facilitated mutagenesis studies on a wide array of precursor peptide sequences, unveiling unique in vitro substrate tolerance of PatD.
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Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; JST, PRESTO, Tokyo 113-0033, Japan.
| | - Yumi Ito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yasuharu Kato
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shotaro Tsunoda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; JST, CREST, Tokyo 113-0033, Japan.
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41
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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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42
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Siodłak D, Staś M, Broda MA, Bujak M, Lis T. Conformational properties of oxazole-amino acids: effect of the intramolecular N-H···N hydrogen bond. J Phys Chem B 2014; 118:2340-50. [PMID: 24528177 DOI: 10.1021/jp4121673] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation β2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(β) double bond is an additional stabilizing interaction. The tendency to adopt the conformation β2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.
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Affiliation(s)
- Dawid Siodłak
- Faculty of Chemistry, University of Opole , Oleska 48, 45-052 Opole, Poland
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Melby JO, Li X, Mitchell DA. Orchestration of enzymatic processing by thiazole/oxazole-modified microcin dehydrogenases. Biochemistry 2014; 53:413-22. [PMID: 24364559 DOI: 10.1021/bi401529y] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Thiazole/oxazole-modified microcins (TOMMs) comprise a structurally diverse family of natural products with varied bioactivities linked by the presence of posttranslationally installed thiazol(in)e and oxazol(in)e heterocycles. The detailed investigation of the TOMM biosynthetic enzymes from Bacillus sp. Al Hakam (Balh) has provided significant insight into heterocycle biosynthesis. Thiazoles and oxazoles are installed by the successive action of an ATP-dependent cyclodehydratase (C- and D-protein) and a FMN-dependent dehydrogenase (B-protein), which are responsible for azoline formation and azoline oxidation, respectively. Although several studies have focused on the mechanism of azoline formation, many details regarding the role of the dehydrogenase (B-protein) in overall substrate processing remain unknown. In this work, we evaluated the involvement of the dehydrogenase in determining the order of ring formation as well as the promiscuity of the Balh and microcin B17 cyclodehydratases to accept a panel of noncognate dehydrogenases. In support of the observed promiscuity, a fluorescence polarization assay was utilized to measure binding of the dehydrogenase to the cyclodehydratase using the intrinsic fluorescence of the FMN cofactor. Ultimately, the noncognate dehydrogenases were shown to possess cyclodehydratase-independent activity. A previous study identified a conserved Lys-Tyr motif to be important for dehydrogenase activity. Using the tools developed in this study, the Lys-Tyr motif was shown neither to alter complex formation with the cyclodehydratase nor the reduction potential. Taken together with the known crystal structure of a homologue, our data suggest that the Lys-Tyr motif is of catalytic importance. Overall, this study provides a greater level of insight into the complex orchestration of enzymatic activity during TOMM biosynthesis.
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Affiliation(s)
- Joel O Melby
- 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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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The Cyanobactin Heterocyclase Enzyme: A Processive Adenylase That Operates with a Defined Order of Reaction. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Koehnke J, Bent AF, Zollman D, Smith K, Houssen WE, Zhu X, Mann G, Lebl T, Scharff R, Shirran S, Botting CH, Jaspars M, Schwarz-Linek U, Naismith JH. The cyanobactin heterocyclase enzyme: a processive adenylase that operates with a defined order of reaction. Angew Chem Int Ed Engl 2013; 52:13991-6. [PMID: 24214017 PMCID: PMC3995012 DOI: 10.1002/anie.201306302] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/03/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Jesko Koehnke
- Biomedical Science Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST (UK)
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Deane CD, Melby JO, Molohon KJ, Susarrey AR, Mitchell DA. Engineering unnatural variants of plantazolicin through codon reprogramming. ACS Chem Biol 2013; 8:1998-2008. [PMID: 23823732 DOI: 10.1021/cb4003392] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plantazolicin (PZN) is a polyheterocyclic natural product derived from a ribosomal peptide that harbors remarkable antibiotic selectivity for the causative agent of anthrax, Bacillus anthracis. To simultaneously establish the structure-activity relationship of PZN and the substrate tolerance of the biosynthetic pathway, an Escherichia coli expression strain was engineered to heterologously produce PZN analogues. Variant PZN precursor genes were produced by site-directed mutagenesis and later screened by mass spectrometry to assess post-translational modification and export by E. coli. From a screen of 72 precursor peptides, 29 PZN variants were detected. This analogue collection provided insight into the selectivity of the post-translational modifying enzymes and established the boundaries of the natural biosynthetic pathway. Unlike other studied thiazole/oxazole-modified microcins, the biosynthetic machinery appeared to be finely tuned toward the production of PZN, such that the cognate enzymes did not process even other naturally occurring sequences from similar biosynthetic clusters. The modifying enzymes were exquisitely selective, installing heterocycles only at predefined positions within the precursor peptides while leaving neighboring residues unmodified. Nearly all substitutions at positions normally harboring heterocycles prevented maturation of a PZN variant, though some exceptions were successfully produced lacking a heterocycle at the penultimate residue. No variants containing additional heterocycles were detected, although several peptide sequences yielded multiple PZN variants as a result of varying oxidation states of select residues. Eleven PZN variants were produced in sufficient quantity to facilitate purification and assessment of their antibacterial activity, providing insight into the structure-activity relationship of PZN.
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Affiliation(s)
- Caitlin D. Deane
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, ∥School of Molecular and Cellular
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Joel O. Melby
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, ∥School of Molecular and Cellular
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Katie J. Molohon
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, ∥School of Molecular and Cellular
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Aziz R. Susarrey
- Department
of Chemistry, ‡Institute for Genomic Biology, and §Department of Microbiology, ∥School of Molecular and Cellular
Biology, 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, ∥School of Molecular and Cellular
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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