151
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Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated ‘Entotheonella’ bacteria. Curr Opin Chem Biol 2016; 31:8-14. [DOI: 10.1016/j.cbpa.2015.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/12/2015] [Accepted: 11/01/2015] [Indexed: 01/14/2023]
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152
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Huang J, Li C, Wang B, Sharon DA, Wu W, Shaik S. Selective Chlorination of Substrates by the Halogenase SyrB2 Is Controlled by the Protein According to a Combined Quantum Mechanics/Molecular Mechanics and Molecular Dynamics Study. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02825] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Huang
- The
State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM,
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chunsen Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Binju Wang
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Dina A. Sharon
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
| | - Wei Wu
- The
State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM,
Fujian Provincial Key Laboratory of Theoretical and Computational
Chemistry and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Sason Shaik
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Israel
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153
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Natural product discovery: past, present, and future. ACTA ACUST UNITED AC 2016; 43:155-76. [DOI: 10.1007/s10295-015-1723-5] [Citation(s) in RCA: 535] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/14/2015] [Indexed: 11/29/2022]
Abstract
Abstract
Microorganisms have provided abundant sources of natural products which have been developed as commercial products for human medicine, animal health, and plant crop protection. In the early years of natural product discovery from microorganisms (The Golden Age), new antibiotics were found with relative ease from low-throughput fermentation and whole cell screening methods. Later, molecular genetic and medicinal chemistry approaches were applied to modify and improve the activities of important chemical scaffolds, and more sophisticated screening methods were directed at target disease states. In the 1990s, the pharmaceutical industry moved to high-throughput screening of synthetic chemical libraries against many potential therapeutic targets, including new targets identified from the human genome sequencing project, largely to the exclusion of natural products, and discovery rates dropped dramatically. Nonetheless, natural products continued to provide key scaffolds for drug development. In the current millennium, it was discovered from genome sequencing that microbes with large genomes have the capacity to produce about ten times as many secondary metabolites as was previously recognized. Indeed, the most gifted actinomycetes have the capacity to produce around 30–50 secondary metabolites. With the precipitous drop in cost for genome sequencing, it is now feasible to sequence thousands of actinomycete genomes to identify the “biosynthetic dark matter” as sources for the discovery of new and novel secondary metabolites. Advances in bioinformatics, mass spectrometry, proteomics, transcriptomics, metabolomics and gene expression are driving the new field of microbial genome mining for applications in natural product discovery and development.
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154
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Biosynthetic manipulation of tryptophan in bacteria: pathways and mechanisms. ACTA ACUST UNITED AC 2016; 22:317-28. [PMID: 25794436 DOI: 10.1016/j.chembiol.2015.02.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 01/19/2023]
Abstract
Tryptophan, the most chemically complex and the least abundant of the 20 common proteinogenic amino acids, is a biosynthetic precursor to a large number of complex microbial natural products. Many of these molecules are promising scaffolds for drug discovery and development. The chemical features of tryptophan, including its ability to undergo enzymatic modifications at almost every atom in its structure and its propensity to undergo spontaneous, non-enzyme catalyzed chemistry, make it a unique biological precursor for the generation of chemical complexity. Here, we review the pathways that enable incorporation of tryptophan into complex metabolites in bacteria, with a focus on recently discovered, unusual metabolic transformations.
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155
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Kittilä T, Schoppet M, Cryle MJ. Online Pyrophosphate Assay for Analyzing Adenylation Domains of Nonribosomal Peptide Synthetases. Chembiochem 2016; 17:576-84. [PMID: 26751610 DOI: 10.1002/cbic.201500555] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Indexed: 12/12/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) produce many important and structurally complex natural products. Because of their architectures, reprogramming NRPSs has long been attempted to access new bioactive compounds. However, detailed characterization of NRPS catalysis and substrate selectivity by adenylation (A) domains is needed to support such efforts. We present a simple coupled NADH/pyrophosphate (PPi ) detection assay for analyzing A domain catalysis in vitro. PPi formation is coupled to the consumption of NADH by four enzymatic steps and is detected spectroscopically (λ=340 nm) for simple analysis. We demonstrate the effectiveness of this assay with several adenylation domains, including a stand-alone A domain (DltA, cell wall biosynthesis) and an embedded A domain (Tcp10, teicoplanin biosynthesis). Substrate acceptance of the Tcp10 A domain was explored for the first time, thus demonstrating the applicability of the assay for complex, multi-domain NRPSs.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Melanie Schoppet
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany. .,EMBL Australia, Monash University, Clayton, Victoria, 3800, Australia. .,The Department of Biochemistry and Molecular Biology and, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, 15 Innovation Walk, Clayton, Victoria, 3800, Australia.
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156
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Kries H, Niquille DL, Hilvert D. A subdomain swap strategy for reengineering nonribosomal peptides. ACTA ACUST UNITED AC 2016; 22:640-8. [PMID: 26000750 DOI: 10.1016/j.chembiol.2015.04.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/31/2015] [Accepted: 04/15/2015] [Indexed: 11/24/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) protect microorganisms from environmental threats by producing diverse siderophores, antibiotics, and other peptide natural products. Their modular molecular structure is also attractive from the standpoint of biosynthetic engineering. Here we evaluate a methodology for swapping module specificities of these mega-enzymes that takes advantage of flavodoxin-like subdomains involved in substrate recognition. Nine subdomains encoding diverse specificities were transplanted into the Phe-specific GrsA initiation module of gramicidin S synthetase. All chimeras could be purified as soluble protein. One construct based on a Val-specific subdomain showed sizable adenylation activity and functioned as a Val-Pro diketopiperazine synthetase upon addition of the proline-specific GrsB1 module. These results suggest that subdomain swapping could be a viable alternative to previous NRPS design approaches targeting binding pockets, domains, or entire modules. The short length of the swapped sequence stretch may facilitate straightforward exploitation of the wealth of existing NRPS modules for combinatorial biosynthesis.
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Affiliation(s)
- Hajo Kries
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zürich, Switzerland.
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157
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Sultana R, Tanneeru K, Kumar ABR, Guruprasad L. Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria. PLoS One 2016; 11:e0146786. [PMID: 26891364 PMCID: PMC4758615 DOI: 10.1371/journal.pone.0146786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022] Open
Abstract
The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
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Affiliation(s)
- Rafiya Sultana
- School of Chemistry, University of Hyderabad, Hyderabad, 500046, India
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158
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Ishikawa F, Kakeya H. A Competitive Enzyme-Linked Immunosorbent Assay System for Adenylation Domains in Nonribosomal Peptide Synthetases. Chembiochem 2016; 17:474-8. [PMID: 26748933 DOI: 10.1002/cbic.201500553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 12/16/2022]
Abstract
We describe a proof-of-concept study of a competitive enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) with active-site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold. A biotin functionality immobilizes the probes onto a streptavidin-coated solid support. Dissociation constants were determined with a series of ligands, including enzyme substrates and a library of sulfamoyloxy-linked aminoacyl/aryl-AMP analogues. As it enables direct readout of protein-ligand interaction, the competitive ELISA technique provided information on comparative structure- activity relationships and insights into the enzyme active-site architecture of NRPS A-domains. These studies indicate that the ELISA technique can accelerate the discovery of small-molecule inhibitors of the A-domains with new scaffolds that perturb the production of NRPS-related virulence factors.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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159
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Reimer JM, Aloise MN, Harrison PM, Schmeing TM. Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Nature 2016; 529:239-42. [PMID: 26762462 DOI: 10.1038/nature16503] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/02/2015] [Indexed: 12/22/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are very large proteins that produce small peptide molecules with wide-ranging biological activities, including environmentally friendly chemicals and many widely used therapeutics. NRPSs are macromolecular machines, with modular assembly-line logic, a complex catalytic cycle, moving parts and many active sites. In addition to the core domains required to link the substrates, they often include specialized tailoring domains, which introduce chemical modifications and allow the product to access a large expanse of chemical space. It is still unknown how the NRPS tailoring domains are structurally accommodated into megaenzymes or how they have adapted to function in nonribosomal peptide synthesis. Here we present a series of crystal structures of the initiation module of an antibiotic-producing NRPS, linear gramicidin synthetase. This module includes the specialized tailoring formylation domain, and states are captured that represent every major step of the assembly-line synthesis in the initiation module. The transitions between conformations are large in scale, with both the peptidyl carrier protein domain and the adenylation subdomain undergoing huge movements to transport substrate between distal active sites. The structures highlight the great versatility of NRPSs, as small domains repurpose and recycle their limited interfaces to interact with their various binding partners. Understanding tailoring domains is important if NRPSs are to be utilized in the production of novel therapeutics.
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Affiliation(s)
- Janice M Reimer
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
| | - Martin N Aloise
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
| | - Paul M Harrison
- Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montréal, Québec H3A 1B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, 3649 Promenade Sir-William-Osler, Montréal, Québec H3G 0B1, Canada
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160
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Ishikawa F, Kakeya H. Affinity Purification Method for the Identification of Nonribosomal Peptide Biosynthetic Enzymes Using a Synthetic Probe for Adenylation Domains. Methods Mol Biol 2016; 1401:63-76. [PMID: 26831701 DOI: 10.1007/978-1-4939-3375-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of inhibitors have been designed based on 5'-O-sulfamoyl adenosine (AMS) that display tight binding characteristics towards the inhibition of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs). We recently developed an affinity probe for A domains that could be used to facilitate the specific isolation and identification of NRPS modules. Our synthetic probe, which is a biotinylated variant of L-Phe-AMS (L-Phe-AMS-biotin), selectively targets the A domains in NRPS modules that recognize and convert L-Phe to an aminoacyl adenylate in whole proteomes. In this chapter, we describe the design and synthesis of L-Phe-AMS-biotin and provide a summary of our work towards the development of a series of protocols for the specific enrichment of NRPS modules using this probe.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
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161
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Duckworth BP, Wilson DJ, Aldrich CC. Measurement of Nonribosomal Peptide Synthetase Adenylation Domain Activity Using a Continuous Hydroxylamine Release Assay. Methods Mol Biol 2016; 1401:53-61. [PMID: 26831700 PMCID: PMC5588023 DOI: 10.1007/978-1-4939-3375-4_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Adenylation is a crucial enzymatic process in the biosynthesis of nonribosomal peptide synthetase (NRPS) derived natural products. Adenylation domains are considered the gatekeepers of NRPSs since they select, activate, and load the carboxylic acid substrate onto a downstream peptidyl carrier protein (PCP) domain of the NRPS. We describe a coupled continuous kinetic assay for NRPS adenylation domains that substitutes the PCP domain with hydroxylamine as the acceptor molecule. The pyrophosphate released from the first-half reaction is then measured using a two-enzyme coupling system, which detects conversion of the chromogenic substrate 7-methylthioguanosine (MesG) to 7-methylthioguanine. From profiling substrate specificity of unknown or engineered adenylation domains to studying chemical inhibition of adenylating enzymes, this robust assay will be of widespread utility in the broad field NRPS enzymology.
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Affiliation(s)
- Benjamin P Duckworth
- Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
| | - Daniel J Wilson
- Center for Drug Design, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford Hall, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
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162
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Brieke C, Maier T, Schröter M, Cryle MJ. Design and synthesis of peptide inhibitor conjugates as probes of the Cytochrome P450s from glycopeptide antibiotic biosynthesis. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00332f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycopeptide antibiotics are important clinical antibiotics that are currently employed against serious Gram-positive bacterial infections.
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Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Theresa Maier
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Martin Schröter
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
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163
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Abstract
The emergence of next-generation sequencing has provided new opportunities in the discovery of new nonribosomal peptides (NRPs) and NRP synthethases (NRPSs). However, there remain challenges for the characterization of these megasynthases. While genetic methods in native hosts are critical in elucidation of the function of fungal NRPS, in vitro assays of intact heterologously expressed proteins provide deeper mechanistic insights in NRPS enzymology. Our previous work in the study of NRPS takes advantage of Saccharomyces cerevisiae strain BJ5464-npgA as a robust and versatile platform for characterization of fungal NRPSs. Here we describe the use of yeast recombination strategies in S. cerevisiae for cloning of the NRPS coding sequence in 2μ-based expression vector; the use of affinity chromatography for purification of NRPS from the total S. cerevisiae soluble protein fraction; and strategies for reconstitution of NRPSs activities in vitro.
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Affiliation(s)
- Ralph A Cacho
- Department of Chemical and Biomolecular Engineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
- Department of Bioengineering, University of California, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA, 90095, USA.
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164
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Ishikawa F, Miyamoto K, Konno S, Kasai S, Kakeya H. Accurate Detection of Adenylation Domain Functions in Nonribosomal Peptide Synthetases by an Enzyme-linked Immunosorbent Assay System Using Active Site-directed Probes for Adenylation Domains. ACS Chem Biol 2015; 10:2816-26. [PMID: 26474351 DOI: 10.1021/acschembio.5b00595] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A significant gap exists between protein engineering and enzymes used for the biosynthesis of natural products, largely because there is a paucity of strategies that rapidly detect active-site phenotypes of the enzymes with desired activities. Herein, we describe a proof-of-concept study of an enzyme-linked immunosorbent assay (ELISA) system for the adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using a combination of active site-directed probes coupled to a 5'-O-N-(aminoacyl)sulfamoyladenosine scaffold with a biotin functionality that immobilizes probe molecules onto a streptavidin-coated solid support. The recombinant NRPSs have a C-terminal His-tag motif that is targeted by an anti-6×His mouse antibody as the primary antibody and a horseradish peroxidase-linked goat antimouse antibody as the secondary antibody. These probes can selectively capture the cognate A domains by ligand-directed targeting. In addition, the ELISA technique detected A domains in the crude cell-free homogenates from the Escherichia coli expression systems. When coupled with a chromogenic substrate, the antibody-based ELISA technique can visualize probe-protein binding interactions, which provides accurate readouts of the A-domain functions in NRPS enzymes. To assess the ELISA-based engineering of the A domains of NRPSs, we reprogramed 2,3-dihydroxybenzoic acid (DHB)-activating enzyme EntE toward salicylic acid (Sal)-activating enzymes and investigated a correlation between binding properties for probe molecules and enzyme catalysts. We generated a mutant of EntE that displayed negligible loss in the kcat/Km value with the noncognate substrate Sal and a corresponding 48-fold decrease in the kcat/Km value with the cognate substrate DHB. The resulting 26-fold switch in substrate specificity was achieved by the replacement of a Ser residue in the active site of EntE with a Cys toward the nonribosomal codes of Sal-activating enzymes. Bringing a laboratory ELISA technique and adenylating enzymes together using a combination of active site-directed probes for the A domains in NRPSs should accelerate both the functional characterization and manipulation of the A domains in NRPSs.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Kengo Miyamoto
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Sho Konno
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Shota Kasai
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy
and Molecular Sciences, Division of Bioinformatics and Chemical Genomics,
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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165
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Ritchie MK, Johnson LC, Clodfelter JE, Pemble CW, Fulp BE, Furdui CM, Kridel SJ, Lowther WT. Crystal Structure and Substrate Specificity of Human Thioesterase 2: INSIGHTS INTO THE MOLECULAR BASIS FOR THE MODULATION OF FATTY ACID SYNTHASE. J Biol Chem 2015; 291:3520-30. [PMID: 26663084 DOI: 10.1074/jbc.m115.702597] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Indexed: 01/12/2023] Open
Abstract
The type I fatty acid synthase (FASN) is responsible for the de novo synthesis of palmitate. Chain length selection and release is performed by the C-terminal thioesterase domain (TE1). FASN expression is up-regulated in cancer, and its activity levels are controlled by gene dosage and transcriptional and post-translational mechanisms. In addition, the chain length of fatty acids produced by FASN is controlled by a type II thioesterase called TE2 (E.C. 3.1.2.14). TE2 has been implicated in breast cancer and generates a broad lipid distribution within milk. The molecular basis for the ability of the TE2 to compete with TE1 for the acyl chain attached to the acyl carrier protein (ACP) domain of FASN is unknown. Herein, we show that human TE1 efficiently hydrolyzes acyl-CoA substrate mimetics. In contrast, TE2 prefers an engineered human acyl-ACP substrate and readily releases short chain fatty acids from full-length FASN during turnover. The 2.8 Å crystal structure of TE2 reveals a novel capping domain insert within the α/β hydrolase core. This domain is reminiscent of capping domains of type II thioesterases involved in polyketide synthesis. The structure also reveals that the capping domain had collapsed onto the active site containing the Ser-101-His-237-Asp-212 catalytic triad. This observation suggests that the capping domain opens to enable the ACP domain to dock and to place the acyl chain and 4'-phosphopantetheinyl-linker arm correctly for catalysis. Thus, the ability of TE2 to prematurely release fatty acids from FASN parallels the role of editing thioesterases involved in polyketide and non-ribosomal peptide synthase synthases.
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Affiliation(s)
- Melissa K Ritchie
- From the Center for Structural Biology and Department of Biochemistry
| | | | - Jill E Clodfelter
- From the Center for Structural Biology and Department of Biochemistry
| | - Charles W Pemble
- From the Center for Structural Biology and Department of Biochemistry
| | - Brian E Fulp
- Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina 27157
| | - Cristina M Furdui
- Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina 27157 Department of Internal Medicine, Section on Molecular Medicine, and
| | - Steven J Kridel
- Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina 27157 Department of Cancer Biology, Wake Forest School of Medicine and
| | - W Todd Lowther
- From the Center for Structural Biology and Department of Biochemistry, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina 27157
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166
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Brieke C, Kratzig V, Haslinger K, Winkler A, Cryle MJ. Rapid access to glycopeptide antibiotic precursor peptides coupled with cytochrome P450-mediated catalysis: towards a biomimetic synthesis of glycopeptide antibiotics. Org Biomol Chem 2015; 13:2012-21. [PMID: 25501135 DOI: 10.1039/c4ob02452d] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding the mechanisms underpinning glycopeptide antibiotic biosynthesis is key to the future ability to reinvent these compounds. For effective in vitro characterization of the crucial later steps of the biosynthesis, facile access to a wide range of substrate peptides as their Coenzyme A (CoA) conjugates is essential. Here we report the development of a rapid route to glycopeptide precursor CoA conjugates that affords both high yields and excellent purities. This synthesis route is applicable to the synthesis of peptide CoA-conjugates containing racemization-prone arylglycine residues: such residues are hallmarks of non-ribosomal peptide synthesis and have previously been inaccessible to peptide synthesis using Fmoc-type chemistry. We have applied this route to generate glycopeptide precursor peptides in their carrier protein-bound form as substrates to explore the specificity of the first oxygenase enzyme from vancomycin biosynthesis (OxyBvan). Our results indicate that OxyBvan is a highly promiscuous catalyst for phenolic coupling of diverse glycopeptide precursors that accepts multiple carrier protein substrates, even on carrier protein domains from alternate glycopeptide biosynthetic machineries. These results represent the first important steps in the development of an in vitro biomimetic synthesis of modified glycopeptide aglycones.
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Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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167
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168
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Shelest E, Heimerl N, Fichtner M, Sasso S. Multimodular type I polyketide synthases in algae evolve by module duplications and displacement of AT domains in trans. BMC Genomics 2015; 16:1015. [PMID: 26611533 PMCID: PMC4661987 DOI: 10.1186/s12864-015-2222-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/16/2015] [Indexed: 11/16/2022] Open
Abstract
Background Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganisms and plants. Here, we have analyzed available full genome sequences of microscopic and macroscopic algae for the presence of type I PKS genes. Results Type I PKS genes are present in 15 of 32 analyzed algal species. In chlorophytes, large proteins in the MDa range are predicted in most sequenced species, and PKSs with free-standing acyltransferase domains (trans-AT PKSs) predominate. In a phylogenetic tree, PKS sequences from different algal phyla form clades that are distinct from PKSs from other organisms such as non-photosynthetic protists or cyanobacteria. However, intermixing is observed in some cases, for example polyunsaturated fatty acid (PUFA) and glycolipid synthases of various origins. Close relationships between type I PKS modules from different species or between modules within the same multimodular enzyme were identified, suggesting module duplications during evolution of algal PKSs. In contrast to type I PKSs, nonribosomal peptide synthetases (NRPSs) are relatively rare in algae (occurrence in 7 of 32 species). Conclusions Our phylogenetic analysis of type I PKSs in algae supports an evolutionary scenario whereby integrated AT domains were displaced to yield trans-AT PKSs. Together with module duplications, the displacement of AT domains may constitute a major mechanism of PKS evolution in algae. This study advances our understanding of the diversity of eukaryotic PKSs and their evolutionary trajectories. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2222-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ekaterina Shelest
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Natalie Heimerl
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Dornburger Str. 159, 07743, Jena, Germany.
| | - Maximilian Fichtner
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Severin Sasso
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Dornburger Str. 159, 07743, Jena, Germany.
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169
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Brieke C, Peschke M, Haslinger K, Cryle MJ. Sequential In Vitro Cyclization by Cytochrome P450 Enzymes of Glycopeptide Antibiotic Precursors Bearing the X‐Domain from Nonribosomal Peptide Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Kristina Haslinger
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
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170
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Brieke C, Peschke M, Haslinger K, Cryle MJ. Sequential In Vitro Cyclization by Cytochrome P450 Enzymes of Glycopeptide Antibiotic Precursors Bearing the X‐Domain from Nonribosomal Peptide Biosynthesis. Angew Chem Int Ed Engl 2015; 54:15715-9. [DOI: 10.1002/anie.201507533] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Kristina Haslinger
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
| | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg (Germany)
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171
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Ishikawa F, Suzuki T, Dohmae N, Kakeya H. A Multiple-Labeling Strategy for Nonribosomal Peptide Synthetases Using Active-Site-Directed Proteomic Probes for Adenylation Domains. Chembiochem 2015; 16:2590-4. [PMID: 26467472 DOI: 10.1002/cbic.201500481] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/07/2022]
Abstract
Genetic approaches have greatly contributed to our understanding of nonribosomal peptide biosynthetic machinery; however, proteomic investigations are limited. Here, we developed a highly sensitive detection strategy for multidomain nonribosomal peptide synthetases (NRPSs) by using a multiple-labeling technique with active-site-directed probes for adenylation domains. When applied to gramicidin S-producing and -nonproducing strains of Aneurinibacillus migulanus (DSM 5759 and DSM 2895, respectively), the multiple technique sensitively detected an active multidomain NRPS (GrsB) in lysates obtained from the organisms. This functional proteomics method revealed an unknown inactive precursor (or other inactive form) of GrsB in the nonproducing strain. This method provides a new option for the direct detection, functional analysis, and high-resolution identification of low-abundance active NRPS enzymes in native proteomic environments.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto, 606-8501, Japan.
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172
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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173
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Konno S, Ishikawa F, Suzuki T, Dohmae N, Burkart MD, Kakeya H. Active site-directed proteomic probes for adenylation domains in nonribosomal peptide synthetases. Chem Commun (Camb) 2015; 51:2262-5. [PMID: 25563804 DOI: 10.1039/c4cc09412c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We describe a general strategy for selective chemical labeling of individual adenylation (A) domains in nonribosomal peptide synthetases (NRPSs) using active site-directed proteomic probes coupled to the 5'-O-N-(aminoacyl)sulfamoyladenosine (AMS) scaffold with a clickable benzophenone functionality. These proteomic tools can greatly facilitate the molecular identification, functional characterization, and profiling of virtually any kind of A domains of NRPS enzymes in complex biological systems.
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Affiliation(s)
- Sho Konno
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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174
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Calcott MJ, Ackerley DF. Portability of the thiolation domain in recombinant pyoverdine non-ribosomal peptide synthetases. BMC Microbiol 2015; 15:162. [PMID: 26268580 PMCID: PMC4535683 DOI: 10.1186/s12866-015-0496-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Non-ribosomal peptide synthetase (NRPS) enzymes govern the assembly of amino acids and related monomers into peptide-like natural products. A key goal of the field is to develop methods to effective recombine NRPS domains or modules, and thereby generate modified or entirely novel products. We previously showed that substitution of the condensation (C) and adenylation (A) domains in module 2 of the pyoverdine synthetase PvdD from Pseudomonas aeruginosa led to synthesis of modified pyoverdines in a minority of cases, but that more often the recombinant enzymes were non-functional. One possible explanation was that the majority of introduced C domains were unable to effectively communicate with the thiolation (T) domain immediately upstream, in the first module of PvdD. RESULTS To test this we first compared the effectiveness of C-A domain substitution relative to T-C-A domain substitution using three different paired sets of domains. Having previously demonstrated that the PvdD A/T domain interfaces are tolerant of domain substitution, we hypothesised that T-C-A domain substitution would lead to more functional recombinant enzymes, by maintaining native T/C domain interactions. Although we successfully generated two recombinant pyoverdines, having a serine or a N5-formyl-N5-hydroxyornithine residue in place of the terminal threonine of wild type pyoverdine, in neither case did the T-C-A domain substitution strategy lead to substantially higher product yield. To more comprehensively examine the abilities of non-native T domains to communicate effectively with the C domain of PvdD module 2 we then substituted the module 1 T domain with 18 different T domains sourced from other pyoverdine NRPS enzymes. In 15/18 cases the recombinant NRPS was functional, including 6/6 cases where the introduced T domain was located upstream of a C domain in its native context. CONCLUSIONS Our data indicate that T domains are generally able to interact effectively with non-native C domains, contrasting with previous findings that they are not generally portable upstream of epimerisation (E) or thioesterase (TE) domains. This offers promise for NRPS recombination efforts, but also raises the possibility that some C domains are unable to efficiently accept non-native peptides at their donor site due to steric constraints or other limitations.
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Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand. .,Centre for Biodiscovery, Victoria University of Wellington, Wellington, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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175
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Nepal KK, Lee RP, Rezenom YH, Watanabe CMH. Probing the Role of N-Acetyl-glutamyl 5-Phosphate, an Acyl Phosphate, in the Construction of the Azabicycle Moiety of the Azinomycins. Biochemistry 2015; 54:4415-8. [DOI: 10.1021/acs.biochem.5b00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keshav K. Nepal
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rachel P. Lee
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yohannes H. Rezenom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Coran M. H. Watanabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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176
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Markova SV, Vysotski ES. Coelenterazine-dependent luciferases. BIOCHEMISTRY (MOSCOW) 2015; 80:714-32. [DOI: 10.1134/s0006297915060073] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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177
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Lee DW, Kim BS. Antimicrobial cyclic peptides for plant disease control. THE PLANT PATHOLOGY JOURNAL 2015; 31:1-11. [PMID: 25774105 PMCID: PMC4356600 DOI: 10.5423/ppj.rw.08.2014.0074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/18/2014] [Accepted: 11/25/2014] [Indexed: 05/11/2023]
Abstract
Antimicrobial cyclic peptides derived from microbes bind stably with target sites, have a tolerance to hydrolysis by proteases, and a favorable degradability under field conditions, which make them an attractive proposition for use as agricultural fungicides. Antimicrobial cyclic peptides are classified according to the types of bonds within the ring structure; homodetic, heterodetic, and complex cyclic peptides, which in turn reflect diverse physicochemical features. Most antimicrobial cyclic peptides affect the integrity of the cell envelope. This is achieved through direct interaction with the cell membrane or disturbance of the cell wall and membrane component biosynthesis such as chitin, glucan, and sphingolipid. These are specific and selective targets providing reliable activity and safety for non-target organisms. Synthetic cyclic peptides produced through combinatorial chemistry offer an alternative approach to develop antimicrobials for agricultural uses. Those synthesized so far have been studied for antibacterial activity, however, the recent advancements in powerful technologies now promise to provide novel antimicrobial cyclic peptides that are yet to be discovered from natural resources.
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Affiliation(s)
| | - Beom Seok Kim
- Corresponding author. Phone) 2-3290-3047, FAX) 2-921-1715, E-mail)
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178
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Kenyon LJ, Sabree ZL. Obligate insect endosymbionts exhibit increased ortholog length variation and loss of large accessory proteins concurrent with genome shrinkage. Genome Biol Evol 2015; 6:763-75. [PMID: 24671745 PMCID: PMC4007534 DOI: 10.1093/gbe/evu055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Extreme genome reduction has been observed in obligate intracellular insect mutualists and is an assumed consequence of fixed, long-term host isolation. Rapid accumulation of mutations and pseudogenization of genes no longer vital for an intracellular lifestyle, followed by deletion of many genes, are factors that lead to genome reduction. Size reductions in individual genes due to small-scale deletions have also been implicated in contributing to overall genome shrinkage. Conserved protein functional domains are expected to exhibit low tolerance for mutations and therefore remain relatively unchanged throughout protein length reduction while nondomain regions, presumably under less selective pressures, would shorten. This hypothesis was tested using orthologous protein sets from the Flavobacteriaceae (phylum: Bacteroidetes) and Enterobacteriaceae (subphylum: Gammaproteobacteria) families, each of which includes some of the smallest known genomes. Upon examination of protein, functional domain, and nondomain region lengths, we found that proteins were not uniformly shrinking with genome reduction, but instead increased length variability and variability was observed in both the functional domain and nondomain regions. Additionally, as complete gene loss also contributes to overall genome shrinkage, we found that the largest proteins in the proteomes of nonhost-restricted bacteroidetial and gammaproteobacterial species often were inferred to be involved in secondary metabolic processes, extracellular sensing, or of unknown function. These proteins were absent in the proteomes of obligate insect endosymbionts. Therefore, loss of genes encoding large proteins not required for host-restricted lifestyles in obligate endosymbiont proteomes likely contributes to extreme genome reduction to a greater degree than gene shrinkage.
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Affiliation(s)
- Laura J Kenyon
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University
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179
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X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis. Nature 2015; 521:105-9. [DOI: 10.1038/nature14141] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/05/2014] [Indexed: 02/06/2023]
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180
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Haslinger K, Redfield C, Cryle MJ. Structure of the terminal PCP domain of the non-ribosomal peptide synthetase in teicoplanin biosynthesis. Proteins 2015; 83:711-21. [PMID: 25586301 DOI: 10.1002/prot.24758] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 01/19/2023]
Abstract
The biosynthesis of the glycopeptide antibiotics, of which teicoplanin and vancomycin are representative members, relies on the combination of non-ribosomal peptide synthesis and modification of the peptide by cytochrome P450 (Oxy) enzymes while the peptide remains bound to the peptide synthesis machinery. We have structurally characterized the final peptidyl carrier protein domain of the teicoplanin non-ribosomal peptide synthetase machinery: this domain is believed to mediate the interactions with tailoring Oxy enzymes in addition to its function as a shuttle for intermediates between multiple non-ribosomal peptide synthetase domains. Using solution state NMR, we have determined structures of this PCP domain in two states, the apo and the post-translationally modified holo state, both of which conform to a four-helix bundle assembly. The structures exhibit the same general fold as the majority of known carrier protein structures, in spite of the complex biosynthetic role that PCP domains from the final non-ribosomal peptide synthetase module must play in glycopeptide antibiotic biosynthesis. These structures thus support the hypothesis that it is subtle rearrangements, rather than dramatic conformational changes, which govern carrier protein interactions and selectivity during non-ribosomal peptide synthesis.
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Affiliation(s)
- Kristina Haslinger
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, 69120, Germany
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181
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Goswami A, Van Lanen SG. Enzymatic strategies and biocatalysts for amide bond formation: tricks of the trade outside of the ribosome. MOLECULAR BIOSYSTEMS 2015; 11:338-53. [PMID: 25418915 PMCID: PMC4304603 DOI: 10.1039/c4mb00627e] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Amide bond-containing (ABC) biomolecules are some of the most intriguing and functionally significant natural products with unmatched utility in medicine, agriculture and biotechnology. The enzymatic formation of an amide bond is therefore a particularly interesting platform for engineering the synthesis of structurally diverse natural and unnatural ABC molecules for applications in drug discovery and molecular design. As such, efforts to unravel the mechanisms involved in carboxylate activation and substrate selection has led to the characterization of a number of structurally and functionally distinct protein families involved in amide bond synthesis. Unlike ribosomal synthesis and thio-templated synthesis using nonribosomal peptide synthetases, which couple the hydrolysis of phosphoanhydride bond(s) of ATP and proceed via an acyl-adenylate intermediate, here we discuss two mechanistically alternative strategies: ATP-dependent enzymes that generate acylphosphate intermediates and ATP-independent transacylation strategies. Several examples highlighting the function and synthetic utility of these amide bond-forming strategies are provided.
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Affiliation(s)
- Anwesha Goswami
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone, Lexington, KY 40536, USA.
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182
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Giessen TW, Altegoer F, Nebel AJ, Steinbach RM, Bange G, Marahiel MA. A Synthetic Adenylation-Domain-Based tRNA-Aminoacylation Catalyst. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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183
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Giessen TW, Altegoer F, Nebel AJ, Steinbach RM, Bange G, Marahiel MA. A synthetic adenylation-domain-based tRNA-aminoacylation catalyst. Angew Chem Int Ed Engl 2015; 54:2492-6. [PMID: 25583137 DOI: 10.1002/anie.201410047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/01/2014] [Indexed: 01/04/2023]
Abstract
The incorporation of non-proteinogenic amino acids represents a major challenge for the creation of functionalized proteins. The ribosomal pathway is limited to the 20-22 proteinogenic amino acids while nonribosomal peptide synthetases (NRPSs) are able to select from hundreds of different monomers. Introduced herein is a fusion-protein-based design for synthetic tRNA-aminoacylation catalysts based on combining NRPS adenylation domains and a small eukaryotic tRNA-binding domain (Arc1p-C). Using rational design, guided by structural insights and molecular modeling, the adenylation domain PheA was fused with Arc1p-C using flexible linkers and achieved tRNA-aminoacylation with both proteinogenic and non-proteinogenic amino acids. The resulting aminoacyl-tRNAs were functionally validated and the catalysts showed broad substrate specificity towards the acceptor tRNA. Our strategy shows how functional tRNA-aminoacylation catalysts can be created for bridging the ribosomal and nonribosomal worlds. This opens up new avenues for the aminoacylation of tRNAs with functional non-proteinogenic amino acids.
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Affiliation(s)
- Tobias W Giessen
- Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg (Germany); LOEWE Center for Synthetic Microbiology (Synmikro), Philipps-University Marburg, Hans-Meerwein-Strasse, 35032 Marburg (Germany).
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185
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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186
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
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Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
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187
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Deshmukh SC, Talukdar P. Stereoselective Synthesis of (2S,3R)-α-Hydroxy-β-Amino Acids (AHBAs): Valinoctin A, (2S,3R)-3-Amino-2-Hydroxydecanoic Acid, and a Fluorescent-Labeled (2S,3R)-AHBA. J Org Chem 2014; 79:11215-25. [DOI: 10.1021/jo501751u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Pinaki Talukdar
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pune, 411008 India
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188
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Haslinger K, Maximowitsch E, Brieke C, Koch A, Cryle MJ. Cytochrome P450 OxyBteiCatalyzes the First Phenolic Coupling Step in Teicoplanin Biosynthesis. Chembiochem 2014; 15:2719-28. [DOI: 10.1002/cbic.201402441] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 01/25/2023]
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189
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Matsuda Y, Wakimoto T, Mori T, Awakawa T, Abe I. Complete Biosynthetic Pathway of Anditomin: Nature’s Sophisticated Synthetic Route to a Complex Fungal Meroterpenoid. J Am Chem Soc 2014; 136:15326-36. [DOI: 10.1021/ja508127q] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yudai Matsuda
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Wakimoto
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical
Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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190
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Genetic manipulation of non-ribosomal peptide synthetases to generate novel bioactive peptide products. Biotechnol Lett 2014; 36:2407-16. [DOI: 10.1007/s10529-014-1642-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/06/2014] [Indexed: 12/25/2022]
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191
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Bayer A, Kazmaier U. Selective Peptide Modifications via Ruthenium-Catalyzed Allylic Alkylations. J Org Chem 2014; 79:8491-7. [DOI: 10.1021/jo501731y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anton Bayer
- Universität des Saarlandes, Institut für Organische Chemie, Campus, Geb. C4.2, D-66123 Saarbrücken, Germany
| | - Uli Kazmaier
- Universität des Saarlandes, Institut für Organische Chemie, Campus, Geb. C4.2, D-66123 Saarbrücken, Germany
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192
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Kries H, Wachtel R, Pabst A, Wanner B, Niquille D, Hilvert D. Reprogramming Nonribosomal Peptide Synthetases for “Clickable” Amino Acids. Angew Chem Int Ed Engl 2014; 53:10105-8. [DOI: 10.1002/anie.201405281] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Indexed: 12/21/2022]
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193
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Kries H, Wachtel R, Pabst A, Wanner B, Niquille D, Hilvert D. Reprogramming Nonribosomal Peptide Synthetases for “Clickable” Amino Acids. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405281] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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194
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Biosynthesis of novel Pyoverdines by domain substitution in a nonribosomal peptide synthetase of Pseudomonas aeruginosa. Appl Environ Microbiol 2014; 80:5723-31. [PMID: 25015884 DOI: 10.1128/aem.01453-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyoverdine is a fluorescent nonribosomal peptide siderophore made by fluorescent pseudomonads. The Pseudomonas aeruginosa nonribosomal peptide synthetase (NRPS) PvdD contains two modules that each incorporate an l-threonine residue at the C-terminal end of pyoverdine. In an attempt to generate modified pyoverdine peptides, we substituted alternative-substrate-specifying adenylation (A) and peptide bond-catalyzing condensation (C) domains into the second module of PvdD. When just the A domain was substituted, the resulting strains produced only wild-type pyoverdine-at high levels if the introduced A domain specified threonine or at trace levels otherwise. The high levels of pyoverdine synthesis observed whenever the introduced A domain specified threonine indicated that these nonnative A domains were able to communicate effectively with the PvdD C domain. Moreover, the unexpected observation that non-threonine-specifying A domains nevertheless incorporated threonine into pyoverdine suggests that the native PvdD C domain exhibited stronger selectivity than these A domains for the incorporated amino acid substrate (i.e., misactivation of a threonine residue by the introduced A domains was more frequent than misincorporation of a nonthreonine residue by the PvdD C domain). In contrast, substitution of both the C and A domains of PvdD generated high yields of rationally modified pyoverdines in two instances, these pyoverdines having either a lysine or a serine residue in place of the terminal threonine. However, C-A domain substitution more commonly yielded a truncated peptide product, likely due to stalling of synthesis on a nonfunctional recombinant NRPS template.
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195
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Haslinger K, Brieke C, Uhlmann S, Sieverling L, Süssmuth RD, Cryle MJ. The Structure of a Transient Complex of a Nonribosomal Peptide Synthetase and a Cytochrome P450 Monooxygenase. Angew Chem Int Ed Engl 2014; 53:8518-22. [DOI: 10.1002/anie.201404977] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 11/11/2022]
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196
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Haslinger K, Brieke C, Uhlmann S, Sieverling L, Süssmuth RD, Cryle MJ. Die Struktur eines transienten Komplexes einer nicht-ribosomalen Peptidsynthetase mit einer P450-Monooxygenase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404977] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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197
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Miller BR, Sundlov JA, Drake EJ, Makin TA, Gulick AM. Analysis of the linker region joining the adenylation and carrier protein domains of the modular nonribosomal peptide synthetases. Proteins 2014; 82:2691-702. [PMID: 24975514 DOI: 10.1002/prot.24635] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 06/06/2014] [Accepted: 06/18/2014] [Indexed: 12/29/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are multimodular proteins capable of producing important peptide natural products. Using an assembly line process, the amino acid substrate and peptide intermediates are passed between the active sites of different catalytic domains of the NRPS while bound covalently to a peptidyl carrier protein (PCP) domain. Examination of the linker sequences that join the NRPS adenylation and PCP domains identified several conserved proline residues that are not found in standalone adenylation domains. We examined the roles of these proline residues and neighboring conserved sequences through mutagenesis and biochemical analysis of the reaction catalyzed by the adenylation domain and the fully reconstituted NRPS pathway. In particular, we identified a conserved LPxP motif at the start of the adenylation-PCP linker. The LPxP motif interacts with a region on the adenylation domain to stabilize a critical catalytic lysine residue belonging to the A10 motif that immediately precedes the linker. Further, this interaction with the C-terminal subdomain of the adenylation domain may coordinate movement of the PCP with the conformational change of the adenylation domain. Through this work, we extend the conserved A10 motif of the adenylation domain and identify residues that enable proper adenylation domain function.
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Affiliation(s)
- Bradley R Miller
- Hauptman-Woodward Medical Research Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York, 14203
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198
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Mining of the pyrrolamide antibiotics analogs in Streptomyces netropsis reveals the amidohydrolase-dependent "iterative strategy" underlying the pyrrole polymerization. PLoS One 2014; 9:e99077. [PMID: 24901640 PMCID: PMC4047045 DOI: 10.1371/journal.pone.0099077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/11/2014] [Indexed: 01/06/2023] Open
Abstract
In biosynthesis of natural products, potential intermediates or analogs of a particular compound in the crude extracts are commonly overlooked in routine assays due to their low concentration, limited structural information, or because of their insignificant bio-activities. This may lead into an incomplete and even an incorrect biosynthetic pathway for the target molecule. Here we applied multiple compound mining approaches, including genome scanning and precursor ion scan-directed mass spectrometry, to identify potential pyrrolamide compounds in the fermentation culture of Streptomyces netropsis. Several novel congocidine and distamycin analogs were thus detected and characterized. A more reasonable route for the biosynthesis of pyrrolamides was proposed based on the structures of these newly discovered compounds, as well as the functional characterization of several key biosynthetic genes of pyrrolamides. Collectively, our results implied an unusual “iterative strategy” underlying the pyrrole polymerization in the biosynthesis of pyrrolamide antibiotics.
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199
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Wang M, Zhao H. Characterization and Engineering of the Adenylation Domain of a NRPS-Like Protein: A Potential Biocatalyst for Aldehyde Generation. ACS Catal 2014; 4:1219-1225. [PMID: 24804152 PMCID: PMC3985451 DOI: 10.1021/cs500039v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/17/2014] [Indexed: 01/24/2023]
Abstract
The adenylation (A) domain acts as the first "gate-keeper" to ensure the activation and thioesterification of the correct monomer to nonribosomal peptide synthetases (NRPSs). Our understanding of the specificity-conferring code and our ability to engineer A domains are critical for increasing the chemical diversity of nonribosomal peptides (NRPs). We recently discovered a novel NRPS-like protein (ATEG_03630) that can activate 5-methyl orsellinic acid (5-MOA) and reduce it to 2,4-dihydroxy-5,6-dimethyl benzaldehyde. A NRPS-like protein is much smaller than multidomain NRPSs, but it still represents the thioesterification half-reaction, which is otherwise missed from a stand-alone A domain. Therefore, a NRPS-like protein may serve as a better model system for A domain engineering. Here, we characterize the substrate specificity of ATEG_03630 and conclude that the hydrogen-bond donor at the 4-position is crucial for substrate recognition. Next, we show that the substrate specificity of ATEG_03630 can be engineered toward our target substrate anthranilate via bioinformatics analysis and mutagenesis. The resultant mutant H358A increased its activity toward anthranilate by 10.9-fold, which led to a 26-fold improvement in specificity. Finally, we demonstrate one-pot chemoenzymatic synthesis of 4-hydroxybenzaldoxime from 4-hydroxybenzoic acid with high yield.
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Affiliation(s)
- Meng Wang
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for
Genomic Biology, Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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200
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Tufar P, Rahighi S, Kraas F, Kirchner D, Löhr F, Henrich E, Köpke J, Dikic I, Güntert P, Marahiel M, Dötsch V. Crystal Structure of a PCP/Sfp Complex Reveals the Structural Basis for Carrier Protein Posttranslational Modification. ACTA ACUST UNITED AC 2014; 21:552-562. [DOI: 10.1016/j.chembiol.2014.02.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/02/2014] [Accepted: 02/06/2014] [Indexed: 11/17/2022]
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