1
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Morandini L, Caulier S, Bragard C, Mahillon J. Bacillus cereus sensu lato antimicrobial arsenal: An overview. Microbiol Res 2024; 283:127697. [PMID: 38522411 DOI: 10.1016/j.micres.2024.127697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/25/2024] [Accepted: 03/16/2024] [Indexed: 03/26/2024]
Abstract
The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.
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Affiliation(s)
| | - Simon Caulier
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Claude Bragard
- Laboratory of Plant Health, Earth and Life Institute, UCLouvain, Louvain-la-Neuve B-1348, Belgium
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2
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. Nat Commun 2024; 15:3574. [PMID: 38678027 PMCID: PMC11055893 DOI: 10.1038/s41467-024-48030-9] [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: 09/29/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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3
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559410. [PMID: 37808672 PMCID: PMC10557607 DOI: 10.1101/2023.09.25.559410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that all CDO-like enzymes are likely enzyme filaments. Our work represents the first structural characterization of a CDO. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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4
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Ogilvie CE, Czekster CM. Cyclic dipeptides and the human microbiome: Opportunities and challenges. Bioorg Med Chem 2023; 90:117372. [PMID: 37343497 DOI: 10.1016/j.bmc.2023.117372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Research into the human microbiome has implicated its constituents in a variety of non-communicable diseases, with certain microbes found to promote health and others leading to dysbiosis and pathogenesis.Microbes communicate and coordinate their behaviour through the secretion of small molecules, such as cyclic dipeptides (CDPs), into their surrounding environment. CDPs are ubiquitous signalling molecules thatexhibit a wide range of biological activities, with particular relevance to human health due to their potential to act as microbiome modulators.
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Affiliation(s)
- Charlene Elizabeth Ogilvie
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
| | - Clarissa Melo Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
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5
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Yee DA, Niwa K, Perlatti B, Chen M, Li Y, Tang Y. Genome mining for unknown-unknown natural products. Nat Chem Biol 2023; 19:633-640. [PMID: 36702957 PMCID: PMC10159913 DOI: 10.1038/s41589-022-01246-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/20/2022] [Indexed: 01/27/2023]
Abstract
Genome mining of biosynthetic pathways with no identifiable core enzymes can lead to discovery of the so-called unknown (biosynthetic route)-unknown (molecular structure) natural products. Here we focused on a conserved fungal biosynthetic pathway that lacks a canonical core enzyme and used heterologous expression to identify the associated natural product, a highly modified cyclo-arginine-tyrosine dipeptide. Biochemical characterization of the pathway led to identification of a new arginine-containing cyclodipeptide synthase (RCDPS), which was previously annotated as a hypothetical protein and has no sequence homology to non-ribosomal peptide synthetase or bacterial cyclodipeptide synthase. RCDPS homologs are widely encoded in fungal genomes; other members of this family can synthesize diverse cyclo-arginine-Xaa dipeptides, and characterization of a cyclo-arginine-tryptophan RCDPS showed that the enzyme is aminoacyl-tRNA dependent. Further characterization of the biosynthetic pathway led to discovery of new compounds whose structures would not have been predicted without knowledge of RCDPS function.
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Affiliation(s)
- Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Kanji Niwa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bruno Perlatti
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Hexagon Bio, Menlo Park, CA, USA
| | - Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Yuqing Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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6
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Sutherland E, Harding CJ, Czekster CM. Active site remodelling of a cyclodipeptide synthase redefines substrate scope. Commun Chem 2022; 5:101. [DOI: 10.1038/s42004-022-00715-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
AbstractCyclodipeptide synthases (CDPSs) generate a wide range of cyclic dipeptides using aminoacylated tRNAs as substrates. Histidine-containing cyclic dipeptides have important biological activities as anticancer and neuroprotective molecules. Out of the 120 experimentally validated CDPS members, only two are known to accept histidine as a substrate yielding cyclo(His-Phe) and cyclo(His-Pro) as products. It is not fully understood how CDPSs select their substrates, and we must rely on bioprospecting to find new enzymes and novel bioactive cyclic dipeptides. Here, we developed an in vitro system to generate an extensive library of molecules using canonical and non-canonical amino acids as substrates, expanding the chemical space of histidine-containing cyclic dipeptide analogues. To investigate substrate selection we determined the structure of a cyclo(His-Pro)-producing CDPS. Three consecutive generations harbouring single, double and triple residue substitutions elucidated the histidine selection mechanism. Moreover, substrate selection was redefined, yielding enzyme variants that became capable of utilising phenylalanine and leucine. Our work successfully engineered a CDPS to yield different products, paving the way to direct the promiscuity of these enzymes to produce molecules of our choosing.
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7
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Zhang S, Zhu J, Fan S, Xie W, Yang Z, Si T. Directed evolution of a cyclodipeptide synthase with new activities via label-free mass spectrometric screening. Chem Sci 2022; 13:7581-7586. [PMID: 35872818 PMCID: PMC9241961 DOI: 10.1039/d2sc01637k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/01/2022] [Indexed: 12/12/2022] Open
Abstract
Directed evolution is a powerful approach to engineer enzymes via iterative creation and screening of variant libraries. However, assay development for high-throughput mutant screening remains challenging, particularly for new catalytic activities. Mass spectrometry (MS) analysis is label-free and well suited for untargeted discovery of new enzyme products but is traditionally limited by slow speed. Here we report an automated workflow for directed evolution of new enzymatic activities via high-throughput library creation and label-free MS screening. For a proof of concept, we chose to engineer a cyclodipeptide synthase (CDPS) that synthesizes diketopiperazine (DKP) compounds with therapeutic potential. In recombinant Escherichia coli, site-saturation mutagenesis (SSM) and error-prone PCR (epPCR) libraries expressing CDPS mutants were automatically created and cultivated on an integrated work cell. Culture supernatants were then robotically processed for matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) MS analysis at a rate of 5 s per sample. The resulting mass spectral data were processed via custom computational algorithms, which performed a multivariant analysis of 108 theoretical mass-to-charge (m/z) values of 190 possible DKP molecules within a mass window of 115–373 Da. An F186L CDPS mutant was isolated to produce cyclo(l-Phe–l-Val), which is undetectable in the product profile of the wild-type enzyme. This robotic, label-free MS screening approach may be generally applicable to engineering other enzymes with new activities in high throughput. A robotic workflow for directed evolution of new enzymatic activities via high-throughput library creation and label-free MS screening.![]()
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Affiliation(s)
- Songya Zhang
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Jing Zhu
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Shuai Fan
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 1000050 China
| | - Wenhao Xie
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhaoyong Yang
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College Beijing 1000050 China
| | - Tong Si
- CAS Key Lib Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
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8
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Canu N, Moutiez M, Belin P, Gondry M. Cyclodipeptide synthases: a promising biotechnological tool for the synthesis of diverse 2,5-diketopiperazines. Nat Prod Rep 2021; 37:312-321. [PMID: 31435633 DOI: 10.1039/c9np00036d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: Up to mid-2019 Cyclodipeptide synthases (CDPSs) catalyse the formation of cyclodipeptides using aminoacylated-tRNA as substrates. The recent characterization of large sets of CDPSs has revealed that they can produce highly diverse products, and therefore have great potential for use in the production of different 2,5-diketopiperazines (2,5-DKPs). Sequence similarity networks (SSNs) are presented as a new, efficient way of classifying CDPSs by specificity and identifying new CDPS likely to display novel specificities. Several strategies for further increasing the diversity accessible with these enzymes are discussed here, including the incorporation of non-canonical amino acids by CDPSs and use of the remarkable diversity of 2,5-DKP-tailoring enzymes discovered in recent years.
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Affiliation(s)
- Nicolas Canu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
| | - Mireille Moutiez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
| | - Pascal Belin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
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9
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Canu N, Tellier C, Babin M, Thai R, Ajel I, Seguin J, Cinquin O, Vinck R, Moutiez M, Belin P, Cintrat JC, Gondry M. Flexizyme-aminoacylated shortened tRNAs demonstrate that only the aminoacylated acceptor arms of the two tRNA substrates are required for cyclodipeptide synthase activity. Nucleic Acids Res 2021; 48:11615-11625. [PMID: 33095883 PMCID: PMC7672478 DOI: 10.1093/nar/gkaa903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 01/15/2023] Open
Abstract
Cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs (AA-tRNAs) to catalyse cyclodipeptide formation in a ping-pong mechanism. Despite intense studies of these enzymes in past years, the tRNA regions of the two substrates required for CDPS activity are poorly documented, mainly because of two limitations. First, previously studied CDPSs use two identical AA-tRNAs to produce homocyclodipeptides, thus preventing the discriminative study of the binding of the two substrates. Second, the range of tRNA analogues that can be aminoacylated by aminoacyl-tRNA synthetases is limited. To overcome the limitations, we studied a new model CDPS that uses two different AA-tRNAs to produce an heterocyclodipeptide. We also developed a production pipeline for the production of purified shortened AA-tRNA analogues (AA-minitRNAs). This method combines the use of flexizymes to aminoacylate a diversity of minitRNAs and their subsequent purifications by anion-exchange chromatography. Finally, we were able to show that aminoacylated molecules mimicking the entire acceptor arms of tRNAs were as effective a substrate as entire AA-tRNAs, thereby demonstrating that the acceptor arms of the two substrates are the only parts of the tRNAs required for CDPS activity. The method developed in this study should greatly facilitate future investigations of the specificity of CDPSs and of other AA-tRNAs-utilizing enzymes.
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Affiliation(s)
- Nicolas Canu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Carine Tellier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Robert Thai
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191, Gif-sur-Yvette, France
| | - Inès Ajel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Jérôme Seguin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Olivier Cinquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France.,Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191 Gif-sur-Yvette, France
| | - Robin Vinck
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191, Gif-sur-Yvette, France.,Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191 Gif-sur-Yvette, France
| | - Mireille Moutiez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Pascal Belin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
| | - Jean-Christophe Cintrat
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, 91191 Gif-sur-Yvette, France
| | - Muriel Gondry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette cedex, France
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10
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Harding CJ, Sutherland E, Hanna JG, Houston DR, Czekster CM. Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme. RSC Chem Biol 2021; 2:230-240. [PMID: 33937777 PMCID: PMC8084100 DOI: 10.1039/d0cb00142b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) produce a variety of cyclic dipeptide products by utilising two aminoacylated tRNA substrates. We sought to investigate the minimal requirements for substrate usage in this class of enzymes as the relationship between CDPSs and their substrates remains elusive. Here, we investigated the Bacillus thermoamylovorans enzyme, BtCDPS, which synthesises cyclo(l-Leu–l-Leu). We systematically tested where specificity arises and, in the process, uncovered small molecules (activated amino esters) that will suffice as substrates, although catalytically poor. We solved the structure of BtCDPS to 1.7 Å and combining crystallography, enzymatic assays and substrate docking experiments propose a model for how the minimal substrates interact with the enzyme. This work is the first report of a CDPS enzyme utilizing a molecule other than aa-tRNA as a substrate; providing insights into substrate requirements and setting the stage for the design of improved simpler substrates. Cyclodipeptide synthases recognize a minimalistic substrate to produce cyclic dipeptides in a tRNA-independent manner.![]()
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Affiliation(s)
- Christopher J Harding
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
| | - Emmajay Sutherland
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
| | - Jane G Hanna
- Arab Academy for Science, Technology, and Maritime Transport (AASTMT) Cairo Campus Egypt
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh Waddington 1 Building, King's Buildings Edinburgh EH9 3BF UK
| | - Clarissa M Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews Fife KY16 9ST UK
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11
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Croitoru A, Babin M, Myllykallio H, Gondry M, Aleksandrov A. Cyclodipeptide Synthases of the NYH Subfamily Recognize tRNA Using an α-Helix Enriched with Positive Residues. Biochemistry 2020; 60:64-76. [PMID: 33331769 DOI: 10.1021/acs.biochem.0c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclodipeptide synthases (CDPSs) perform nonribosomal protein synthesis using two aminoacyl-tRNA substrates to produce cyclodipeptides. At present, there are no structural details of the CDPS:tRNA interaction available. Using AlbC, a CDPS that produces cyclo(l-Phe-l-Phe), the interaction between AlbC and its Phe-tRNA substrate was investigated. Simulations of models of the AlbC:tRNA complex, proposed by rigid-body docking or homology modeling, demonstrated that interactions with residues of an AlbC α-helix, α4, significantly contribute to the free energy of binding of AlbC to tRNA. Individual residue contributions to the tRNA binding free energy of the discovered binding mode explain well the available biochemical data, and the results of in vivo assay experiments performed in this work and guided by simulations. In molecular dynamics simulations, the phenylalanyl group predominantly occupied the two positions observed in the experimental structure of AlbC in the dipeptide intermediate state, suggesting that tRNAs of the first and second substrates interact with AlbC in a similar manner. Overall, given the high degree of sequence and structural similarity among the members of the CDPS NYH protein subfamily, the mechanism of the protein:tRNA interaction is expected to be pertinent to a wide range of proteins interacting with tRNA.
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Affiliation(s)
- Anastasia Croitoru
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
| | - Morgan Babin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, F-91128 Palaiseau, France
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12
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Yuan S, Yong X, Zhao T, Li Y, Liu J. Research Progress of the Biosynthesis of Natural Bio-Antibacterial Agent Pulcherriminic Acid in Bacillus. Molecules 2020; 25:E5611. [PMID: 33260656 PMCID: PMC7731078 DOI: 10.3390/molecules25235611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 11/16/2022] Open
Abstract
Pulcherriminic acid is a cyclic dipeptide found mainly in Bacillus and yeast. Due to the ability of pulcherriminic acid to chelate Fe3+ to produce reddish brown pulcherrimin, microorganisms capable of synthesizing pulcherriminic acid compete with other microorganisms for environmental iron ions to achieve bacteriostatic effects. Therefore, studying the biosynthetic pathway and their enzymatic catalysis, gene regulation in the process of synthesis of pulcherriminic acid in Bacillus can facilitate the industrial production, and promote the wide application in food, agriculture and medicine industries. After initially discussing, this review summarizes current research on the synthesis of pulcherriminic acid by Bacillus, which includes the crystallization of key enzymes, molecular catalytic mechanisms, regulation of synthetic pathways, and methods to improve efficiency in synthesizing pulcherriminic acid and its precursors. Finally, possible applications of pulcherriminic acid in the fermented food, such as Chinese Baijiu, applying combinatorial biosynthesis will be summarized.
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Affiliation(s)
- Siqi Yuan
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Luzhou Laojiao Group Co. Ltd., Airentang Square, Jiangyang District, Luzhou 646000, China
| | - Xihao Yong
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Ting Zhao
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Yuan Li
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
| | - Jun Liu
- Sichuan University of Science & Engineering, Xueyuan Street 180#, Huixing Rd., Zigong 643000, China; (S.Y.); (X.Y.); (T.Z.)
- Wuliangye Group Co. Ltd., No. 150 Minjiang West Road, Yibin 644000, China
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13
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Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E. Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. RNA (NEW YORK, N.Y.) 2020; 26:1589-1602. [PMID: 32680846 PMCID: PMC7566563 DOI: 10.1261/rna.075184.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNAPhe to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNAPhe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jérôme Seguin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Muriel Gondry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
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14
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Zhang Z, van der Donk WA. Nonribosomal Peptide Extension by a Peptide Amino-Acyl tRNA Ligase. J Am Chem Soc 2019; 141:19625-19633. [PMID: 31751505 DOI: 10.1021/jacs.9b07111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The catalytic use of a small peptide scaffold for the biosynthesis of amino acid-derived natural products is a recently discovered new biosynthetic strategy. During this process, a peptide-amino acyl tRNA ligase (PEARL) adds amino acids to the C-terminus of a small peptide scaffold in an ATP- and tRNA-dependent process. The mechanism of this unusual transformation is currently not known. In this study, we present a detailed biochemical and mechanistic study of TglB (UniProtKB-F3HQJ1), a PEARL that catalyzes the addition of Cys to the C-terminus of the peptide TglA in the biosynthesis of 3-thiaglutamate in the plant pathogen Pseudomonas syringae. TglB recognizes several important residues close to the C-terminus of TglA to perform its activity and is tolerant with respect to the last amino acid of its substrate peptide. The enzyme recognizes the acceptor stem of tRNACys, as micro- and minihelices, truncated versions of full-length tRNACys that contain the acceptor stem, were also accepted. Mutagenesis of conserved residues in TglB identified several key residues for catalysis and did not support the possibility of TglB adopting various ping-pong mechanisms to catalyze the amino acid addition reaction. Using isotopic labeling studies, we demonstrate that ATP is used to directly phosphorylate the C-terminal carboxylate of TglA. Collectively, the data support a general mechanism for the amino acid addition reaction catalyzed by this class of enzyme.
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Affiliation(s)
- Zhengan Zhang
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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15
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Strategy for the Biosynthesis of Short Oligopeptides: Green and Sustainable Chemistry. Biomolecules 2019; 9:biom9110733. [PMID: 31766233 PMCID: PMC6920838 DOI: 10.3390/biom9110733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Short oligopeptides are some of the most promising and functionally important amide bond-containing components, with widespread applications. Biosynthesis of these oligopeptides may potentially become the ultimate strategy because it has better cost efficiency and environmental-friendliness than conventional solid phase peptide synthesis and chemo-enzymatic synthesis. To successfully apply this strategy for the biosynthesis of structurally diverse amide bond-containing components, the identification and selection of specific biocatalysts is extremely important. Given that perspective, this review focuses on the current knowledge about the typical enzymes that might be potentially used for the synthesis of short oligopeptides. Moreover, novel enzymatic methods of producing desired peptides via metabolic engineering are highlighted. It is believed that this review will be helpful for technological innovation in the production of desired peptides.
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16
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Gomes NGM, Pereira RB, Andrade PB, Valentão P. Double the Chemistry, Double the Fun: Structural Diversity and Biological Activity of Marine-Derived Diketopiperazine Dimers. Mar Drugs 2019; 17:md17100551. [PMID: 31569621 PMCID: PMC6835637 DOI: 10.3390/md17100551] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/14/2022] Open
Abstract
While several marine natural products bearing the 2,5-diketopiperazine ring have been reported to date, the unique chemistry of dimeric frameworks appears to remain neglected. Frequently reported from marine-derived strains of fungi, many naturally occurring diketopiperazine dimers have been shown to display a wide spectrum of pharmacological properties, particularly within the field of cancer and antimicrobial therapy. While their structures illustrate the unmatched power of marine biosynthetic machinery, often exhibiting unsymmetrical connections with rare linkage frameworks, enhanced binding ability to a variety of pharmacologically relevant receptors has been also witnessed. The existence of a bifunctional linker to anchor two substrates, resulting in a higher concentration of pharmacophores in proximity to recognition sites of several receptors involved in human diseases, portrays this group of metabolites as privileged lead structures for advanced pre-clinical and clinical studies. Despite the structural novelty of various marine diketopiperazine dimers and their relevant bioactive properties in several models of disease, to our knowledge, this attractive subclass of compounds is reviewed here for the first time.
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Affiliation(s)
- Nelson G M Gomes
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, nº 228, Porto 4050-313, Portugal.
| | - Renato B Pereira
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, nº 228, Porto 4050-313, Portugal.
| | - Paula B Andrade
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, nº 228, Porto 4050-313, Portugal.
| | - Patrícia Valentão
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, R. Jorge Viterbo Ferreira, nº 228, Porto 4050-313, Portugal.
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17
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Shi J, Xu X, Zhao EJ, Zhang B, Li W, Zhao Y, Jiao RH, Tan RX, Ge HM. Genome Mining and Enzymatic Total Biosynthesis of Purincyclamide. Org Lett 2019; 21:6825-6829. [DOI: 10.1021/acs.orglett.9b02461] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Er Juan Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wei Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
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18
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Dubois P, Correia I, Le Chevalier F, Dubois S, Jacques I, Canu N, Moutiez M, Thai R, Gondry M, Lequin O, Belin P. Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids. Sci Rep 2019; 9:9208. [PMID: 31239480 PMCID: PMC6592928 DOI: 10.1038/s41598-019-45519-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/05/2019] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole diketopiperazine (DKP) alkaloids are important bioactive molecules or their precursors. In the context of synthetic biology, efficient means for their biological production would increase their chemical diversification and the discovery of novel bioactive compounds. Here, we prove the suitability of the Escherichia coli chassis for the production of prenylated indole DKP alkaloids. We used enzyme combinations not found in nature by co-expressing bacterial cyclodipeptide synthases (CDPSs) that assemble the DKP ring and fungal prenyltransferases (PTs) that transfer the allylic moiety from the dimethylallyl diphosphate (DMAPP) to the indole ring of tryptophanyl-containing cyclodipeptides. Of the 11 tested combinations, seven resulted in the production of eight different prenylated indole DKP alkaloids as determined by LC-MS/MS and NMR characterization. Two were previously undescribed. Engineering E. coli by introducing a hybrid mevalonate pathway for increasing intracellular DMAPP levels improved prenylated indole DKP alkaloid production. Purified product yields of 2–26 mg/L per culture were obtained from culture supernatants. Our study paves the way for the bioproduction of novel prenylated indole DKP alkaloids in a tractable chassis that can exploit the cyclodipeptide diversity achievable with CDPSs and the numerous described PT activities.
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Affiliation(s)
- Pavlina Dubois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Isabelle Correia
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Fabien Le Chevalier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | | | - Isabelle Jacques
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France.,Isabelle B. Jacques, APTEEUS, Institut Pasteur de Lille, Lille, France
| | - Nicolas Canu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Mireille Moutiez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Robert Thai
- SIMOPRO, CEA, 91198, Gif-sur-Yvette, cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France.
| | - Pascal Belin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France.
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19
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Borgman P, Lopez RD, Lane AL. The expanding spectrum of diketopiperazine natural product biosynthetic pathways containing cyclodipeptide synthases. Org Biomol Chem 2019; 17:2305-2314. [PMID: 30688950 DOI: 10.1039/c8ob03063d] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microorganisms are remarkable chemists, with enzymes as their tools for executing multi-step syntheses to yield myriad natural products. Microbial synthetic aptitudes are illustrated by the structurally diverse 2,5-diketopiperazine (DKP) family of bioactive nonribosomal peptide natural products. Nonribosomal peptide synthetases (NRPSs) have long been recognized as catalysts for formation of DKP scaffolds from two amino acid substrates. Cyclodipeptide synthases (CDPSs) are more recently recognized catalysts of DKP assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. CDPS-encoding genes are typically found in genomic neighbourhoods with genes encoding additional biosynthetic enzymes. These include oxidoreductases, cytochrome P450s, prenyltransferases, methyltransferases, and cyclases, which equip the DKP scaffold with groups that diversify chemical structures and confer biological activity. These tailoring enzymes have been characterized from nine CDPS-containing biosynthetic pathways to date, including four during the last year. In this review, we highlight these nine DKP pathways, emphasizing recently characterized tailoring reactions and connecting new developments to earlier findings. Featured pathways encompass a broad spectrum of chemistry, including the formation of challenging C-C and C-O bonds, regioselective methylation, a unique indole alkaloid DKP prenylation strategy, and unprecedented peptide-nucleobase bond formation. These CDPS-containing pathways also provide intriguing models of metabolic pathway evolution across related and divergent microorganisms, and open doors to synthetic biology approaches for generation of DKP combinatorial libraries. Further, bioinformatics analyses support that much unique genetically encoded DKP tailoring potential remains unexplored, suggesting opportunities for further expansion of Nature's biosynthetic spectrum. Together, recent studies of DKP pathways demonstrate the chemical ingenuity of microorganisms, highlight the wealth of unique enzymology provided by bacterial biosynthetic pathways, and suggest an abundance of untapped biosynthetic potential for future exploration.
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Affiliation(s)
- Paul Borgman
- Department of Chemistry, University of North Florida, 1 UNF Dr, Jacksonville, FL 32224, USA.
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20
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Abstract
Communication between and within communities of cells or independent organisms is a crucial prerequisite for species survival. In response to variations in the extracellular environment, the collective behavior of cell populations can be coordinated by regulating community-level gene expression. This mechanism is strongly conserved during evolution, being shared both by bacterial communities and central nervous system cells. Notably, cyclic dipeptides (CDPs) are molecules that are implicated in these quorum sensing behaviors in both settings. Bacteria coordinate their collective behavior by producing CDPs (quorum sensing inducers) that enhance the capacity of individual members of the community to detect these signals and thus amplify the community-level response. In this review, we highlight recent data indicating that strikingly similar molecular mechanisms control communications between glial and neuronal cells to maintain homeostasis in the central nervous system, with a specific focus on the role of the thyrotropin-releasing hormone—derived CDP cyclo(His-Pro) in the protection against neurotoxic insults.
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21
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Structural basis for partition of the cyclodipeptide synthases into two subfamilies. J Struct Biol 2018; 203:17-26. [DOI: 10.1016/j.jsb.2018.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 11/19/2022]
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22
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Abstract
The formation of ordered nanostructures by molecular self-assembly of proteins and peptides represents one of the principal directions in nanotechnology. Indeed, polyamides provide superior features as materials with diverse physical properties. A reductionist approach allowed the identification of extremely short peptide sequences, as short as dipeptides, which could form well-ordered amyloid-like β-sheet-rich assemblies comparable to supramolecular structures made of much larger proteins. Some of the peptide assemblies show remarkable mechanical, optical, and electrical characteristics. Another direction of reductionism utilized a natural noncoded amino acid, α-aminoisobutryic acid, to form short superhelical assemblies. The use of this exceptional helix inducer motif allowed the fabrication of single heptad repeats used in various biointerfaces, including their use as surfactants and DNA-binding agents. Two additional directions of the reductionist approach include the use of peptide nucleic acids (PNAs) and coassembly techniques. The diversified accomplishments of the reductionist approach, as well as the exciting future advances it bears, are discussed.
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Affiliation(s)
- Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, Department of Materials Science and Engineering, Tel Aviv University, Tel Aviv 6997801, Israel;
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23
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Schmitt E, Bourgeois G, Gondry M, Aleksandrov A. Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue. Sci Rep 2018; 8:7031. [PMID: 29728603 PMCID: PMC5935735 DOI: 10.1038/s41598-018-25479-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/20/2018] [Indexed: 11/23/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) form various cyclodipeptides from two aminoacyl tRNAs via a stepwise mechanism with the formation of a dipeptidyl enzyme intermediate. As a final step of the catalytic reaction, the dipeptidyl group undergoes intramolecular cyclization to generate the target cyclodipeptide product. In this work, we investigated the cyclization reaction in the cyclodipeptide synthase AlbC using QM/MM methods and free energy simulations. The results indicate that the catalytic Y202 residue is in its neutral protonated form, and thus, is not likely to serve as a general base during the reaction. We further demonstrate that the reaction relies on the conserved residue Y202 serving as a proton relay, and the direct proton transfer from the amino group to S37 of AlbC is unlikely. Calculations reveal that the hydroxyl group of tyrosine is more suitable for the proton transfer than hydroxyl groups of other amino acids, such as serine and threonine. Results also show that the residues E182, N40, Y178 and H203 maintain the correct conformation of the dipeptide needed for the cyclization reaction. The mechanism discovered in this work relies on the amino groups conserved among the entire CDPS family and, thus is expected to be universal among CDPSs.
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Affiliation(s)
- Emmanuelle Schmitt
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, F-91128, Palaiseau, France
| | - Gabrielle Bourgeois
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, F-91128, Palaiseau, France
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, F-91128, Palaiseau, France.
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24
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Liu J, Yu H, Li SM. Expanding tryptophan-containing cyclodipeptide synthase spectrum by identification of nine members from Streptomyces strains. Appl Microbiol Biotechnol 2018; 102:4435-4444. [PMID: 29574613 DOI: 10.1007/s00253-018-8908-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/28/2018] [Indexed: 02/05/2023]
Abstract
Cyclodipeptide synthases (CDPSs) comprise normally 200-300 amino acid residues and are mainly found in bacteria. They hijack aminoacyl-tRNAs from the ribosomal machinery for cyclodipeptide formation. In this study, nine new CDPS genes from eight Streptomyces strains were cloned into pET28a vector and expressed in Escherichia coli. Structural elucidation of the isolated products led to the identification of one cyclo-L-Trp-L-Leu, two cyclo-L-Trp-L-Pro, and three cyclo-L-Trp-L-Trp synthases. Other three CDPSs produce cyclo-L-Trp-L-Ala or cyclo-L-Trp-L-Tyr as the major cyclodipeptide. Total product yields of 46 to 211 mg/L E. coli culture were obtained. Our findings represent rare examples of CDPS family derived from actinobacteria that form various tryptophan-containing cyclodipeptides. Furthermore, this study highlights the potential of the microbial machinery for tryptophan-containing cyclodipeptide biosynthesis and provides valid experimental basis for further combination of these CDPS genes with other modification genes in synthetic biology.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Huili Yu
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.
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25
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Canu N, Belin P, Thai R, Correia I, Lequin O, Seguin J, Moutiez M, Gondry M. Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases. Angew Chem Int Ed Engl 2018; 57:3118-3122. [DOI: 10.1002/anie.201712536] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Nicolas Canu
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Pascal Belin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Robert Thai
- SIMOPRO; CEA-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Isabelle Correia
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Olivier Lequin
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Jérôme Seguin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mireille Moutiez
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Muriel Gondry
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
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26
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Canu N, Belin P, Thai R, Correia I, Lequin O, Seguin J, Moutiez M, Gondry M. Incorporation of Non-canonical Amino Acids into 2,5-Diketopiperazines by Cyclodipeptide Synthases. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Nicolas Canu
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Pascal Belin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Robert Thai
- SIMOPRO; CEA-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Isabelle Correia
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Olivier Lequin
- Sorbonne Université; Ecole Normale Supérieure; PSL University; CNRS; Laboratoire des Biomolécules (LBM); 75005 Paris France
| | - Jérôme Seguin
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mireille Moutiez
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Muriel Gondry
- Institute for Integrated Biology of the Cell (I2BC); CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
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27
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Gondry M, Jacques IB, Thai R, Babin M, Canu N, Seguin J, Belin P, Pernodet JL, Moutiez M. A Comprehensive Overview of the Cyclodipeptide Synthase Family Enriched with the Characterization of 32 New Enzymes. Front Microbiol 2018; 9:46. [PMID: 29483897 PMCID: PMC5816076 DOI: 10.3389/fmicb.2018.00046] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) use as substrates two amino acids activated as aminoacyl-tRNAs to synthesize cyclodipeptides in secondary metabolites biosynthetic pathways. Since the first description of a CDPS in 2002, the number of putative CDPSs in databases has increased exponentially, reaching around 800 in June 2017. They are likely to be involved in numerous biosynthetic pathways but the diversity of their products is still under-explored. Here, we describe the activity of 32 new CDPSs, bringing the number of experimentally characterized CDPSs to about 100. We detect 16 new cyclodipeptides, one of which containing an arginine which has never been observed previously. This brings to 75 the number of cyclodipeptides formed by CDPSs out of the possible 210 natural ones. We also identify several consensus sequences related to the synthesis of a specific cyclodipeptide, improving the predictive model of CDPS specificity. The improved prediction method enables to propose the main product synthesized for about 80% of the CDPS sequences available in databases and opens the way for the deciphering of CDPS-dependent pathways. Analysis of phylum distribution and predicted activity for all CDPSs identified in databases shows that the experimentally characterized set is representative of the whole family. Our work also demonstrates that some cyclodipeptides, precursors of diketopiperazines with interesting pharmacological properties and previously described as being synthesized by fungal non-ribosomal peptide synthetases, can also be produced by CDPSs in bacteria.
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Affiliation(s)
- Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Isabelle B Jacques
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Thai
- SIMOPRO, Institut Frédéric Joliot, CEA-Saclay, Gif-sur-Yvette, France
| | - Morgan Babin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nicolas Canu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jérôme Seguin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pascal Belin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mireille Moutiez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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28
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Stamatelopoulou E, Agriopoulou S, Dourtoglou E, Chatzilazarou A, Drosou F, Marinea M, Dourtoglou V. Diketopiperazines in wines. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/09571264.2018.1433137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Eygenia Stamatelopoulou
- Department of Food Technology, Technological Educational Institute of Peloponnese, Kalamata, Greece
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
| | - Sofia Agriopoulou
- Department of Food Technology, Technological Educational Institute of Peloponnese, Kalamata, Greece
| | - Euthalia Dourtoglou
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
| | - Arhontoula Chatzilazarou
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
| | - Fotini Drosou
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
| | - Marina Marinea
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
| | - Vassilis Dourtoglou
- Department of Oenology and Beverage Technology, Technological Educational Institute of Athens, Athens, Greece
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29
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Global analysis of prokaryotic tRNA-derived cyclodipeptide biosynthesis. BMC Genomics 2018; 19:45. [PMID: 29334896 PMCID: PMC5767969 DOI: 10.1186/s12864-018-4435-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery. RESULTS We developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures. We leveraged this tool to conduct a global analysis of tRNA-derived cyclodipeptide biosynthesis in 93,107 prokaryotic genomes, and compared predicted cyclodipeptides to known cyclodipeptide synthase products and all known chemically characterized cyclodipeptides. By integrating predicted chemical structures and gene cluster architectures, we created a unified map of known and unknown genetically encoded cyclodipeptides. CONCLUSIONS Our analysis suggests that sizeable regions of the chemical space encoded within sequenced prokaryotic genomes remain unexplored. Our map of the landscape of genetically encoded cyclodipeptides provides candidates for targeted discovery of novel compounds. The integration of our pipeline into a user-friendly web application provides a resource for further discovery of cyclodipeptides in newly sequenced prokaryotic genomes.
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Brockmeyer K, Li SM. Mutations of Residues in Pocket P1 of a Cyclodipeptide Synthase Strongly Increase Product Formation. JOURNAL OF NATURAL PRODUCTS 2017; 80:2917-2922. [PMID: 29064250 DOI: 10.1021/acs.jnatprod.7b00430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Expression of a cyclodipeptide synthase gene from Nocardiopsis prasina (CDPS-Np) in Escherichia coli resulted in the formation of cyclo-(l-Tyr-l-Tyr) (1) as the minor and cyclo-(l-Tyr-l-Phe) (2) as the major products. Site-directed mutagenesis revealed a strong influence on product accumulation of the amino acid residues in pocket P1. An 8-fold increase in product formation for 1 and 10-fold for 2 were detected in the double mutant T82V_Y196F compared with the wild type.
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Affiliation(s)
- Kirsten Brockmeyer
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
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31
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Mishra AK, Choi J, Choi SJ, Baek KH. Cyclodipeptides: An Overview of Their Biosynthesis and Biological Activity. Molecules 2017; 22:molecules22101796. [PMID: 29065531 PMCID: PMC6151668 DOI: 10.3390/molecules22101796] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/06/2023] Open
Abstract
Cyclodipeptides (CDP) represent a diverse family of small, highly stable, cyclic peptides that are produced as secondary functional metabolites or side products of protein metabolism by bacteria, fungi, and animals. They are widespread in nature, and exhibit a broad variety of biological and pharmacological activities. CDP synthases (CDPSs) and non-ribosomal peptide synthetases (NRPSs) catalyze the biosynthesis of the CDP core structure, which is further modified by tailoring enzymes often associated with CDP biosynthetic gene clusters. In this review, we provide a comprehensive summary of CDP biosynthetic pathways and modifying enzymes. We also discuss the biological properties of some known CDPs and their possible applications in metabolic engineering.
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Affiliation(s)
- Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Jaehyuk Choi
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
| | - Seong-Jin Choi
- Department of Biotechnology, Daegu Catholic University, Gyeongsan 38430, Korea.
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea.
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32
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Zhao Q, Yung TK, Wang X, Tam WY. Correction of numerical aperture effect on reflection phase measurement using a thick-gap Fabry-Perot etalon. APPLIED OPTICS 2017; 56:4392-4397. [PMID: 29047868 DOI: 10.1364/ao.56.004392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We propose a method for the measurement of the reflection phase using a thick-gap Fabry-Perot (FP) etalon interferometry technique with correction for the numerical aperture effect of the optical setup. The setup is first calibrated using a known sample by comparing the reflectance from a two-beam interference model for the FP etalon with experimental data. We then apply the correction to a sample of interest and obtain the reflection phase of the sample. Our method can be used to measure the reflection phase of a small sample and could lead to practical applications in optical characterization of metamaterials. Moreover, the principle of our approach could be generalized to other systems in the correction of numerical aperture effect due to microscopic objectives.
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33
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Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017; 7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022] Open
Abstract
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.
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34
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Jakubowski H. Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †. Life (Basel) 2017; 7:life7010006. [PMID: 28208756 PMCID: PMC5370406 DOI: 10.3390/life7010006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
- Department of Biochemistry and Biotechnology, University of Life Sciences, Poznan 60-632, Poland.
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35
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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36
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Caetano-Anollés D, Caetano-Anollés G. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. Life (Basel) 2016; 6:life6040043. [PMID: 27918435 PMCID: PMC5198078 DOI: 10.3390/life6040043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 01/10/2023] Open
Abstract
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, 24306 Plön, Germany.
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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37
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Ulrich EC, van der Donk WA. Cameo appearances of aminoacyl-tRNA in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:29-36. [PMID: 27599269 PMCID: PMC5161580 DOI: 10.1016/j.cbpa.2016.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 11/19/2022]
Abstract
The breadth of unprecedented enzymatic reactions performed during the formation of microbial natural products has continued to expand as new biosynthetic gene clusters are unearthed by genome mining. Enzymes that use aminoacyl-tRNA (aa-tRNA) outside of the translation machinery have been known for decades, and accounts of their use in natural product biosynthesis are just beginning to accumulate. This review will highlight the recent discoveries and advances in our mechanistic understanding of aa-tRNA-dependent enzymes that play key roles in the biosynthesis of a growing number of microbial natural products.
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Affiliation(s)
- Emily C Ulrich
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.
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38
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Spectrophotometric assays for monitoring tRNA aminoacylation and aminoacyl-tRNA hydrolysis reactions. Methods 2016; 113:3-12. [PMID: 27780756 DOI: 10.1016/j.ymeth.2016.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases play a central role in protein synthesis, catalyzing the attachment of amino acids to their cognate tRNAs. Here, we describe a spectrophotometric assay for tyrosyl-tRNA synthetase in which the Tyr-tRNA product is cleaved, regenerating the tRNA substrate. As tRNA is the limiting substrate in the assay, recycling it substantially increases the sensitivity of the assay while simultaneously reducing its cost. The tRNA aminoacylation reaction is monitored spectrophotometrically by coupling the production of AMP to the conversion of NAD+ to NADH. We have adapted the tyrosyl-tRNA synthetase assay to monitor: (1) aminoacylation of tRNA by l- or d-tyrosine, (2) cyclodipeptide formation by cyclodipeptide synthases, (3) hydrolysis of d-aminoacyl-tRNAs by d-tyrosyl-tRNA deacylase, and (4) post-transfer editing by aminoacyl-tRNA synthetases. All of these assays are continuous and homogenous, making them amenable for use in high-throughput screens of chemical libraries. In the case of the cyclodipeptide synthase, d-tyrosyl-tRNA deacylase, and post-transfer editing assays, the aminoacyl-tRNAs are generated in situ, avoiding the need to synthesize and purify aminoacyl-tRNA substrates prior to performing the assays. Lastly, we describe how the tyrosyl-tRNA synthetase assay can be adapted to monitor the activity of other aminoacyl-tRNA synthetases and how the approach to regenerating the tRNA substrate can be used to increase the sensitivity and decrease the cost of commercially available aminoacyl-tRNA synthetase assays.
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39
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Yung TK, Gao W, Leung HM, Zhao Q, Wang X, Tam WY. Measurement of reflection phase using thick-gap Fabry-Perot etalon. APPLIED OPTICS 2016; 55:7301-7306. [PMID: 27661366 DOI: 10.1364/ao.55.007301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report measurement of the reflection phase of a dielectric (glass)/titanium (Ti) surface in the visible wavelength using a thick-gap Fabry-Perot (FP) interferometry technique. Using a two-beam interference model for the reflection peaks and troughs of the FP etalon, we obtain the air-gap spacing of the etalon and, more importantly, the reflection phase of the etalon substrate. We find systematic dependence of the as-measured reflection phase on the air-gap spacing due to the numerical aperture effect of the measuring objective. However, the relative reflection phase of Ti with respect to glass is independent of the air-gap spacing. As a demonstration of our approach in the optical characterization of small metamaterial samples, we also measure the reflection phase of a micron-sized 2D Au sawtooth nanoarray. The experiment is in good agreement with the model simulation.
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40
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James ED, Knuckley B, Alqahtani N, Porwal S, Ban J, Karty JA, Viswanathan R, Lane AL. Two Distinct Cyclodipeptide Synthases from a Marine Actinomycete Catalyze Biosynthesis of the Same Diketopiperazine Natural Product. ACS Synth Biol 2016; 5:547-53. [PMID: 26641496 DOI: 10.1021/acssynbio.5b00120] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diketopiperazine natural products are structurally diverse and offer many biological activities. Cyclodipeptide synthases (CDPSs) were recently unveiled as a novel enzyme family that employs aminoacyl-tRNAs as substrates for 2,5-diketopiperazine assembly. Here, the Nocardiopsis sp. CMB-M0232 genome is predicted to encode two CDPSs, NozA and NcdA. Metabolite profiles from E. coli expressing these genes and assays with purified recombinant enzymes revealed that NozA and NcdA catalyze cyclo(l-Trp-l-Trp) (1) biosynthesis from tryptophanyl-tRNA and do not accept other aromatic aminoacyl-tRNA substrates. Fidelity is uncommon among characterized CDPSs, making NozA and NcdA important CDPS family additions. Further, 1 was previously supported as a biosynthetic precursor of the nocardioazines; the current study suggests that Nocardiopsis sp. may derive this precursor from both NozA and NcdA. This study offers a rare example of a single bacterium encoding multiple phylogenetically distinct enzymes that yield the same secondary metabolite and provides tools for chemoenzymatic syntheses of indole alkaloid diketopiperazines.
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Affiliation(s)
- Elle D. James
- Department of Chemistry, University of North Florida, 1 UNF
Drive, Jacksonville, Florida 32224, United States
| | - Bryan Knuckley
- Department of Chemistry, University of North Florida, 1 UNF
Drive, Jacksonville, Florida 32224, United States
| | - Norah Alqahtani
- Department of Chemistry, Case Western Reserve University, Millis Science
Center Room 216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
| | - Suheel Porwal
- Department of Chemistry, Case Western Reserve University, Millis Science
Center Room 216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
| | - Jisun Ban
- Department of Chemistry, University of North Florida, 1 UNF
Drive, Jacksonville, Florida 32224, United States
| | - Jonathan A. Karty
- Mass Spectrometry Facility, Indiana University, Department of Chemistry, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Rajesh Viswanathan
- Department of Chemistry, Case Western Reserve University, Millis Science
Center Room 216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
| | - Amy L. Lane
- Department of Chemistry, University of North Florida, 1 UNF
Drive, Jacksonville, Florida 32224, United States
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41
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Jakubowski H. Aminoacyl-tRNA synthetases and the evolution of coded peptide synthesis: the Thioester World. FEBS Lett 2016; 590:469-81. [PMID: 26831912 DOI: 10.1002/1873-3468.12085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 11/10/2022]
Abstract
Coded peptide synthesis must have been preceded by a prebiotic stage, in which thioesters played key roles. Fossils of the Thioester World are found in extant aminoacyl-tRNA synthetases (AARSs). Indeed, studies of the editing function reveal that AARSs have a thiol-binding site in their catalytic modules. The thiol-binding site confers the ability to catalyze aminoacyl~coenzyme A thioester synthesis and peptide bond formation. Genomic comparisons show that AARSs are structurally related to proteins involved in sulfur and coenzyme A metabolisms and peptide bond synthesis. These findings point to the origin of the amino acid activation and peptide bond synthesis functions in the Thioester World and suggest that the present-day AARSs had originated from ancestral forms that were involved in noncoded thioester-dependent peptide synthesis.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health, Newark, NJ, USA.,Institute of Bioorganic Chemistry, Poznań, Poland.,Department of Biochemistry and Biotechnology, University of Life Sciences, Poznań, Poland
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42
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Analysis of 51 cyclodipeptide synthases reveals the basis for substrate specificity. Nat Chem Biol 2015; 11:721-7. [DOI: 10.1038/nchembio.1868] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 06/05/2015] [Indexed: 11/08/2022]
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