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Sengupta S, Pabbaraja S, Mehta G. Natural products from the human microbiome: an emergent frontier in organic synthesis and drug discovery. Org Biomol Chem 2024; 22:4006-4030. [PMID: 38669195 DOI: 10.1039/d4ob00236a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Often referred to as the "second genome", the human microbiome is at the epicenter of complex inter-habitat biochemical networks like the "gut-brain axis", which has emerged as a significant determinant of cognition, overall health and well-being, as well as resistance to antibiotics and susceptibility to diseases. As part of a broader understanding of the nexus between the human microbiome, diseases and microbial interactions, whether encoded secondary metabolites (natural products) play crucial signalling roles has been the subject of intense scrutiny in the recent past. A major focus of these activities involves harvesting the genomic potential of the human microbiome via bioinformatics guided genome mining and culturomics. Through these efforts, an impressive number of structurally intriguing antibiotics, with enhanced chemical diversity vis-à-vis conventional antibiotics have been isolated from human commensal bacteria, thereby generating considerable interest in their total synthesis and expanding their therapeutic space for drug discovery. These developments augur well for the discovery of new drugs and antibiotics, particularly in the context of challenges posed by mycobacterial resistance and emerging new diseases. The current landscape of various synthetic campaigns and drug discovery initiatives on antibacterial natural products from the human microbiome is captured in this review with an intent to stimulate further activities in this interdisciplinary arena among the new generation.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
| | - Srihari Pabbaraja
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad-500007, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Hyderabad-500046, India.
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2
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Lee H, Park SH, Kim J, Lee J, Koh MS, Lee JH, Kim S. Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305946. [PMID: 37987032 PMCID: PMC10787088 DOI: 10.1002/advs.202305946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiyoon Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehak Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min Sun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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3
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Advances in the Synthesis and Analysis of Biologically Active Phosphometabolites. Int J Mol Sci 2023; 24:ijms24043150. [PMID: 36834560 PMCID: PMC9961378 DOI: 10.3390/ijms24043150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Phosphorus-containing metabolites cover a large molecular diversity and represent an important domain of small molecules which are highly relevant for life and represent essential interfaces between biology and chemistry, between the biological and abiotic world. The large but not unlimited amount of phosphate minerals on our planet is a key resource for living organisms on our planet, while the accumulation of phosphorus-containing waste is associated with negative effects on ecosystems. Therefore, resource-efficient and circular processes receive increasing attention from different perspectives, from local and regional levels to national and global levels. The molecular and sustainability aspects of a global phosphorus cycle have become of much interest for addressing the phosphorus biochemical flow as a high-risk planetary boundary. Knowledge of balancing the natural phosphorus cycle and the further elucidation of metabolic pathways involving phosphorus is crucial. This requires not only the development of effective new methods for practical discovery, identification, and high-information content analysis, but also for practical synthesis of phosphorus-containing metabolites, for example as standards, as substrates or products of enzymatic reactions, or for discovering novel biological functions. The purpose of this article is to review the advances which have been achieved in the synthesis and analysis of phosphorus-containing metabolites which are biologically active.
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Single-exonuclease nanocircuits reveal the RNA degradation dynamics of PNPase and demonstrate potential for RNA sequencing. Nat Commun 2023; 14:552. [PMID: 36725855 PMCID: PMC9892577 DOI: 10.1038/s41467-023-36278-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
The degradation process of RNA is decisive in guaranteeing high-fidelity translation of genetic information in living organisms. However, visualizing the single-base degradation process in real time and deciphering the degradation mechanism at the single-enzyme level remain formidable challenges. Here, we present a reliable in-situ single-PNPase-molecule dynamic electrical detector based on silicon nanowire field-effect transistors with ultra-high temporal resolution. These devices are capable of realizing real-time and label-free monitoring of RNA analog degradation with single-base resolution, including RNA analog binding, single-nucleotide hydrolysis, and single-base movement. We discover a binding event of the enzyme (near the active site) with the nucleoside, offering a further understanding of the RNA degradation mechanism. Relying on systematic analyses of independent reads, approximately 80% accuracy in RNA nucleoside sequencing is achieved in a single testing process. This proof-of-concept sets up a Complementary Metal Oxide Semiconductor (CMOS)-compatible playground for the development of high-throughput detection technologies toward mechanistic exploration and single-molecule sequencing.
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5
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Manganese(II)/cobalt(II) co-catalyzed phosphorylation of 8-aminoquinoline amides to construct Csp2-P bond. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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6
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S51 Family Peptidases Provide Resistance to Peptidyl-Nucleotide Antibiotic McC. mBio 2022; 13:e0080522. [PMID: 35467414 PMCID: PMC9239234 DOI: 10.1128/mbio.00805-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microcin C (McC)-like compounds are natural Trojan horse peptide-nucleotide antibiotics produced by diverse bacteria. The ribosomally synthesized peptide parts of these antibiotics are responsible for their facilitated transport into susceptible cells. Once inside the cell, the peptide part is degraded, releasing the toxic payload, an isoaspartyl-nucleotide that inhibits aspartyl-tRNA synthetase, an enzyme essential for protein synthesis. Bacteria that produce microcin C-like compounds have evolved multiple ways to avoid self-intoxication. Here, we describe a new strategy through the action of S51 family peptidases, which we name MccG. MccG cleaves the toxic isoaspartyl-nucleotide, rendering it inactive. While some MccG homologs are encoded by gene clusters responsible for biosynthesis of McC-like compounds, most are encoded by standalone genes whose products may provide a basal level of resistance to peptide-nucleotide antibiotics in phylogenetically distant bacteria.
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Jajula K, Kumar RA, Kishore R, Thommandru PR, Shrikanth R, Satyanarayana S, Kishore PVVN. Silver( i)-catalyzed dehydrogenative cross-coupling of 2-aroylbenzofurans with phosphites. NEW J CHEM 2022. [DOI: 10.1039/d1nj06077e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The silver(i)-catalyzed dehydrogenative cross-coupling reaction of 2-aroylbenzofurans with phosphites to afford 2-aroyl-3-phosphonylbenzofurans is reported.
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Affiliation(s)
- Kashanna Jajula
- Department of Chemistry, Rajiv Gandhi University of Knowledge Technologies-Basar, Nirmal-504107, India
| | - Rathod Aravind Kumar
- Semiochemical Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Ravada Kishore
- Department of Chemistry, GITAM Institute of Science, GITAM (Deemed to be University), Visakhapatnam 530045, India
| | - Prakash Raj Thommandru
- Department of Chemistry, GITAM Institute of Science, GITAM (Deemed to be University), Visakhapatnam 530045, India
| | - Ravula Shrikanth
- Department of Chemistry, Rajiv Gandhi University of Knowledge Technologies-Basar, Nirmal-504107, India
- Department of Chemistry, Osmania University, Hyderabad 500007, India
| | | | - Pilli V. V. N. Kishore
- Chemistry Division, Department of Science and Humanities, VFSTR (Deemed to be University), Vadlamudi, Guntur-522213, India
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8
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Zhu YY, Niu Y, Niu YN, Yang SD. Recent advances in the synthesis and applications of phosphoramides. Org Biomol Chem 2021; 19:10296-10313. [PMID: 34812834 DOI: 10.1039/d1ob01566d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Phosphoramide, as an important framework of many biologically active molecules, has attracted widespread attention in recent decades. It is not only widely used in pharmaceuticals because of its excellent biological activities, but it also shows good performance in organic dyes, flame retardants and extractors. Thus, it is of great significance to develop effective and convenient methods for the synthesis of phosphoramides. In this review, the recent advancements made in the synthesis routes and applications of phosphoramides are discussed. The synthetic strategies of phosphoramides can be separated into five categories: phosphorus halides as the substrate, phosphates as the substrate, phosphorus hydrogen as the substrate, azides as the substrate and other methods. The latest examples of these methods are provided and some representative mechanisms are also described.
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Affiliation(s)
- Yuan-Yuan Zhu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yuan Niu
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
| | - Yan-Ning Niu
- Department of Teaching and Research, Nanjing Forestry University, Huaian 223003, P. R. China
| | - Shang-Dong Yang
- State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, China.
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9
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Bauman KD, Butler KS, Moore BS, Chekan JR. Genome mining methods to discover bioactive natural products. Nat Prod Rep 2021; 38:2100-2129. [PMID: 34734626 PMCID: PMC8597713 DOI: 10.1039/d1np00032b] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Indexed: 12/22/2022]
Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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10
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Karimi-Nami R, Adib M, Heydari F, Rajai-Daryasarei S, Karakaya I. Phosphorylation of 2-Aryl Quinoxaline Derivatives via C-H/P-H Cross Coupling under Transition-Metal-Free Conditions. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1983619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Rahman Karimi-Nami
- Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Mehdi Adib
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Forouzan Heydari
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | | | - Idris Karakaya
- Department of Chemistry, College of Basic Sciences, Gebze Technical University, Gebze, Turkey
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11
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Wang S, Ma S, Yang J, Li W, Li D, Yang J. Copper‐Phosphine Mediated Oxidative Phosphorylation of Aromatic Amines and P(OR)
3
under Aerobic Conditions. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shihaozhi Wang
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
| | - Shidi Ma
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
| | - Jiale Yang
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
| | - Wenshuang Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
| | - Dianjun Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
| | - Jinhui Yang
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering College of Chemistry and Chemical Engineering Ningxia University Yinchuan 750021 China
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12
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Gholivand K, Sabaghian M, Eshaghi Malekshah R. Synthesis, characterization, cytotoxicity studies, theoretical approach of adsorptive removal and molecular calculations of four new phosphoramide derivatives and related graphene oxide. Bioorg Chem 2021; 115:105193. [PMID: 34339976 DOI: 10.1016/j.bioorg.2021.105193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/26/2021] [Accepted: 07/17/2021] [Indexed: 01/05/2023]
Abstract
In this study, four novel phosphoramide ligands (L1-L4) are synthesized and characterized by 31PNMR, 1HNMR, MASS, and FT-IR spectroscopies. In vitro cell growth inhibition is studied by the MTT assay to evaluate the cytotoxicity of ligands against MCF-7 cell line; the result of the assay demonstrates that all ligands significantly suppress the proliferation of breast cancer cells in a concentration-dependent manner. The calculated IC50 values are in the range of 3.6-10.77 µg ml-1, of which the lowest value is attributed to L1. Then a facile approach was developed to functionalize graphene oxide (GO) surface by L1. The data which are obtained by XRD, FT-IR, and EDX analysis confirmed the deposition of phosphoramide on the surface of GO. The cell viability of GO-L1 compound at different concentrations is investigated in 24 h experiment. Excellent synergistic antitumor effects of GO and L1 lead to a decrease in IC50 value up to 2.13 μg ml-1. The Quantum calculations of compounds are used to study energies and HOMO and LUMO values, dipole moments (µ), global hardness (η), global softness (σ), and electrophilicity index (ω) using DMol3 module in Material studio2017. The docking calculations are performed to describe the mode of the binding to DNA and DNA polymerase IIα. Adsorption calculations of ligands (L1-L4) on GO sheet in the presence of water showed that L1 and L2 were located on GO via π electrons of anisole ring. While, L3 and L4 were located on GO by π - π interactions of aniline ring.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
| | - Marzie Sabaghian
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
| | - Rahime Eshaghi Malekshah
- Medical Biomaterial Research Centre (MBRC), Tehran University of Medical Sciences, Tehran, Iran.
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13
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Nguyen NA, Lin Z, Mohanty I, Garg N, Schmidt EW, Agarwal V. An Obligate Peptidyl Brominase Underlies the Discovery of Highly Distributed Biosynthetic Gene Clusters in Marine Sponge Microbiomes. J Am Chem Soc 2021; 143:10221-10231. [PMID: 34213321 DOI: 10.1021/jacs.1c03474] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Marine sponges are prolific sources of bioactive natural products, several of which are produced by bacteria symbiotically associated with the sponge host. Bacteria-derived natural products, and the specialized bacterial symbionts that synthesize them, are not shared among phylogenetically distant sponge hosts. This is in contrast to nonsymbiotic culturable bacteria in which the conservation of natural products and natural product biosynthetic gene clusters (BGCs) is well established. Here, we demonstrate the widespread conservation of a BGC encoding a cryptic ribosomally synthesized and post-translationally modified peptide (RiPP) in microbiomes of phylogenetically and geographically dispersed sponges from the Pacific and Atlantic oceans. Detection of this BGC was enabled by mining for halogenating enzymes in sponge metagenomes, which, in turn, allowed for the description of a broad-spectrum regiospecific peptidyl tryptophan-6-brominase which possessed no chlorination activity. In addition, we demonstrate the cyclodehydrative installation of azoline heterocycles in proteusin RiPPs. This is the first demonstration of halogenation and cyclodehydration for proteusin RiPPs and the enzymes catalyzing these transformations were found to competently interact with other previously described proteusin substrate peptides. Within a sponge microbiome, many different generalized bacterial taxa harbored this BGC with often more than 50 copies of the BGC detected in individual sponge metagenomes. Moreover, the BGC was found in all sponges queried that possess high diversity microbiomes but it was not detected in other marine invertebrate microbiomes. These data shed light on conservation of cryptic natural product biosynthetic potential in marine sponges that was not detected by traditional natural product-to-BGC (meta)genome mining.
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Affiliation(s)
- Nguyet A Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ipsita Mohanty
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Zhong T, Zheng X, Yin C, Shen Q, Yu C. Copper-Catalyzed Phosphorylation of 2,3-Allenoic Acids and Phosphine Oxide: Access to Phosphorylated Butenolides. J Org Chem 2021; 86:9699-9710. [PMID: 34184529 DOI: 10.1021/acs.joc.1c00998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated a novel Cu-catalyzed annulation of 2,3-allenoic acids with diphenylphosphine oxide, leading to the formation of 4-phosphate butenolides in up to 88% yield. The formation of the C-P bond provides new avenues for the functionalization of different furan-2(5H)-ones, with favorable features such as suitable functional group tolerance and mild synthesis conditions.
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Affiliation(s)
- Tianshuo Zhong
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Xiangyun Zheng
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Chuanliu Yin
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Qitao Shen
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
| | - Chuanming Yu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, P.R. China
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15
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Travin DY, Severinov K, Dubiley S. Natural Trojan horse inhibitors of aminoacyl-tRNA synthetases. RSC Chem Biol 2021; 2:468-485. [PMID: 34382000 PMCID: PMC8323819 DOI: 10.1039/d0cb00208a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
For most antimicrobial compounds with intracellular targets, getting inside the cell is the major obstacle limiting their activity. To pass this barrier some antibiotics mimic the compounds of specific interest for the microbe (siderophores, peptides, carbohydrates, etc.) and hijack the transport systems involved in their active uptake followed by the release of a toxic warhead inside the cell. In this review, we summarize the information about the structures, biosynthesis, and transport of natural inhibitors of aminoacyl-tRNA synthetases (albomycin, microcin C-related compounds, and agrocin 84) that rely on such "Trojan horse" strategy to enter the cell. In addition, we provide new data on the composition and distribution of biosynthetic gene clusters reminiscent of those coding for known Trojan horse aminoacyl-tRNA synthetases inhibitors. The products of these clusters are likely new antimicrobials that warrant further investigation.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
- Waksman Institute for Microbiology, Rutgers, Piscataway New Jersey USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology Moscow Russia
- Institute of Gene Biology, Russian Academy of Sciences Moscow Russia
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Ning Z, Peng X, Bai R, Liu S, Li Z, Jiao L. Iridium Catalyzed C—H Amidation of Benzamides with Phosphoryl Azides in Ionic Liquids. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202104039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Ahmadabad FK, Pourayoubi M, Nečas M. Syntheses, Characterizations and Crystal Structures of Two New Racemic Amidophosphoesters: rac-(C6H5O)(cyclo-C6H11NH)P(O)N(C4H8)NP(O)(NH-cyclo-C6H11)(OC6H5) and rac-(p-CH3-C6H4NH)P(O)(OC6H4-p-CH3)(OC6H5). CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520070020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Gulevskyy AK, Akhatova YS, Nikolchenko AY. Cryoprotective agents affect amino acids incorporation into total proteins in cells of lymphoid organs and liver of experimental animals. UKRAINIAN BIOCHEMICAL JOURNAL 2020. [DOI: 10.15407/ubj92.05.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Abstract
The Escherichia coli microcin C (McC) and related compounds are potent Trojan horse peptide-nucleotide antibiotics. The peptide part facilitates transport into sensitive cells. Inside the cell, the peptide part is degraded by nonspecific peptidases releasing an aspartamide-adenylate containing a phosphoramide bond. This nonhydrolyzable compound inhibits aspartyl-tRNA synthetase. In addition to the efficient export of McC outside the producing cells, special mechanisms have evolved to avoid self-toxicity caused by the degradation of the peptide part inside the producers. Here, we report that histidine-triad (HIT) hydrolases encoded in biosynthetic clusters of some McC homologs or by standalone genes confer resistance to McC-like compounds by hydrolyzing the phosphoramide bond in toxic aspartamide-adenosine, rendering them inactive.IMPORTANCE Uncovering the mechanisms of resistance is a required step for countering the looming antibiotic resistance crisis. In this communication, we show how universally conserved histidine-triad hydrolases provide resistance to microcin C, a potent inhibitor of bacterial protein synthesis.
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20
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Travin DY, Bikmetov D, Severinov K. Translation-Targeting RiPPs and Where to Find Them. Front Genet 2020; 11:226. [PMID: 32296456 PMCID: PMC7136475 DOI: 10.3389/fgene.2020.00226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
Prokaryotic translation is among the major targets of diverse natural products with antibacterial activity including several classes of clinically relevant antibiotics. In this review, we summarize the information about the structure, biosynthesis, and modes of action of translation inhibiting ribosomally synthesized and post-translationally modified peptides (RiPPs). Azol(in)e-containing RiPPs are known to target translation, and several new compounds inhibiting the ribosome have been characterized recently. We performed a systematic search for biosynthetic gene clusters (BGCs) of azol(in)e-containing RiPPs. This search uncovered several groups of clusters that likely direct the synthesis of novel compounds, some of which may be targeting the ribosome.
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Affiliation(s)
- Dmitrii Y Travin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Bikmetov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,Waksman Institute for Microbiology, Rutgers, Piscataway, NJ, United States
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21
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Wang X, Ou Y, Peng Z, Yu G, Huang Y, Li X, Huo Y, Chen Q. TBHP/NH 4I-Mediated Direct N-H Phosphorylation of Imines and Imidates. J Org Chem 2019; 84:14949-14956. [PMID: 31622097 DOI: 10.1021/acs.joc.9b02301] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A direct and practical metal-free N-H phosphorylation has been achieved via the TBHP/NH4I-mediated cross-dehydrogenative coupling (CDC) reactions between imines/imidates and P(O)H compounds. This transformation provides an efficient synthetic route to the construction of P-N bonds with good functional group compatibility, leading to the formation of N-phosphorylimines and N-phosphorylimidates in up to 95% yield (33 examples) under mild conditions.
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Affiliation(s)
- Xiaofeng Wang
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Yingcong Ou
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Zhenbo Peng
- Chemical Engineering College , Ningbo Polytechnic , Ningbo 315800 , China
| | - Guodian Yu
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Yuanting Huang
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Xianwei Li
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Yanping Huo
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China
| | - Qian Chen
- School of Chemical Engineering and Light Industry , Guangdong University of Technology , Guangzhou 510006 , China.,Key Laboratory of Functional Molecular Engineering of Guangdong Province , South China University of Technology , Guangzhou 510640 , China
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22
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Cheng Z, Bown L, Piercey B, Bignell DRD. Positive and Negative Regulation of the Virulence-Associated Coronafacoyl Phytotoxin in the Potato Common Scab Pathogen Streptomyces scabies. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1348-1359. [PMID: 31107631 DOI: 10.1094/mpmi-03-19-0070-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The potato common scab pathogen Streptomyces scabies produces N-coronafacoyl-l-isoleucine (CFA-Ile), which is a member of the coronafacoyl family of phytotoxins that are synthesized by multiple plant pathogenic bacteria. The CFA-Ile biosynthetic gene cluster contains a regulatory gene, cfaR, which directly controls the expression of the phytotoxin structural genes. In addition, a gene designated orf1 encodes a predicted ThiF family protein and is cotranscribed with cfaR, suggesting that it also plays a role in the regulation of CFA-Ile production. In this study, we demonstrated that CfaR is an essential activator of coronafacoyl phytotoxin production, while ORF1 is dispensable for phytotoxin production and may function as a helper protein for CfaR. We also showed that CFA-Ile inhibits the ability of CfaR to bind to the promoter region driving expression of the phytotoxin biosynthetic genes and that elevated CFA-Ile production by overexpression of both cfaR and orf1 in S. scabies increases the severity of disease symptoms induced by the pathogen during colonization of potato tuber tissue. Overall, our study reveals novel insights into the regulatory mechanisms controlling CFA-Ile production in S. scabies and it provides further evidence that CFA-Ile is an important virulence factor for this organism.
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Affiliation(s)
- Zhenlong Cheng
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Luke Bown
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Brandon Piercey
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
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23
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Li Q, Sun X, Yang X, Wu M, Sun S, Chen X. Transition-metal-free amination phosphoryl azide for the synthesis of phosphoramidates. RSC Adv 2019; 9:16040-16043. [PMID: 35521381 PMCID: PMC9064390 DOI: 10.1039/c9ra03389k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023] Open
Abstract
A facile and efficient approach to phosphoramidates was developed via amination of phosphoryl azides. A variety of phosphoramidates were obtained in one step with good to excellent yields under a mild reaction system. The process uses easily available amines as a N source and offers a new opportunity for P–N bond formation. A facile and efficient approach to phosphoramidates was developed via amination of phosphoryl azides.![]()
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Affiliation(s)
- Qing Li
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | | | - Xiaoqin Yang
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Minghu Wu
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Shaofa Sun
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
| | - Xiuling Chen
- Non-power Nuclear Technology Collaborative Innovation Center, School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology Xianning 437100 China +86-715-8338007
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24
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Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor. mBio 2019; 10:mBio.00768-19. [PMID: 31040244 PMCID: PMC6495379 DOI: 10.1128/mbio.00768-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli microcin C (McC) is a representative member of peptide-nucleotide antibiotics produced by diverse microorganisms. The vast majority of biosynthetic gene clusters responsible for McC-like compound production encode 7-amino-acid-long precursor peptides, which are C-terminally modified by dedicated biosynthetic enzymes with a nucleotide moiety to produce a bioactive compound. In contrast, the sequences of McC-like compound precursor peptides are not conserved. Here, we studied the consequences of E. coli McC precursor peptide length increase on antibiotic production and activity. We show that increasing the precursor peptide length strongly decreases McC production by affecting multiple biosynthetic steps, suggesting that the McC biosynthesis system has evolved under significant functional constraints to maintain the precursor peptide length. Microcin C (McC) is a peptide adenylate antibiotic produced by Escherichiacoli cells bearing a plasmid-borne mcc gene cluster. Most MccA precursors, encoded by validated mcc operons from diverse bacteria, are 7 amino acids long, but the significance of this precursor length conservation has remained unclear. Here, we created derivatives of E. colimcc operons encoding longer precursors and studied their synthesis and bioactivities. We found that increasing the precursor length to 11 amino acids and beyond strongly decreased antibiotic production. We found this decrease to depend on several parameters. First, reiterative synthesis of the MccA peptide by the ribosome was decreased at longer mccA open reading frames, leading to less efficient competition with other messenger RNAs. Second, the presence of a formyl group at the N-terminal methionine of the heptameric peptide had a strong stimulatory effect on adenylation by the MccB enzyme. No such formyl group stimulation was observed for longer peptides. Finally, the presence of the N-terminal formyl on the heptapeptide adenylate stimulated bioactivity, most likely at the uptake stage. Together, these factors should contribute to optimal activity of McC-like compounds as 7-amino-acid peptide moieties and suggest convergent evolution of several steps of the antibiotic biosynthesis pathway and their adjustment to sensitive cell uptake machinery to create a potent drug.
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25
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Baulig A, Helmle I, Bader M, Wolf F, Kulik A, Al-Dilaimi A, Wibberg D, Kalinowski J, Gross H, Kaysser L. Biosynthetic reconstitution of deoxysugar phosphoramidate metalloprotease inhibitors using an N-P-bond-forming kinase. Chem Sci 2019; 10:4486-4490. [PMID: 31057776 PMCID: PMC6482885 DOI: 10.1039/c9sc00641a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Phosphoramidon is a potent metalloprotease inhibitor and a widespread tool in cell biology research. It contains a dipeptide backbone that is uniquely linked to a 6-deoxysugar via a phosphoramidate bridge. Herein, we report the identification of a gene cluster for the formation of phosphoramidon and its detailed characterization. In vitro reconstitution of the biosynthesis established TalE as a phosphoramidate-forming kinase and TalC as the glycosyltransferase which installs the l-rhamnose moiety by phosphoester linkage.
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Affiliation(s)
- Alexandra Baulig
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Irina Helmle
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany .
| | - Marius Bader
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Felix Wolf
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Andreas Kulik
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT) , Microbiology/Biotechnology , University of Tübingen , 72076 Tübingen , Germany
| | - Arwa Al-Dilaimi
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec) , Bielefeld University , 33615 Bielefeld , Germany
| | - Harald Gross
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology , Pharmaceutical Institute , University of Tübingen , 72076 Tübingen , Germany . .,German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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26
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Du YL, Ryan KS. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat Prod Rep 2019; 36:430-457. [DOI: 10.1039/c8np00049b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review reactions catalyzed by pyridoxal phosphate-dependent enzymes, highlighting enzymes reported in the recent natural product biosynthetic literature.
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Affiliation(s)
- Yi-Ling Du
- Institute of Pharmaceutical Biotechnology
- Zhejiang University School of Medicine
- Hangzhou
- China
| | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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27
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Dong SH, Kulikovsky A, Zukher I, Estrada P, Dubiley S, Severinov K, Nair SK. Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor. Chem Sci 2018; 10:2391-2395. [PMID: 30881667 PMCID: PMC6385645 DOI: 10.1039/c8sc03173h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023] Open
Abstract
The N-formyl moiety of the peptide precursor directs the biosynthesis of the RiPP trojan horse nucleotide antibiotic McC.
Microcin C7 (McC) is a peptide antibiotic modified by a linkage of the terminal isoAsn amide to AMP via a phosphoramidate bond. Post-translational modification on this ribosomally produced heptapeptide precursor is carried out by MccB, which consumes two equivalents of ATP to generate the N–P linkage. We demonstrate that MccB only efficiently processes the precursor heptapeptide that retains the N-formylated initiator Met (fMet). Binding studies and kinetic measurements evidence the role of the N-formyl moiety. Structural data show that the N-formyl peptide binding results in an ordering of residues in the MccB “crossover loop”, which dictates specificity in homologous ubiquitin activating enzymes. The N-formyl peptide exhibits substrate inhibition, and cannot be displaced from MccB by the desformyl counterpart. Such substrate inhibition may be a strategy to avert unwanted McC buildup and avert toxicity in the cytoplasm of producing organisms.
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Affiliation(s)
- Shi-Hui Dong
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . .,Carl Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Illinois , USA
| | - Alexey Kulikovsky
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . .,Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia.,Center for Life Sciences , Skolkov Institute of Science and Technology , 3 Nobel str. , 143026 Moscow , Russia
| | - Inna Zukher
- Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia
| | - Paola Estrada
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA .
| | - Svetlana Dubiley
- Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia.,Center for Life Sciences , Skolkov Institute of Science and Technology , 3 Nobel str. , 143026 Moscow , Russia
| | - Konstantin Severinov
- Institute of Gene Biology , Russian Academy of Science , 34/5 Vavilo str. , 11934 Moscow , Russia.,Center for Life Sciences , Skolkov Institute of Science and Technology , 3 Nobel str. , 143026 Moscow , Russia.,Waksman Institute for Microbiology , 190 Frelinghuysen Road , Piscataway , New Jersey , USA .
| | - Satish K Nair
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Illinois , USA . .,Carl Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Illinois , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Illinois , USA
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28
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Taylor ZW, Chamberlain AR, Raushel FM. Substrate Specificity and Chemical Mechanism for the Reaction Catalyzed by Glutamine Kinase. Biochemistry 2018; 57:5447-5455. [PMID: 30142271 DOI: 10.1021/acs.biochem.8b00811] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni, a leading cause of gastroenteritis worldwide, has a unique O-methyl phosphoramidate (MeOPN) moiety attached to its capsular polysaccharide. Investigations into the biological role of MeOPN have revealed that it contributes to the pathogenicity of C. jejuni, and this modification is important for the colonization of C. jejuni. Previously, the reactions catalyzed by four enzymes (Cj1418-Cj1415) from C. jejuni that are required for the biosynthesis of the phosphoramidate modification have been elucidated. Cj1418 (l-glutamine kinase) catalyzes the formation of the initial phosphoramidate bond with the ATP-dependent phosphorylation of the amide nitrogen of l-glutamine. Here we show that Cj1418 catalyzes the phosphorylation of l-glutamine through a three-step reaction mechanism via the formation of covalent pyrophosphorylated ( Enz-X-Pβ-Pγ) and phosphorylated ( Enz-X-Pβ) intermediates. In the absence of l-glutamine, the enzyme was shown to catalyze a positional isotope exchange (PIX) reaction within β-[18O4]-ATP in support of the formation of the Enz-X-Pβ-Pγintermediate. In the absence of ATP, the enzyme was shown to catalyze a molecular isotope exchange (MIX) reaction between l-glutamine phosphate and [15N-amide]-l-glutamine in direct support of the Enz-X-Pβintermediate. The active site nucleophile has been identified as His-737 based on the lack of activity of the H737N mutant and amino acid sequence comparisons. The enzyme was shown to also catalyze the phosphorylation of d-glutamine, γ-l-glutamyl hydroxamate, γ-l-glutamyl hydrazide, and β-l-aspartyl hydroxamate, in addition to l-glutamine.
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Affiliation(s)
- Zane W Taylor
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Alexandra R Chamberlain
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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29
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Tsibulskaya D, Mokina O, Kulikovsky A, Piskunova J, Severinov K, Serebryakova M, Dubiley S. The Product of Yersinia pseudotuberculosis mcc Operon Is a Peptide-Cytidine Antibiotic Activated Inside Producing Cells by the TldD/E Protease. J Am Chem Soc 2017; 139:16178-16187. [PMID: 29045133 DOI: 10.1021/jacs.7b07118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microcin C is a heptapeptide-adenylate antibiotic produced by some strains of Escherichia coli. Its peptide part is responsible for facilitated transport inside sensitive cells where it is proteolyzed with release of a toxic warhead-a nonhydrolyzable aspartamidyl-adenylate, which inhibits aspartyl-tRNA synthetase. Recently, a microcin C homologue from Bacillus amyloliquefaciens containing a longer peptide part modified with carboxymethyl-cytosine instead of adenosine was described, but no biological activity of this compound was revealed. Here, we characterize modified peptide-cytidylate from Yersinia pseudotuberculosis. As reported for B. amyloliquefaciens homologue, the initially synthesized compound contains a long peptide that is biologically inactive. This compound is subjected to endoproteolytic processing inside producing cells by the evolutionary conserved TldD/E protease. As a result, an 11-amino acid long peptide with C-terminal modified cytosine residue is produced. This compound is exported outside the producing cell and is bioactive, inhibiting sensitive cells in the same way as E. coli microcin C. Proteolytic processing inside producing cells is a novel strategy of peptide-nucleotide antibiotics biosynthesis that may help control production levels and avoid toxicity to the producer.
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Affiliation(s)
- Darya Tsibulskaya
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Olga Mokina
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Alexey Kulikovsky
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia.,Department of Biochemistry, University of Illinois at Urbana-Champaign , 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Julia Piskunova
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Konstantin Severinov
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia.,Waksman Institute for Microbiology , 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020, United States
| | - Marina Serebryakova
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Leninskie Gory 1, Bldg. 40, Moscow 119991, Russia
| | - Svetlana Dubiley
- Institute of Gene Biology , Russian Academy of Science, 34/5 Vavilov str., 119334 Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
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30
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Koroniak-Szejn K, Tomaszewska J, Koroniak H. The synthesis of new fluorinated or nonfluorinated sugar phosphonates and phosphoramidates as building blocks in the synthesis of modified hyaluronic acid subunits. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2017.1311332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Henryk Koroniak
- Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
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31
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Ageitos J, Sánchez-Pérez A, Calo-Mata P, Villa T. Antimicrobial peptides (AMPs): Ancient compounds that represent novel weapons in the fight against bacteria. Biochem Pharmacol 2017; 133:117-138. [DOI: 10.1016/j.bcp.2016.09.018] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/19/2016] [Indexed: 01/01/2023]
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32
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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33
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Mousa WK, Athar B, Merwin NJ, Magarvey NA. Antibiotics and specialized metabolites from the human microbiota. Nat Prod Rep 2017; 34:1302-1331. [DOI: 10.1039/c7np00021a] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human microbiota associated with each body site produce specialized molecules to kill human pathogens. Advanced bioinformatics tools will help to discover unique microbiome chemistry.
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Affiliation(s)
- Walaa K. Mousa
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Bilal Athar
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nishanth J. Merwin
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nathan A. Magarvey
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
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34
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Serebryakova M, Tsibulskaya D, Mokina O, Kulikovsky A, Nautiyal M, Van Aerschot A, Severinov K, Dubiley S. A Trojan-Horse Peptide-Carboxymethyl-Cytidine Antibiotic from Bacillus amyloliquefaciens. J Am Chem Soc 2016; 138:15690-15698. [PMID: 27934031 PMCID: PMC5152938 DOI: 10.1021/jacs.6b09853] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Microcin
C and related antibiotics are Trojan-horse peptide-adenylates.
The peptide part is responsible for facilitated transport inside the
sensitive cell, where it gets processed to release a toxic warhead—a
nonhydrolyzable aspartyl-adenylate, which inhibits aspartyl-tRNA synthetase.
Adenylation of peptide precursors is carried out by MccB THIF-type
NAD/FAD adenylyltransferases. Here, we describe a novel microcin C-like
compound from Bacillus amyloliquefaciens. The B. amyloliquefaciens MccB demonstrates an unprecedented
ability to attach a terminal cytidine monophosphate to cognate precursor
peptide in cellular and cell free systems. The cytosine moiety undergoes
an additional modification—carboxymethylation—that is
carried out by the C-terminal domain of MccB and the MccS enzyme that
produces carboxy-SAM, which serves as a donor of the carboxymethyl
group. We show that microcin C-like compounds carrying terminal cytosines
are biologically active and target aspartyl-tRNA synthetase, and that
the carboxymethyl group prevents resistance that can occur due to
modification of the warhead. The results expand the repertoire of
known enzymatic modifications of peptides that can be used to obtain
new biological activities while avoiding or limiting bacterial resistance.
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Affiliation(s)
- Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Leninskie Gory 1, Bldg. 40, Moscow 119991, Russia
| | - Darya Tsibulskaya
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia
| | - Olga Mokina
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Alexey Kulikovsky
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
| | - Manesh Nautiyal
- KU Leuven , O&N Rega, Medicinal Chemistry, Herestraat 49 10, B-3000 Leuven, Belgium
| | - Arthur Van Aerschot
- KU Leuven , O&N Rega, Medicinal Chemistry, Herestraat 49 10, B-3000 Leuven, Belgium
| | - Konstantin Severinov
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia.,Waksman Institute for Microbiology , 190 Frelinghuysen Road, Piscataway, New Jersey 08854-8020, United States
| | - Svetlana Dubiley
- Institute of Gene Biology, Russian Academy of Science , 34/5 Vavilov str., 119334 Moscow, Russia.,Skolkovo Institute of Science and Technology , 3 Nobel str., 143026 Moscow, Russia
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35
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Cheung WL, Chen M, Maksimov MO, Link AJ. Lasso Peptide Biosynthetic Protein LarB1 Binds Both Leader and Core Peptide Regions of the Precursor Protein LarA. ACS CENTRAL SCIENCE 2016; 2:702-709. [PMID: 27800552 PMCID: PMC5084080 DOI: 10.1021/acscentsci.6b00184] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Lasso peptides are a member of the superclass of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Like all RiPPs, lasso peptides are derived from a gene-encoded precursor protein. The biosynthesis of lasso peptides requires two enzymatic activities: proteolytic cleavage between the leader peptide and the core peptide in the precursor protein, accomplished by the B enzymes, and ATP-dependent isopeptide bond formation, accomplished by the C enzymes. In a subset of lasso peptide biosynthetic gene clusters from Gram-positive organisms, the B enzyme is split between two proteins. One such gene cluster is found in the organism Rhodococcus jostii, which produces the antimicrobial lasso peptide lariatin. The B enzyme in R. jostii is split between two open reading frames, larB1 and larB2, both of which are required for lariatin biosynthesis. While the cysteine catalytic triad is found within the LarB2 protein, LarB1 is a PqqD homologue expected to bind to the lariatin precursor LarA based on its structural homology to other RiPP leader peptide binding domains. We show that LarB1 binds to the leader peptide of the lariatin precursor protein LarA with a sub-micromolar affinity. We used photocrosslinking with the noncanonical amino acid p-azidophenylalanine and mass spectrometry to map the interaction of LarA and LarB1. This analysis shows that the LarA leader peptide interacts with a conserved motif within LarB1 and, unexpectedly, the core peptide of LarA also binds to LarB1 in several positions. A Rosetta model built from distance restraints from the photocrosslinking experiments shows that the scissile bond between the leader peptide and core peptide in LarA is in a solvent-exposed loop.
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Affiliation(s)
- Wai Ling Cheung
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Maria
Y. Chen
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Mikhail O. Maksimov
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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36
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Qi J, Wan D, Ma H, Liu Y, Gong R, Qu X, Sun Y, Deng Z, Chen W. Deciphering Carbamoylpolyoxamic Acid Biosynthesis Reveals Unusual Acetylation Cycle Associated with Tandem Reduction and Sequential Hydroxylation. Cell Chem Biol 2016; 23:935-44. [DOI: 10.1016/j.chembiol.2016.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 07/05/2016] [Accepted: 07/11/2016] [Indexed: 01/27/2023]
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37
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Ghodge SV, Biernat KA, Bassett SJ, Redinbo MR, Bowers AA. Post-translational Claisen Condensation and Decarboxylation en Route to the Bicyclic Core of Pantocin A. J Am Chem Soc 2016; 138:5487-90. [PMID: 27088303 DOI: 10.1021/jacs.5b13529] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pantocin A (PA) is a member of the growing family of ribosomally encoded and post-translationally modified peptide natural products (RiPPs). PA is much smaller than most known RiPPs, a tripeptide with a tight bicyclic core that appears to be cleaved from the middle of a larger 30-residue precursor peptide. We show here that the enzyme PaaA catalyzes the double dehydration and decarboxylation of two glutamic acid residues in the 30-residue precursor PaaP. Further truncates of PaaP leader and follower peptide sequences demonstrate the different impacts of these two regions on PaaA-mediated tailoring and delineate an essential role for the follower sequence in the decarboxylation step. The crystal structure of apo PaaA is reported, allowing identification of structural features that set PaaA apart from other homologous enzymes that typically do not catalyze such extended post-translational chemistry. Together, these data reveal how additional chemistry can be extracted from a ubiquitous enzyme family toward ribosomally derived peptide natural product biosynthesis and suggest that more examples of such enzymes likely exist in untapped genomic space.
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Affiliation(s)
- Swapnil V Ghodge
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill , Eshelmann School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Kristen A Biernat
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Sarah Jane Bassett
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill , Eshelmann School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill , Eshelmann School of Pharmacy, Chapel Hill, North Carolina 27599, United States
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38
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Bahri L, Barhoumi-Slimi T, Sanhoury MAK, Ben Dhia MT. Synthesis and Characterization of New Variously Substituted Allylic Phosphates. HETEROATOM CHEMISTRY 2016. [DOI: 10.1002/hc.21316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Leila Bahri
- Laboratory of Structural Organic Chemistry: Synthesis and Physicochemical Studies, Department of Chemistry; Faculty of Sciences of Tunis, University of Tunis El Manar; 2092 Tunis Tunisia
| | - T. Barhoumi-Slimi
- Laboratory of Structural Organic Chemistry: Synthesis and Physicochemical Studies, Department of Chemistry; Faculty of Sciences of Tunis, University of Tunis El Manar; 2092 Tunis Tunisia
- Institut Supérieur des Sciences et Technologie de l'Environnement; Carthage University; Technopole Borj Cedria Hammam Lif 2050 Tunisa
| | - M. A. K. Sanhoury
- Laboratory of Structural Organic Chemistry: Synthesis and Physicochemical Studies, Department of Chemistry; Faculty of Sciences of Tunis, University of Tunis El Manar; 2092 Tunis Tunisia
| | - M. T. Ben Dhia
- Laboratory of Structural Organic Chemistry: Synthesis and Physicochemical Studies, Department of Chemistry; Faculty of Sciences of Tunis, University of Tunis El Manar; 2092 Tunis Tunisia
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39
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Meazza M, Kowalczuk A, Shirley L, Yang JW, Guo H, Rios R. Organophotocatalytic Synthesis of Phosphoramidates. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201501068] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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Gao M, Li Y, Xie L, Chauvin R, Cui X. Direct phosphonation of quinoxalin-2(1H)-ones under transition-metal-free conditions. Chem Commun (Camb) 2016; 52:2846-9. [DOI: 10.1039/c5cc08049e] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A direct C–H bond phosphonation of quinoxalin-2(1H)-ones with H-phosphonates, H-phosphinates or H-phosphine oxides has been developed.
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Affiliation(s)
- Ming Gao
- Engineering Research Center of Molecular Medicine
- Ministry of Education
- Key Laboratory of Xiamen Marine and Gene Drugs
- Institutes of Molecular Medicine and School of Biomedical Sciences
- Huaqiao University
| | - Yi Li
- Engineering Research Center of Molecular Medicine
- Ministry of Education
- Key Laboratory of Xiamen Marine and Gene Drugs
- Institutes of Molecular Medicine and School of Biomedical Sciences
- Huaqiao University
| | - Lijuan Xie
- Engineering Research Center of Molecular Medicine
- Ministry of Education
- Key Laboratory of Xiamen Marine and Gene Drugs
- Institutes of Molecular Medicine and School of Biomedical Sciences
- Huaqiao University
| | - Remi Chauvin
- Engineering Research Center of Molecular Medicine
- Ministry of Education
- Key Laboratory of Xiamen Marine and Gene Drugs
- Institutes of Molecular Medicine and School of Biomedical Sciences
- Huaqiao University
| | - Xiuling Cui
- Engineering Research Center of Molecular Medicine
- Ministry of Education
- Key Laboratory of Xiamen Marine and Gene Drugs
- Institutes of Molecular Medicine and School of Biomedical Sciences
- Huaqiao University
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41
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Sun M, Sun S, Qiao H, Yang F, Zhu Y, Kang J, Wu Y, Wu Y. Silver(i)-promoted C5–H phosphonation of 8-aminoquinoline amides with H-phosphonates. Org Chem Front 2016. [DOI: 10.1039/c6qo00379f] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An efficient protocol for silver(i)-promoted C5–H phosphonation of 8-aminoquinoline amides with dialkyl H-phosphonates was developed.
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Affiliation(s)
- Mengmeng Sun
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Suyan Sun
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Huijie Qiao
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Fan Yang
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Yu Zhu
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Jianxun Kang
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
| | - Yusheng Wu
- Tetranov Biopharm
- LLC
- Zhengzhou
- China
- Collaborative Innovation Center of New Drug Research and Safety Evaluation
| | - Yangjie Wu
- The College of Chemistry and Molecular Engineering
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou 450052
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42
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Peng P, Peng L, Wang G, Wang F, Luo Y, Lei A. Visible light mediated aerobic radical C–H phosphorization toward arylphosphonates. Org Chem Front 2016. [DOI: 10.1039/c6qo00049e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A visible light mediated radical C–H phosphorization of benzothiazoles with O2 as the sole oxidant toward the synthesis of arylphosphonates was developed.
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Affiliation(s)
- Pan Peng
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
| | - Long Peng
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
| | - Guangyu Wang
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
| | - Fangyu Wang
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
| | - Yi Luo
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
| | - Aiwen Lei
- College of Chemistry and Molecular Sciences
- the Institute for Advanced Studies (IAS)
- Wuhan University
- Wuhan
- P. R. China
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43
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Cochrane RVK, Norquay AK, Vederas JC. Natural products and their derivatives as tRNA synthetase inhibitors and antimicrobial agents. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00274a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tRNA synthetase enzymes are promising targets for development of therapeutic agents against infections by parasitic protozoans (e.g. malaria), fungi and yeast, as well as bacteria resistant to current antibiotics.
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Affiliation(s)
| | - A. K. Norquay
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
| | - J. C. Vederas
- Department of Chemistry
- University of Alberta
- Edmonton
- T6G 2G2 Canada
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44
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Abstract
Developments in the use of genomics to guide natural product discovery and a recent emphasis on understanding the molecular mechanisms of microbiota-host interactions have converged on the discovery of small molecules from the human microbiome. Here, we review what is known about small molecules produced by the human microbiota. Numerous molecules representing each of the major metabolite classes have been found that have a variety of biological activities, including immune modulation and antibiosis. We discuss technologies that will affect how microbiota-derived molecules are discovered in the future and consider the challenges inherent in finding specific molecules that are critical for driving microbe-host and microbe-microbe interactions and understanding their biological relevance.
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Affiliation(s)
- Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Michael A Fischbach
- Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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45
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Enzymatic Synthesis and Functional Characterization of Bioactive Microcin C-Like Compounds with Altered Peptide Sequence and Length. J Bacteriol 2015. [PMID: 26195597 DOI: 10.1128/jb.00271-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Escherichia coli microcin C (McC) consists of a ribosomally synthesized heptapeptide attached to a modified adenosine. McC is actively taken up by sensitive Escherichia coli strains through the YejABEF transporter. Inside the cell, McC is processed by aminopeptidases, which release nonhydrolyzable aminoacyl adenylate, an inhibitor of aspartyl-tRNA synthetase. McC is synthesized by the MccB enzyme, which terminally adenylates the MccA heptapeptide precursor MRTGNAN. Earlier, McC analogs with shortened peptide lengths were prepared by total chemical synthesis and were shown to have strongly reduced biological activity due to decreased uptake. Variants with longer peptides were difficult to synthesize, however. Here, we used recombinant MccB to prepare and characterize McC-like molecules with altered peptide moieties, including extended peptide lengths. We find that N-terminal extensions of E. coli MccA heptapeptide do not affect MccB-catalyzed adenylation and that some extended-peptide-length McC analogs show improved biological activity. When the peptide length reaches 20 amino acids, both YejABEF and SbmA can perform facilitated transport of toxic peptide adenylates inside the cell. A C-terminal fusion of the carrier maltose-binding protein (MBP) with the MccA peptide is also recognized by MccB in vivo and in vitro, allowing highly specific adenylation and/or radioactive labeling of cellular proteins. IMPORTANCE Enzymatic adenylation of chemically synthesized peptides allowed us to generate biologically active derivatives of the peptide-nucleotide antibiotic microcin C with improved bioactivity and altered entry routes into target cells, opening the way for development of various McC-based antibacterial compounds not found in nature.
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46
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Kim H, Park J, Kim JG, Chang S. Synthesis of Phosphoramidates: A Facile Approach Based on the C–N Bond Formation via Ir-Catalyzed Direct C–H Amidation. Org Lett 2014; 16:5466-9. [DOI: 10.1021/ol502722j] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hyunwoo Kim
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Juhyeon Park
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Jeung Gon Kim
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
| | - Sukbok Chang
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
- Center
for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 305-701, Korea
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47
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Zukher I, Novikova M, Tikhonov A, Nesterchuk MV, Osterman IA, Djordjevic M, Sergiev PV, Sharma CM, Severinov K. Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C. Nucleic Acids Res 2014; 42:11891-902. [PMID: 25274735 PMCID: PMC4231749 DOI: 10.1093/nar/gku880] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Microcin C (McC) is a peptide–nucleotide antibiotic produced by Escherichia coli cells harboring a plasmid-borne operon mccABCDE. The heptapeptide MccA is converted into McC by adenylation catalyzed by the MccB enzyme. Since MccA is a substrate for MccB, a mechanism that regulates the MccA/MccB ratio likely exists. Here, we show that transcription from a promoter located upstream of mccA directs the synthesis of two transcripts: a short highly abundant transcript containing the mccA ORF and a longer minor transcript containing mccA and downstream ORFs. The short transcript is generated when RNA polymerase terminates transcription at an intrinsic terminator located in the intergenic region between the mccA and mccB genes. The function of this terminator is strongly attenuated by upstream mcc sequences. Attenuation is relieved and transcription termination is induced when ribosome binds to the mccA ORF. Ribosome binding also makes the mccA RNA exceptionally stable. Together, these two effects—ribosome-induced transcription termination and stabilization of the message—account for very high abundance of the mccA transcript that is essential for McC production. The general scheme appears to be evolutionary conserved as ribosome-induced transcription termination also occurs in a homologous operon from Helicobacter pylori.
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Affiliation(s)
- Inna Zukher
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA St. Petersburg State Polytechnical University, St. Petersburg, Russia
| | - Maria Novikova
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Anton Tikhonov
- Institute of Molecular Genetics of the Russian Academy of Sciences, Moscow, Russia
| | | | - Ilya A Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Petr V Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Cynthia M Sharma
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany
| | - Konstantin Severinov
- Institute of Gene Biology of the Russian Academy of Sciences, Moscow, Russia Waksman Institute for Microbiology and Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA St. Petersburg State Polytechnical University, St. Petersburg, Russia Skolkovo Institute of Science and Technology, Skolkovo, Russia
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48
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Kulikovsky A, Serebryakova M, Bantysh O, Metlitskaya A, Borukhov S, Severinov K, Dubiley S. The molecular mechanism of aminopropylation of peptide-nucleotide antibiotic microcin C. J Am Chem Soc 2014; 136:11168-75. [PMID: 25026542 DOI: 10.1021/ja505982c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Translation inhibitor microcin C (McC) is a heptapeptide with an aspartate α-carboxyl group linked to AMP via phosphoramidate bond. Modification of the McC phosphate by an aminopropyl moiety increases the biological activity by ~10-fold. Here, we determine the pathway of the aminopropylation reaction of McC. We show that the MccD enzyme uses S-adenosyl methionine to transfer 3-amino-3-carboxypropyl group onto a phosphate of an McC maturation intermediate consisting of adenylated heptapeptide. The carboxyl group is removed by the MccE enzyme, yielding mature McC. MccD is an inefficient enzyme that requires for its action the product of Escherichia coli mtn gene, a 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase, which hydrolyses 5'-methylthioadenosine, the product of MccD-catalyzed reaction, thus stimulating the amino-3-carboxypropylation reaction. Both MccD and MccE are capable of modifying McC-like compounds with divergent peptide moieties, opening way for preparation of more potent peptidyl-adenylates.
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Affiliation(s)
- Alexey Kulikovsky
- Institute of Gene Biology and ∥Institute of Molecular Genetics, Russian Academy of Sciences , Moscow 119991, Russia
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49
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Enzymatic synthesis of bioinformatically predicted microcin C-like compounds encoded by diverse bacteria. mBio 2014; 5:e01059-14. [PMID: 24803518 PMCID: PMC4010828 DOI: 10.1128/mbio.01059-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT The Trojan horse Escherichia coli antibiotic microcin C (McC) consists of a heptapeptide attached to adenosine through a phosphoramidate linkage. McC is synthesized by the MccB enzyme, which terminally adenylates the ribosomally synthesized heptapeptide precursor MccA. The peptide part is responsible for McC uptake; it is degraded inside the cell to release a toxic nonhydrolyzable aspartyl-adenylate. Bionformatic analysis reveals that diverse bacterial genomes encoding mccB homologues also contain adjacent short open reading frames that may encode MccA-like adenylation substrates. Using chemically synthesized predicted peptide substrates and recombinant cognate MccB protein homologs, adenylated products were obtained in vitro for predicted MccA peptide-MccB enzyme pairs from Helicobacter pylori, Streptococcus thermophilus, Lactococcus johnsonii, Bartonella washoensis, Yersinia pseudotuberculosis, and Synechococcus sp. Some adenylated products were shown to inhibit the growth of E. coli by targeting aspartyl-tRNA synthetase, the target of McC. IMPORTANCE Our results prove that McC-like adenylated peptides are widespread and are encoded by both Gram-negative and Gram-positive bacteria and by cyanobacteria, opening ways for analyses of physiological functions of these compounds and for creation of microcin C-like antibiotics targeting various bacteria.
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50
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Wang H, Cui X, Pei Y, Zhang Q, Bai J, Wei D, Wu Y. Direct regioselective phosphonation of heteroaryl N-oxides with H-phosphonates under metal and external oxidant free conditions. Chem Commun (Camb) 2014; 50:14409-11. [DOI: 10.1039/c4cc07060g] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A direct C–H/P–H functionalization of heteroaryl N-oxides with H-phosphonates under metal and oxidant free conditions was developed. Various heteroaryl phosphonate derivatives were obtained in up to 92% yield in a chemo- and regioselective manner.
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Affiliation(s)
- Hui Wang
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Xiuling Cui
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Yu Pei
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Qianqian Zhang
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Jie Bai
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Donghui Wei
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| | - Yangjie Wu
- Department of Chemistry
- Henan Key Laboratory of Chemical Biology and Organic Chemistry
- Key Laboratory of Applied Chemistry of Henan Universities
- Zhengzhou University
- Zhengzhou, P. R. China
| |
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