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Xue D, Zou H, Qiu Y, Lv W, Madden MD, Xu M, Lian X, Pulliam C, Older EA, Hou L, Campbell A, de Rond T, Awakawa T, Yuan C, Moore BS, Li J. Discovery of acylsulfenic acid-featuring natural product sulfenicin and characterization of its biosynthesis. Nat Chem 2025:10.1038/s41557-025-01833-9. [PMID: 40394187 DOI: 10.1038/s41557-025-01833-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Accepted: 04/14/2025] [Indexed: 05/22/2025]
Abstract
Life's organic molecules are built with diverse functional groups that enable various importance biological functions. As such, the discovery of unique functional groups in nature can expand our understanding of the natural world. Here we report the genome-aided discovery of sulfenicin, a polyketide-non-ribosomal peptide hybrid natural product from a marine Streptomyces bacterium bearing a unique acylsulfenic acid functionality. Through a series of heterologous biosynthesis, functional genetics and enzymatic reconstitution experiments, we show that this previously described synthetic functional group is biologically assembled by a set of enzymes from both primary and secondary metabolism, including a flavin-dependent S-hydroxylase that hydroxylates the sulfur atom of a thiocarboxylic acid. Although public databases so far include no parallel for the sulfenicin biosynthetic gene cluster, enzymes catalysing the production of acylsulfenic acid are widely distributed in bacterial genomes, implying that this labile functional group may similarly have a broad distribution among specialized metabolites.
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Affiliation(s)
- Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Hongbin Zou
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yanping Qiu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Wei Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Michael D Madden
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Mingming Xu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Xiaoying Lian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Conor Pulliam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Lukuan Hou
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Andrew Campbell
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Takayoshi Awakawa
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA
- RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA.
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA.
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2
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Rice AJ, Sword TT, Chengan K, Mitchell DA, Mouncey NJ, Moore SJ, Bailey CB. Cell-free synthetic biology for natural product biosynthesis and discovery. Chem Soc Rev 2025; 54:4314-4352. [PMID: 40104998 PMCID: PMC11920963 DOI: 10.1039/d4cs01198h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Indexed: 03/20/2025]
Abstract
Natural products have applications as biopharmaceuticals, agrochemicals, and other high-value chemicals. However, there are challenges in isolating natural products from their native producers (e.g. bacteria, fungi, plants). In many cases, synthetic chemistry or heterologous expression must be used to access these important molecules. The biosynthetic machinery to generate these compounds is found within biosynthetic gene clusters, primarily consisting of the enzymes that biosynthesise a range of natural product classes (including, but not limited to ribosomal and nonribosomal peptides, polyketides, and terpenoids). Cell-free synthetic biology has emerged in recent years as a bottom-up technology applied towards both prototyping pathways and producing molecules. Recently, it has been applied to natural products, both to characterise biosynthetic pathways and produce new metabolites. This review discusses the core biochemistry of cell-free synthetic biology applied to metabolite production and critiques its advantages and disadvantages compared to whole cell and/or chemical production routes. Specifically, we review the advances in cell-free biosynthesis of ribosomal peptides, analyse the rapid prototyping of natural product biosynthetic enzymes and pathways, highlight advances in novel antimicrobial discovery, and discuss the rising use of cell-free technologies in industrial biotechnology and synthetic biology.
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Affiliation(s)
- Andrew J Rice
- Department of Biochemistry, School of Medicine - Basic Sciences, Vanderbilt University Medical Research Building-IV, Nashville, Tennessee, 37232, USA
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, TN, USA
| | | | - Douglas A Mitchell
- Department of Biochemistry, School of Medicine - Basic Sciences, Vanderbilt University Medical Research Building-IV, Nashville, Tennessee, 37232, USA
- Department of Chemistry, Vanderbilt University, Medical Research Building-IV, Nashville, Tennessee, 37232, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Simon J Moore
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Constance B Bailey
- School of Chemistry, University of Sydney, Camperdown, NSW, 2001, Australia.
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3
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Weeks AM. PEARLs of wisdom for ribosome-independent peptide bond synthesis. Proc Natl Acad Sci U S A 2025; 122:e2504930122. [PMID: 40258159 PMCID: PMC12054794 DOI: 10.1073/pnas.2504930122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2025] Open
Affiliation(s)
- Amy M. Weeks
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI53706
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4
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Yu Z, Abe I. Recently discovered heteromeric enzymes in natural product biosynthesis. J Biol Chem 2025; 301:108516. [PMID: 40246025 DOI: 10.1016/j.jbc.2025.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 04/07/2025] [Accepted: 04/09/2025] [Indexed: 04/19/2025] Open
Abstract
The abundant diversity and elegant complexity in the chemical structures of natural products have attracted vigorous investigations of the chemistry and enzymology underlying their biosynthetic processes over the past few decades. Among the biochemical events, the formation of complexes of heteromeric enzymes has been observed in the biosynthesis of several natural products and metabolic pathways. In this review, we aim to consolidate the recently discovered cases of heteromeric enzymes in natural product biosynthesis and metabolism, in order to clarify the genetic and structural bases leading to the formation of these heteromeric complexes and provide insights for the rational redesign of proteins in biosynthetic machineries.
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Affiliation(s)
- Zhongtian Yu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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5
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Seshadri K, Abad AND, Nagasawa KK, Yost KM, Johnson CW, Dror MJ, Tang Y. Synthetic Biology in Natural Product Biosynthesis. Chem Rev 2025; 125:3814-3931. [PMID: 40116601 DOI: 10.1021/acs.chemrev.4c00567] [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: 03/23/2025]
Abstract
Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.
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Affiliation(s)
- Kaushik Seshadri
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Abner N D Abad
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Kyle K Nagasawa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Karl M Yost
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Colin W Johnson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Moriel J Dror
- Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, California 90095, United States
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Padhi C, Zhu L, Chen JY, Moreira R, van der Donk WA. Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho -Tyrosines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.04.647296. [PMID: 40291698 PMCID: PMC12026744 DOI: 10.1101/2025.04.04.647296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that possess many activities that are of potential translational interest. Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), until recently termed domain of unknown function 692 (DUF692), have been gaining interest because of their involvement in a range of biochemical reactions that are remarkable from a chemical perspective. Over 13,500 putative MNIO-encoding biosynthetic gene clusters (BGCs) have been identified by sequence similarity networks (SSNs). In this study, we identified a set of precursor peptides containing a conserved FHAFRF-motif in MNIO-encoding BGCs. These BGCs follow a conserved synteny with genes encoding an MNIO, a RiPP recognition element (RRE)-containing partner protein, an arginase, and a B12-dependent radical SAM enzyme (rSAM). Using heterologous reconstitution of a representative BGC from Peribacillus simplex ( pbs cluster) in E. coli , we demonstrated that the MNIO in conjunction with the partner protein catalyzes ortho -hydroxylation of each of the phenylalanine residues in the conserved FRF-motif, the arginase forms an ornithine by deguanidination of the arginine in the motif, and the B12-rSAM crosslinks the ortho -Tyr side side chains by a C-C linkage forming a novel macrocyclic molecule. Substrate scope studies suggested tolerance of the MNIO and the B12-rSAM towards substituting the Phe residues with tyrosines in the conserved motif with the position of hydroxylation and crosslinking being maintained. Overall, this study expands the diverse array of posttranslational modifications catalyzed by MNIOs and B12-rSAM enzymes. TOC Graphic
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7
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Ramos-Figueroa J, Liang H, van der Donk WA. Substrate recognition by a peptide-aminoacyl-tRNA ligase. Proc Natl Acad Sci U S A 2025; 122:e2423858122. [PMID: 40106349 PMCID: PMC11962472 DOI: 10.1073/pnas.2423858122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Accepted: 02/18/2025] [Indexed: 03/22/2025] Open
Abstract
The continuing discovery of new peptide-aminoacyl-tRNA ligases (PEARLs) has unveiled a diverse array of enzymes with the unique potential to append amino acids to the C terminus of substrate peptides in an aminoacyl-tRNA-dependent manner. To date, PEARLs have been reported that can conjugate Cys, Ala, Trp, Gly, Leu, Asn, and Thr residues, but the basis of peptide substrate and aminoacyl-tRNA recognition is not known. Cell-free expression (CFE) has emerged as a powerful tool to rapidly assay activity of substrate variants, and we used the technique in this study to investigate the peptide substrate specificity of the PEARL [Formula: see text]. This enzyme that adds Trp was discovered previously during genome mining for ribosomally synthesized and posttranslational modified peptides (RiPPs). The enzyme is remarkably tolerant of changes to the C-terminal amino acid of the peptide substrate, and truncation and replacement experiments suggest a minimal sequence requirement. An AlphaFold3 model provided insights into binding interactions of the substrate peptide BhaA-Ala to [Formula: see text] and also generated predictions for tRNA, ATP, and Mg2+ binding modes that were tested by site-directed mutagenesis. The data suggest that several highly conserved residues in PEARLs recognize the 3'-CCA sequence present in all tRNAs. The minimal sequence required for Trp incorporation by [Formula: see text] was employed as a protein tag for C-terminal labeling of eGFP, lysozyme, and MBP with Trp and 5-Br-Trp.
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Affiliation(s)
- Josseline Ramos-Figueroa
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- HHMI, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Haoqian Liang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- HHMI, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
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8
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Awakawa T. Biosynthesis of unique natural product scaffolds by Fe(II)/αKG-dependent oxygenases. J Nat Med 2025; 79:303-313. [PMID: 39915427 PMCID: PMC11880133 DOI: 10.1007/s11418-025-01880-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Accepted: 01/21/2025] [Indexed: 03/06/2025]
Abstract
Fe(II)/αKG-dependent oxygenases are multifunctional oxidases responsible for the formation of unique natural product skeletons. Studies of these enzymes are important because the knowledge of their catalytic functions, enzyme structures, and reaction mechanisms can be used to create non-natural enzymes through mutation and synthesize non-natural compounds. In this review, I will introduce the research we have conducted on two fungal Fe(II)/αKG-dependent oxygenases, TlxI-J and TqaL. TlxI-J is the first Fe(II)/αKG-dependent oxygenase type enzyme heterodimer that catalyzes consecutive oxidation reactions, hydroxylation followed by retro-aldol or ketal formation, to form the complex skeletons of meroterpenoids. TqaL is the first naturally occurring aziridine synthase, and I will discuss the mechanism of its unique C-N bond formation in nonproteinogenic amino acid biosynthesis. This review will advance research on the discovery of new enzymes and the analysis of their functions by reviewing the structures and functions of these extraordinary Fe(II)/αKG-dependent oxygenases, and promote their use in the synthesis of new natural medicines.
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Affiliation(s)
- Takayoshi Awakawa
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, 351-0198, Japan.
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9
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Mirza S, Ahmad MS. Applications of MicroED in structural biology and structure-based drug discovery. Biochim Biophys Acta Gen Subj 2025; 1869:130758. [PMID: 39761934 DOI: 10.1016/j.bbagen.2025.130758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 01/02/2025] [Accepted: 01/02/2025] [Indexed: 01/11/2025]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging method for the structure determination of proteins and peptides, enzyme-inhibitor complexes. Several structures of biomolecules, including lysozyme, proteinase K, adenosine receptor A2A, insulin, xylanase, thermolysin, DNA, and Granulovirus occlusion bodies, have been successfully determined through MicroED. As MicroED uses very small crystals for structure determination, therefore, it has several advantages over conventional X-ray diffraction methods. In this review article, we discussed the most recent developments in the field of MicroED and its applications for the structural determination of different types of peptides, proteins, enzymes, DNA, and enzyme-inhibitor-complexed structures.
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Affiliation(s)
- Salma Mirza
- Dow University of Health Sciences, Ojha, Karachi 74200, Pakistan
| | - Malik Shoaib Ahmad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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10
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Most MM, Boll LB, Gödtel P, Pianowski ZL, Lewandowski B. Glucose-derived receptors for photo-controlled binding of amino acid esters in water. Commun Chem 2025; 8:50. [PMID: 39972110 PMCID: PMC11840139 DOI: 10.1038/s42004-025-01445-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 02/04/2025] [Indexed: 02/21/2025] Open
Abstract
Selective receptors of amino acids in aqueous media are highly sought after as they may enable the creation of novel diagnostic and sensing tools. Photoswitchable receptors are particularly attractive for such purposes as their response and selectivity towards bioanalytes can be modulated using light. Herein we report glucose-based photoswitchable receptors of amino-acid methyl esters and biogenic amines in water. The tetra-ortho-fluoroazobenzene unit in the receptors structure allows to control the distance between their binding sites using light. The Z-isomers of both receptors, having these sites in closer proximity, bind lysine, ornithine and arginine esters significantly stronger compared to E-isomers, where the binding sites are further apart.
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Affiliation(s)
- Mario M Most
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131, Karlsruhe, Germany
| | - Linus B Boll
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Peter Gödtel
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131, Karlsruhe, Germany
| | - Zbigniew L Pianowski
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131, Karlsruhe, Germany.
- Institute of Biological and Chemical Systems - Functional Molecular Systems IBCS-FMS, Karlsruhe Institute of Technology (KIT), Kaiserstrasse 12, 76131, Karlsruhe, Germany.
| | - Bartosz Lewandowski
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland.
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11
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Rudenko AY, Mariasina SS, Ozhiganov RM, Sergiev PV, Polshakov VI. Enzymatic Reactions of S-Adenosyl- L-Methionine: Synthesis and Applications. BIOCHEMISTRY. BIOKHIMIIA 2025; 90:S105-S134. [PMID: 40164155 DOI: 10.1134/s0006297924604210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 10/29/2024] [Accepted: 11/08/2024] [Indexed: 04/02/2025]
Abstract
S-adenosyl-L-methionine (SAM, AdoMet) is a ubiquitous biomolecule present in all living organisms, playing a central role in a wide array of biochemical reactions and intracellular regulatory pathways. It is the second most common participant in enzymatic reactions in living systems, following adenosine triphosphate (ATP). This review provides a comprehensive analysis of enzymatic reactions involving SAM, whether as a product, a reactant (cosubstrate), or as a non-consumable enzyme cofactor. The discussion encompasses various methods for SAM synthesis, including biotechnological, chemical, and enzymatic approaches. Particular emphasis is placed on the biochemical reactions where SAM functions as a cosubstrate, notably in trans-alkylation reactions, where it acts as a key methyl group donor. Beyond methylation, SAM also serves as a precursor for the synthesis of other molecular building blocks, which are explored in a dedicated section. The review also addresses the role of SAM as a non-consumable cofactor in enzymatic processes, highlighting its function as a prosthetic group for certain protein enzymes and its ability to form complexes with ribozymes. In addition, bioorthogonal systems involving SAM analogues are discussed. These systems employ engineered enzyme-cofactor pairs designed to enable highly selective interactions between target SAM analogues and specific enzymes, facilitating precise reactions even in the presence of other SAM-dependent enzymes. The concluding section explores practical applications of SAM analogues, including their use as selective inhibitors in clinical medicine and as components of reporter systems.
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Affiliation(s)
- Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sofia S Mariasina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Petr V Sergiev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Leprevost L, Jünger S, Lippens G, Guillaume C, Sicoli G, Oliveira L, Falcone E, de Santis E, Rivera-Millot A, Billon G, Stellato F, Henry C, Antoine R, Zirah S, Dubiley S, Li Y, Jacob-Dubuisson F. A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to metal stress. Proc Natl Acad Sci U S A 2024; 121:e2408304121. [PMID: 39602266 PMCID: PMC11626156 DOI: 10.1073/pnas.2408304121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 10/15/2024] [Indexed: 11/29/2024] Open
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a structurally diverse group of natural products that bacteria employ in their survival strategies. Herein, we characterized the structure, the biosynthetic pathway, and the mode of action of a RiPP family called bufferins. With thousands of homologous biosynthetic gene clusters throughout the bacterial phylogenetic tree, bufferins form by far the largest family of RiPPs modified by multinuclear nonheme iron-dependent oxidases (MNIO, DUF692 family). Using Caulobacter vibrioides bufferins as a model, we showed that the conserved Cys residues of their precursors are transformed into 5-thiooxazoles, further expanding the reaction range of MNIO enzymes. This rare modification is installed in conjunction with a partner protein of the DUF2063 family. Bufferin precursors are rare examples of bacterial RiPPs found to feature an N-terminal Sec signal peptide allowing them to be exported by the ubiquitous Sec pathway. We reveal that bufferins are involved in copper homeostasis, and their metal-binding propensity requires the thiooxazole heterocycles. Bufferins enhance bacterial growth under copper stress by complexing excess metal ions. Our study thus describes a large family of RiPP metallophores and unveils a widespread but overlooked metal homeostasis mechanism in bacteria.
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Affiliation(s)
- Laura Leprevost
- Univ. Lille, CNRS, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, LilleF-59000, France
| | - Sophie Jünger
- Unit Molecules of Communication and Adaptation of Microorganisms, UMR 7245 CNRS, Museum National d'Histoire Naturelle, Paris75005, France
| | - Guy Lippens
- Toulouse Biotechnology Institute, CNRS/Institut National de la Recherche en Agronomie, Alimentation et Environnement/Institut National des Sciences Appliquées, Toulouse31077, France
| | - Céline Guillaume
- Unit Molecules of Communication and Adaptation of Microorganisms, UMR 7245 CNRS, Museum National d'Histoire Naturelle, Paris75005, France
| | - Giuseppe Sicoli
- CNRS, UMR 8516 Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Université de Lille, LilleF-59000, France
| | - Lydie Oliveira
- Institut National de la Recherche en Agronomie, Alimentation et Environnement-AgroParisTech-Université Paris-Saclay, Microbiologie des aliments au service de la santé, Jouy-en Josas78352, France
| | - Enrico Falcone
- Laboratoire de Chimie de Coordination, CNRS UPR 8241, Toulouse31077, France
| | - Emiliano de Santis
- Department of Physics, University of Rome Tor Vergata and Istituto Nazionale di Fisica Nucleare, Rome00133, Italy
| | - Alex Rivera-Millot
- Univ. Lille, CNRS, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, LilleF-59000, France
| | - Gabriel Billon
- CNRS, UMR 8516 Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Université de Lille, LilleF-59000, France
| | - Francesco Stellato
- Department of Physics, University of Rome Tor Vergata and Istituto Nazionale di Fisica Nucleare, Rome00133, Italy
| | - Céline Henry
- Institut National de la Recherche en Agronomie, Alimentation et Environnement-AgroParisTech-Université Paris-Saclay, Microbiologie des aliments au service de la santé, Jouy-en Josas78352, France
| | - Rudy Antoine
- Univ. Lille, CNRS, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, LilleF-59000, France
| | - Séverine Zirah
- Unit Molecules of Communication and Adaptation of Microorganisms, UMR 7245 CNRS, Museum National d'Histoire Naturelle, Paris75005, France
| | - Svetlana Dubiley
- Toulouse Biotechnology Institute, CNRS/Institut National de la Recherche en Agronomie, Alimentation et Environnement/Institut National des Sciences Appliquées, Toulouse31077, France
| | - Yanyan Li
- Unit Molecules of Communication and Adaptation of Microorganisms, UMR 7245 CNRS, Museum National d'Histoire Naturelle, Paris75005, France
| | - Françoise Jacob-Dubuisson
- Univ. Lille, CNRS, INSERM, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - Center for Infection and Immunity of Lille, LilleF-59000, France
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13
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Zhong L, Tan X, Yang W, Li P, Ye L, Luo Q, Hou H. Bioactive matters based on natural product for cardiovascular diseases. SMART MATERIALS IN MEDICINE 2024; 5:542-565. [DOI: 10.1016/j.smaim.2024.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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14
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Li F, Liu R, Li W, Xie M, Qin S. Synchrotron Radiation: A Key Tool for Drug Discovery. Bioorg Med Chem Lett 2024; 114:129990. [PMID: 39406298 DOI: 10.1016/j.bmcl.2024.129990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/22/2024] [Accepted: 10/11/2024] [Indexed: 10/25/2024]
Abstract
Synchrotron radiation is extensively utilized in the domains of materials science, physical chemistry, and life science, resulting from its high intensity, exceptional monochromaticity, superior collimation, and broad wave spectrum. This top-notch light source has also made significant contributions to the progress of biomedicine. The advancement of synchrotron radiation-based X-ray and protein crystallography technologies has created new prospects for drug discovery. These innovative techniques have opened up exciting avenues in the field. The investigation of protein crystal structures and the elucidation of the spatial configuration of biological macromolecules have revealed intricate details regarding the modes of protein binding. Furthermore, the screening of crystal polymorphs and ligands has laid the groundwork for rational drug modification and the improvement of drug physicochemical properties. As science and technology continue to advance, the techniques for analyzing structures using synchrotron radiation sources and the design of corresponding crystallographic beamline stations are undergoing continuous enhancement. These cutting-edge tools and facilities are expected to expedite the drug development process and rectify the current situation of a lack of targeted drugs.
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Affiliation(s)
- Fengcheng Li
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Runze Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Wenjun Li
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Mingyuan Xie
- Institute of Advanced Science Facilities, Shenzhen, Guangdong 518107, China.
| | - Song Qin
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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15
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Fu B, Yang H, Kountz DJ, Lundahl MN, Beller HR, Broderick WE, Broderick JB, Hoffman BH, Balskus EP. Discovery of a New Class of Aminoacyl Radical Enzymes Expands Nature's Known Radical Chemistry. J Am Chem Soc 2024; 146:29645-29655. [PMID: 39392720 PMCID: PMC11528403 DOI: 10.1021/jacs.4c10348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/24/2024] [Accepted: 10/02/2024] [Indexed: 10/13/2024]
Abstract
Radical enzymes, including the evolutionarily ancient glycyl radical enzyme (GRE) family, catalyze chemically challenging reactions that are involved in a myriad of important biological processes. All GREs possess an essential, conserved backbone glycine that forms a stable, catalytically essential α-carbon radical. Through close examination of the GRE family, we unexpectedly identified hundreds of noncanonical GRE homologs that encode either an alanine, serine, or threonine in place of the catalytic glycine residue. Contrary to a long-standing belief, we experimentally demonstrate that these aminoacyl radical enzymes (AAREs) form stable α-carbon radicals on the three cognate residues when activated by partner activating enzymes. The previously unrecognized AAREs are widespread in microbial genomes, highlighting their biological importance and potential for exhibiting new reactivity. Collectively, these studies expand the known radical chemistry of living systems while raising questions about the evolutionary emergence of the AAREs.
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Affiliation(s)
- Beverly Fu
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Hao Yang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Duncan J. Kountz
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
| | - Maike N. Lundahl
- Department
of Chemistry and Biochemistry, Montana State
University, Bozeman, Montana 59717, United States
| | - Harry R. Beller
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada
| | - William E. Broderick
- Department
of Chemistry and Biochemistry, Montana State
University, Bozeman, Montana 59717, United States
| | - Joan B. Broderick
- Department
of Chemistry and Biochemistry, Montana State
University, Bozeman, Montana 59717, United States
| | - Brian H. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Emily P. Balskus
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Howard Hughes
Medical Institute, Harvard University, Cambridge, Massachusetts 02138, United States
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16
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Chen H, Kim S, Ting CP. Total Synthesis of (±)-3-Thiaglutamate. Tetrahedron Lett 2024; 149:155246. [PMID: 39295961 PMCID: PMC11407705 DOI: 10.1016/j.tetlet.2024.155246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
The total synthesis of (±)-3-thiaglutamate is reported. Central to our strategy is an thiol addition to an imine to form the thioaminal of the natural product. The resulting thioaminal product is then subjected to triflic acid global deprotection to produce 3-thiaglutamate as a triflate salt. This work constitutes the first total synthesis of 3-thiaglutamate and demonstrates that the hemithioaminal group in 3-thiaglutamate can be stabilized under acidic conditions.
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Affiliation(s)
- Hao Chen
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, 02453, United States
| | - Sohjeong Kim
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, 02453, United States
| | - Chi P Ting
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA, 02453, United States
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17
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Protein interactions in human pathogens revealed through deep learning. Nat Microbiol 2024; 9:2642-2652. [PMID: 39294458 PMCID: PMC11445079 DOI: 10.1038/s41564-024-01791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/23/2024] [Indexed: 09/20/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of these complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here we developed RoseTTAFold2-Lite, a rapid deep learning model that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1,923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer-membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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Affiliation(s)
- Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Minkyung Baek
- Department of Biological Sciences, Seoul National University, Seoul, South Korea.
| | - Yaxi Wang
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Aditya Krishnakumar
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine A Tower
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Blake A Jackson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Thulasi Warrier
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deborah T Hung
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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18
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Simke W, Walker ME, Calderone LA, Putz AT, Patteson JB, Vitro CN, Zizola CF, Redinbo MR, Pandelia ME, Grove TL, Li B. Structural Basis for Methine Excision by a Heme Oxygenase-like Enzyme. ACS CENTRAL SCIENCE 2024; 10:1524-1536. [PMID: 39220707 PMCID: PMC11363339 DOI: 10.1021/acscentsci.4c00015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024]
Abstract
Heme oxygenase-like domain-containing oxidases (HDOs) are a rapidly expanding enzyme family that typically use dinuclear metal cofactors instead of heme. FlcD, an HDO from the opportunistic pathogen Pseudomonas aeruginosa, catalyzes the excision of an oxime carbon in the biosynthesis of the copper-containing antibiotic fluopsin C. We show that FlcD is a dioxygenase that catalyzes a four-electron oxidation. Crystal structures of FlcD reveal a mononuclear iron in the active site, which is coordinated by two histidines, one glutamate, and the oxime of the substrate. Enzyme activity, Mössbauer spectroscopy, and electron paramagnetic resonance spectroscopy analyses support the usage of a mononuclear iron cofactor. This cofactor resembles that of mononuclear non-heme iron-dependent enzymes and breaks the paradigm of dinuclear HDO cofactors. This study begins to illuminate the catalytic mechanism of methine excision and indicates convergent evolution of different lineages of mononuclear iron-dependent enzymes.
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Affiliation(s)
- William
C. Simke
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Morgan E. Walker
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Logan A. Calderone
- Department
of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Andrew T. Putz
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Jon B. Patteson
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Caitlin N. Vitro
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Cynthia F. Zizola
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Matthew R. Redinbo
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
- Integrated
Program for Biological and Genome Sciences, Department of Biochemistry
and Biophysics, and Department of Microbiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Maria-Eirini Pandelia
- Department
of Biochemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Bo Li
- Department
of Chemistry, The University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
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19
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Reyes RM, Rosenzweig AC. Purification and biochemical characterization of methanobactin biosynthetic enzymes. Methods Enzymol 2024; 702:171-187. [PMID: 39155110 PMCID: PMC11622243 DOI: 10.1016/bs.mie.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Methanobactin (Mbn) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that binds Cu(I) with high affinity. The copper-chelating thioamide/oxazolone groups in Mbn are installed on the precursor peptide MbnA by the core enzyme complex, MbnBC, which includes the multinuclear non-heme iron-dependent oxidase (MNIO) MbnB and its RiPP recognition element-containing partner protein MbnC. For the extensively characterized Mbn biosynthetic gene cluster (BGC) from the methanotroph Methylosinus trichosporium OB3b, the tailoring aminotransferase MbnN further modifies MbnA after leader sequence cleavage by an unknown mechanism. Here we detail methods to express and purify M. trichosporium OB3b MbnBC and MbnN along with protocols for assessing MbnA modification by MbnBC and MbnN aminotransferase activity. In addition, we describe crystallization and structure determination of MbnBC. These procedures can be adapted for other MNIOs and partner proteins encoded in Mbn and Mbn-like BGCs. Furthermore, these methods provide a first step toward in vitro biosynthesis of Mbns and related natural products as potential therapeutics.
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Affiliation(s)
- Reyvin M Reyes
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, United States.
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20
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Manley OM, Shriver TJ, Xu T, Melendrez IA, Palacios P, Robson SA, Guo Y, Kelleher NL, Ziarek JJ, Rosenzweig AC. A multi-iron enzyme installs copper-binding oxazolone/thioamide pairs on a nontypeable Haemophilus influenzae virulence factor. Proc Natl Acad Sci U S A 2024; 121:e2408092121. [PMID: 38968106 PMCID: PMC11252979 DOI: 10.1073/pnas.2408092121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/01/2024] [Indexed: 07/07/2024] Open
Abstract
The multinuclear nonheme iron-dependent oxidases (MNIOs) are a rapidly growing family of enzymes involved in the biosynthesis of ribosomally synthesized, posttranslationally modified peptide natural products (RiPPs). Recently, a secreted virulence factor from nontypeable Haemophilus influenzae (NTHi) was found to be expressed from an operon, which we designate the hvf operon, that also encodes an MNIO. Here, we show by Mössbauer spectroscopy that the MNIO HvfB contains a triiron cofactor. We demonstrate that HvfB works together with HvfC [a RiPP recognition element (RRE)-containing partner protein] to perform six posttranslational modifications of cysteine residues on the virulence factor precursor peptide HvfA. Structural characterization by tandem mass spectrometry and NMR shows that these six cysteine residues are converted to oxazolone and thioamide pairs, similar to those found in the RiPP methanobactin. Like methanobactin, the mature virulence factor, which we name oxazolin, uses these modified residues to coordinate Cu(I) ions. Considering the necessity of oxazolin for host cell invasion by NTHi, these findings point to a key role for copper during NTHi infection. Furthermore, oxazolin and its biosynthetic pathway represent a potential therapeutic target for NTHi.
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Affiliation(s)
- Olivia M. Manley
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Tucker J. Shriver
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Tian Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Isaac A. Melendrez
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Philip Palacios
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA15213
| | - Scott A. Robson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA15213
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Chemistry, Northwestern University, Evanston, IL60208
| | - Joshua J. Ziarek
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, IL60208
- Department of Chemistry, Northwestern University, Evanston, IL60208
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21
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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22
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Richter D, Piel J. Novel types of RiPP-modifying enzymes. Curr Opin Chem Biol 2024; 80:102463. [PMID: 38729090 DOI: 10.1016/j.cbpa.2024.102463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024]
Abstract
Novel discoveries in natural product biosynthesis reveal hidden bioactive compounds and expand our knowledge in enzymology. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products featuring diverse non-canonical amino acids introduced by maturation enzymes as a class-defining characteristic. Underexplored RiPP sources, such as the human microbiome, the oceans, uncultured microorganisms, and plants are rich hunting grounds for novel enzymology. Unusual α- and β-amino acids, peptide cleavages, lipidations, diverse macrocyclizations, and other features expand the range of chemical groups that are installed in RiPPs by often promiscuous enzymes. This review highlights the search for novelty in RiPP enzymology in the past two years, with respect to the discovery of new biochemical modifications but also towards novel applications.
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Affiliation(s)
- Daniel Richter
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
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23
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Chen JY, van der Donk WA. Multinuclear non-heme iron dependent oxidative enzymes (MNIOs) involved in unusual peptide modifications. Curr Opin Chem Biol 2024; 80:102467. [PMID: 38772214 PMCID: PMC11806912 DOI: 10.1016/j.cbpa.2024.102467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024]
Abstract
Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), formerly known as domain of unknown function 692 (DUF692), are involved in the post-translational modification of peptides during the biosynthesis of peptide-based natural products. These enzymes catalyze highly unusual and diverse chemical modifications. Several class-defining features of this large family (>14 000 members) are beginning to emerge. Structurally, the enzymes are characterized by a TIM-barrel fold and a set of conserved residues for a di- or tri-iron binding site. They use molecular oxygen to modify peptide substrates, often in a four-electron oxidation taking place at a cysteine residue. This review summarizes the current understanding of MNIOs. Four modifications are discussed in detail: oxazolone-thioamide formation, β-carbon excision, hydantoin-macrocycle formation, and 5-thiooxazole formation. Briefly discussed are two other reactions that do not take place on Cys residues.
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Affiliation(s)
- Jeff Y Chen
- Department of Chemistry, The Carl R. Woese Institute for Genomic Biology, The Howard Hughes Medical Institute at the University of Illinois at Urbana-Champaign, 1206 W Gregory Drive, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, The Carl R. Woese Institute for Genomic Biology, The Howard Hughes Medical Institute at the University of Illinois at Urbana-Champaign, 1206 W Gregory Drive, Urbana, IL 61801, USA.
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24
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Gao Y, Zhong Z, Zhang D, Zhang J, Li YX. Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining. MICROBIOME 2024; 12:94. [PMID: 38790030 PMCID: PMC11118758 DOI: 10.1186/s40168-024-01807-y] [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: 11/11/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored. RESULTS Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome. CONCLUSIONS This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. Video Abstract.
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Affiliation(s)
- Ying Gao
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Zheng Zhong
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Dengwei Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Jian Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Yong-Xin Li
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China.
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25
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Ramos Figueroa J, Zhu L, van der Donk WA. Unexpected Transformations during Pyrroloiminoquinone Biosynthesis. J Am Chem Soc 2024; 146:14235-14245. [PMID: 38719200 PMCID: PMC11117183 DOI: 10.1021/jacs.4c03677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Pyrroloiminoquinone-containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP- and tRNA-dependent manner catalyzed by a PEptide Aminoacyl-tRNA Ligase (PEARL). The indole of Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes from two gene clusters, which show that the previously proposed pathway is incorrect and that Nature's route toward pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, amino groups in pyrroloiminoquinones are derived from (at least) three different sources, glycine, asparagine, and leucine, all introduced in a tRNA-dependent manner. We also show that an FAD-dependent putative glycine oxidase (Amm14) is required for the process that incorporates the nitrogens from glycine and leucine and that a quinone reductase is required for the incorporation of asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes, such as the glutamyl-tRNA-dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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26
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of Macrocyclic Peptides with C-Terminal β-Amino-α-keto Acid Groups by Three Different Metalloenzymes. ACS CENTRAL SCIENCE 2024; 10:1022-1032. [PMID: 38799663 PMCID: PMC11117315 DOI: 10.1021/acscentsci.4c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configuration of the atropisomer formed upon biaryl cross-linking. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Danielle L. Gray
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Toby J. Woods
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kristen M. Flatt
- Materials
Research Laboratory, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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27
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Jodts RJ, Ho MB, Reyes RM, Park YJ, Doan PE, Rosenzweig AC, Hoffman BM. Initial Steps in Methanobactin Biosynthesis: Substrate Binding by the Mixed-Valent Diiron Enzyme MbnBC. Biochemistry 2024; 63:1170-1177. [PMID: 38587906 PMCID: PMC11613419 DOI: 10.1021/acs.biochem.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The MbnBC enzyme complex converts cysteine residues in a peptide substrate, MbnA, to oxazolone/thioamide groups during the biosynthesis of copper chelator methanobactin (Mbn). MbnBC belongs to the mixed-valent diiron oxygenase (MVDO) family, of which members use an Fe(II)Fe(III) cofactor to react with dioxygen for substrate modification. Several crystal structures of the inactive Fe(III)Fe(III) form of MbnBC alone and in complex with MbnA have been reported, but a mechanistic understanding requires determination of the oxidation states of the crystallographically observed Fe ions in the catalytically active Fe(II)Fe(III) state, along with the site of MbnA binding. Here, we have used electron nuclear double resonance (ENDOR) spectroscopy to determine such structural and electronic properties of the active site, in particular, the mode of substrate binding to the MV state, information not accessible by X-ray crystallography alone. The oxidation states of the two Fe ions were determined by 15N ENDOR analysis. The presence and locations of both bridging and terminal exogenous solvent ligands were determined using 1H and 2H ENDOR. In addition, 2H ENDOR using an isotopically labeled MbnA substrate indicates that MbnA binds to the Fe(III) ion of the cluster via the sulfur atom of its N-terminal modifiable cysteine residue, with displacement of a coordinated solvent ligand as shown by complementary 1H ENDOR. These results, which underscore the utility of ENDOR in studying MVDOs, provide a molecular picture of the initial steps in Mbn biosynthesis.
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Affiliation(s)
- Richard J. Jodts
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Madeline B. Ho
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Reyvin M. Reyes
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Yun Ji Park
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Peter E. Doan
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Amy C. Rosenzweig
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Brian M. Hoffman
- Departments of Chemistry and Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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28
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Pang C, Xu Y, Ma X, Li S, Zhou S, Tian H, Wang M, Han B. Design, synthesis, and evaluation of novel arecoline-linked amino acid derivatives for insecticidal and antifungal activities. Sci Rep 2024; 14:9392. [PMID: 38658769 PMCID: PMC11043403 DOI: 10.1038/s41598-024-60053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
A series of arecoline derivatives with amino acid moieties were designed and synthesised using an acylamide condensation strategy, taking arecoline as the foundational structure. The insecticidal efficacy of these compounds against Aphis craccivora and Tetranychus cinnabarinus was evaluated. Notably, derivatives 3h and 3i demonstrated superior insecticidal activity compared with arecoline. Additionally, 3h and 3i showed good fungicidal effectiveness against two types of plant fungi. Moreover, molecular docking analyses suggested that 3h and 3i could affect the nervous systems of A. craccivora and T. cinnabarinus by binding to neuronal nicotinic acetylcholine receptors. These findings suggest that compounds 3h and 3i represent promising leads for further development in insecticide and fungicide research.
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Affiliation(s)
- Chaohai Pang
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China.
| | - Yuan Xu
- Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, International Joint Research Center of Human-machine Intelligent Collaborative for Tumor Precision Diagnosis and Treatment of Hainan Province, Hainan provincial key laboratory of research and development on tropical herbs, School of Pharmacy, Hainan Medical University, Haikou, 571199, China
| | - Xionghui Ma
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China.
| | - Shuhuai Li
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China.
| | - Shengfu Zhou
- Shenzhen Bay Laboratory, BayRay Innovation Center, Shenzhen, 518000, China
| | - Hai Tian
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China
| | - Mingyue Wang
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China
| | - Bingjun Han
- Hainan Provincial Key Laboratory of Quality and Safety for Tropical Fruits and Vegetables, Key Laboratory of Quality and Safety Control of Subtropical Fruits and Vegetables, Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Haikou, 571101, China
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29
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Humphreys IR, Zhang J, Baek M, Wang Y, Krishnakumar A, Pei J, Anishchenko I, Tower CA, Jackson BA, Warrier T, Hung DT, Peterson SB, Mougous JD, Cong Q, Baker D. Essential and virulence-related protein interactions of pathogens revealed through deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589144. [PMID: 38645026 PMCID: PMC11030334 DOI: 10.1101/2024.04.12.589144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Identification of bacterial protein-protein interactions and predicting the structures of the complexes could aid in the understanding of pathogenicity mechanisms and developing treatments for infectious diseases. Here, we developed a deep learning-based pipeline that leverages residue-residue coevolution and protein structure prediction to systematically identify and structurally characterize protein-protein interactions at the proteome-wide scale. Using this pipeline, we searched through 78 million pairs of proteins across 19 human bacterial pathogens and identified 1923 confidently predicted complexes involving essential genes and 256 involving virulence factors. Many of these complexes were not previously known; we experimentally tested 12 such predictions, and half of them were validated. The predicted interactions span core metabolic and virulence pathways ranging from post-transcriptional modification to acid neutralization to outer membrane machinery and should contribute to our understanding of the biology of these important pathogens and the design of drugs to combat them.
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30
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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31
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Gao Y, Zhu Y, Awakawa T, Abe I. Unusual cysteine modifications in natural product biosynthesis. RSC Chem Biol 2024; 5:293-311. [PMID: 38576726 PMCID: PMC10989515 DOI: 10.1039/d4cb00020j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/08/2024] [Indexed: 04/06/2024] Open
Abstract
l-Cysteine is a highly reactive amino acid that is modified into a variety of chemical structures, including cysteine sulfinic acid in human metabolic pathways, and sulfur-containing scaffolds of amino acids, alkaloids, and peptides in natural product biosynthesis. Among the modification enzymes responsible for these cysteine-derived compounds, metalloenzymes constitute an important family of enzymes that catalyze a wide variety of reactions. Therefore, understanding their reaction mechanisms is important for the biosynthetic production of cysteine-derived natural products. This review mainly summarizes recent mechanistic investigations of metalloenzymes, with a particular focus on recently discovered mononuclear non-heme iron (NHI) enzymes, dinuclear NHI enzymes, and radical-SAM enzymes involved in unusual cysteine modifications in natural product biosynthesis.
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Affiliation(s)
- Yaojie Gao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuhao Zhu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- RIKEN Center for Sustainable Resource Science Wako Saitama 351-0198 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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32
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Tang S, Hao Q, Huang Y, Zhao S, Hu K. Highly selective and sensitive histamine and tryptamine analysis using SiO 2@AuNPs@PDA molecularly imprinted polymer coupled with SALDI-TOF MS. Talanta 2024; 270:125538. [PMID: 38086223 DOI: 10.1016/j.talanta.2023.125538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/07/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
A combination of SiO2@AuNPs@PDA molecularly imprinted and surface-assisted laser desorption/ionization-time-of-flight mass spectrometry (SALDI-TOF MS) was devised as a method for highly specific and ultrasensitive detection of two biogenic amines-histamine (HIS) and tryptamine (TRP)-in real samples. In this strategy, AuNPs modified amino-abundant silica nanospheres (SiO2@AuNPs). The prepared SiO2@AuNPs were used as a substrate to synthesize a molecularly imprinted polymer (MIP) through in situ dopamine self-polymerization with HIS and TRP as the template molecules (SiO2@AuNP@PDA-MIP). The as-prepared MIP structure, properties, and target-analyte identification conditions were characterized and optimized and it was used as the matrix for MS. Compared to the case of nonimprinted materials, the imprinting function endowed the matrix with a higher selectivity for capturing the target molecules. The enriched analytes were directly and rapidly identified using SALDI-TOF MS without elution. Meanwhile, the proposed method has low background interference, good reproducibility and stability, high salt tolerance, and satisfactory linearity (R2 > 0.99), and it enables ultrasensitive detection of HIS and TRP (limits of detection for HIS and TRP were 0.2 and 0.1 ng mL-1, respectively). Moreover, the proposed method was applied to analyze samples of real beer, sausage, and chicken, and the results agreed with those obtained via liquid chromatography-MS, suggesting that the method has excellent practical applications in the field of food safety.
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Affiliation(s)
- Shuiping Tang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Qing Hao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Yong Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Shulin Zhao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China
| | - Kun Hu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources/Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, PR China.
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33
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Chioti VT, Clark KA, Ganley JG, Han EJ, Seyedsayamdost MR. N-Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster. J Am Chem Soc 2024; 146:7313-7323. [PMID: 38452252 PMCID: PMC11062405 DOI: 10.1021/jacs.3c11740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
DUF692 multinuclear iron oxygenases (MNIOs) are an emerging family of tailoring enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Three members, MbnB, TglH, and ChrH, have been characterized to date and shown to catalyze unusual and complex transformations. Using a co-occurrence-based bioinformatic search strategy, we recently generated a sequence similarity network of MNIO-RiPP operons that encode one or more MNIOs adjacent to a transporter. The network revealed >1000 unique gene clusters, evidence of an unexplored biosynthetic landscape. Herein, we assess an MNIO-RiPP cluster from this network that is encoded in Proteobacteria and Actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes a 23-residue precursor peptide, two MNIOs, a RiPP recognition element, and a transporter. Using both in vivo and in vitro methods, we show that one MNIO, homologous to MbnB, installs an oxazolone-thioamide at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO catalyzes N-Cα bond cleavage of the penultimate Asn to generate a C-terminally amidated peptide. This transformation expands the reaction scope of the enzyme family, marks the first example of an MNIO-catalyzed modification that does not involve Cys, and sets the stage for future exploration of other MNIO-RiPPs.
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Affiliation(s)
- Vasiliki T Chioti
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jack G Ganley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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34
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Figueroa JR, Zhu L, van der Donk WA. Unexpected transformations during pyrroloiminoquinone biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584671. [PMID: 38559119 PMCID: PMC10979984 DOI: 10.1101/2024.03.12.584671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pyrroloiminoquinone containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP and tRNA dependent manner catalyzed by a PEptide Amino-acyl tRNA ligase (PEARL). The indole of the Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes that show that the proposed pathway is incorrect and that Nature's route towards pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, the amino groups in pyrroloiminoquinones are derived from three different sources, glycine, asparagine, and leucine, all introduced in a tRNA dependent manner. We also show that an FAD-dependent putative glycine oxidase is required for the process that incorporates the nitrogens from glycine and leucine, and that a quinone reductase is required for the incorporation of the asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes such as the glutamyl-tRNA dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lingyang Zhu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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35
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Eslami SM, van der Donk WA. Proteases Involved in Leader Peptide Removal during RiPP Biosynthesis. ACS BIO & MED CHEM AU 2024; 4:20-36. [PMID: 38404746 PMCID: PMC10885120 DOI: 10.1021/acsbiomedchemau.3c00059] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/27/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) have received much attention in recent years because of their promising bioactivities and the portability of their biosynthetic pathways. Heterologous expression studies of RiPP biosynthetic enzymes identified by genome mining often leave a leader peptide on the final product to prevent toxicity to the host and to allow the attachment of a genetically encoded affinity purification tag. Removal of the leader peptide to produce the mature natural product is then carried out in vitro with either a commercial protease or a protease that fulfills this task in the producing organism. This review covers the advances in characterizing these latter cognate proteases from bacterial RiPPs and their utility as sequence-dependent proteases. The strategies employed for leader peptide removal have been shown to be remarkably diverse. They include one-step removal by a single protease, two-step removal by two dedicated proteases, and endoproteinase activity followed by aminopeptidase activity by the same protease. Similarly, the localization of the proteolytic step varies from cytoplasmic cleavage to leader peptide removal during secretion to extracellular leader peptide removal. Finally, substrate recognition ranges from highly sequence specific with respect to the leader and/or modified core peptide to nonsequence specific mechanisms.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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36
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Haymaker A, Nannenga BL. Advances and applications of microcrystal electron diffraction (MicroED). Curr Opin Struct Biol 2024; 84:102741. [PMID: 38086321 PMCID: PMC10882645 DOI: 10.1016/j.sbi.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 02/08/2024]
Abstract
Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography.
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Affiliation(s)
- Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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37
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of macrocyclic peptides with C-terminal β-amino-α-keto acid groups by three different metalloenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564719. [PMID: 37965205 PMCID: PMC10635010 DOI: 10.1101/2023.10.30.564719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new class involving modifications installed by a cytochrome P450, a multi-nuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-L-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes encoded by the BGC were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization with 2D-NMR and Marfey's method on the resulting RiPP demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C crosslink between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid while the methyltransferase acted on the β-carbon of the α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configurations of the atropisomer that formed upon biaryl crosslinking. The conserved Cys residue in the precursor peptide was not modified as in all other characterized MNIO-containing BGCs; However, mutational analyses demonstrated that it was essential for the MNIO activity on the C-terminal Asp. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to discover new macrocyclic RiPPs and that RiPPs remain a significant source of previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Danielle L. Gray
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Toby J. Woods
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chandrashekhar Padhi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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38
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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 ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Sho Hee Park
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Jiyoon Kim
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Jaehak Lee
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Min Sun Koh
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Jung Ho Lee
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
| | - Seokhee Kim
- Department of ChemistrySeoul National University1 Gwanak‐ro, Gwanak‐guSeoul08826Republic of Korea
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39
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Yu Y, van der Donk WA. PEARL-catalyzed peptide bond formation after chain reversal during the biosynthesis of non-ribosomal peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573212. [PMID: 38187666 PMCID: PMC10769383 DOI: 10.1101/2023.12.23.573212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic sequence towards these compounds. The putative lantibiotic dehydratase catalyzes peptide bond formation that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS catalyzes the formation of a ureido group, and bioinformatics analysis revealed distinct active site residues of ureido-generating condensation (UreaC) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and non-ribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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40
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Danelius E, Bu G, Wieske LHE, Gonen T. MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations. ACS Chem Biol 2023; 18:2582-2589. [PMID: 37944119 PMCID: PMC10728894 DOI: 10.1021/acschembio.3c00611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as to act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally, and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles that have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material and that different conformations of flexible compounds can be derived from the same experiment. These results will have an impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- Emma Danelius
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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41
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Gao ZH, Guo XY, Liu YZ, Zhang QM, Tong XJ, Qiu LH. Trinickia violacea sp. nov. and Trinickia terrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917540 DOI: 10.1099/ijsem.0.006147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
Two Gram-stain negative, aerobic and rod-shaped bacterial strains, DHOD12T and 7GSK02T, were isolated from forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOD12T grew at 4-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.5-6.5) and in the presence of 0-1.5 % (w/v; optimum, 0-0.5 %)NaCl; while strain 7GSK02T grew at 12-42 °C (optimum, 28-33 °C), pH 4.0-8.5 (optimum, pH 5.0-6.0) and in the presence of 0-0.5 % (w/v; optimum, 0 %) NaCl. Strains DHOD12T and 7GSK02T had the highest 16S rRNA sequence similarities of 98.0 and 98.3 % with the same species Trinickia mobilis DHG64T, respectively, and 98.4 % between themselves. In the 16S rRNA phylogeny, they formed a clade that was sister to a major cluster consisting of all described Trinickia species. Phylogenomic analyses with the UBCG and PhyloPhlAn methods consistently showed that strains DHOD12T and 7GSK02T formed a clade with T. mobilis DHG64T that was a sister of a cluster containing the remainder of the Trinickia species. The DNA G+C contents of strains DHOD12T and 7GSK02T were 63.1 and 64.6 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity values of strains DHOD12T, 7GSK02T and their closely related strains were in the ranges of 21.6-31.4 % and 77.1-86.9 %, respectively. These two strains had the same major respiratory quinone, ubiquinone-8, and both had C16 : 0, C17 : 0 cyclo and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as their major fatty acids. Their major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Genomic analysis indicated that the two strains could have the potential to degrade aromatic compounds like other Trinickia species. On the basis of phenotypic and phylogenetic results, strains DHOD12T and 7GSK02T represent two novel species of the genus Trinickia, for which the names Trinickia violacea sp. nov. (type strain DHOD12T=LMG 30258T=CGMCC 1.15436T) and Trinickia terrae sp. nov. (type strain 7GSK02T=CGMCC 1.15432T=KCTC 62468T) are proposed.
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Affiliation(s)
- Zeng-Hong Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xiu-Yin Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Yi-Zhi Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Qiu-Mei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Xin-Jie Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
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42
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Zheng Y, Xu X, Fu X, Zhou X, Dou C, Yu Y, Yan W, Yang J, Xiao M, van der Donk WA, Zhu X, Cheng W. Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis. Structure 2023; 31:1220-1232.e5. [PMID: 37652001 PMCID: PMC10880893 DOI: 10.1016/j.str.2023.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
Structural diverse natural products like ribosomally synthesized and posttranslationally modified peptides (RiPPs) display a wide range of biological activities. Currently, the mechanism of an uncommon reaction step during the biosynthesis of 3-thiaglutamate (3-thiaGlu) is poorly understood. The removal of the β-carbon from the Cys in the TglA-Cys peptide catalyzed by the TglHI holoenzyme remains elusive. Here, we present three crystal structures of TglHI complexes with and without bound iron, which reveal that the catalytic pocket is formed by the interaction of TglH-TglI and that its activation is conformation dependent. Biochemical assays suggest a minimum of two iron ions in the active cluster, and we identify the position of a third iron site. Collectively, our study offers insights into the activation and catalysis mechanisms of the non-heme dioxygen-dependent holoenzyme TglHI. Additionally, it highlights the evolutionary and structural conservation in the DUF692 family of biosynthetic enzymes that produce diverse RiPPs.
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Affiliation(s)
- Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoqing Xu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoli Fu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xuerong Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China; Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong 637000, China
| | - Chao Dou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yue Yu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weizhu Yan
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Jingyuan Yang
- Core Facilities of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minqin Xiao
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Wilfred A van der Donk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Xiaofeng Zhu
- College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.
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43
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Chen X, Li B. How nature incorporates sulfur and selenium into bioactive natural products. Curr Opin Chem Biol 2023; 76:102377. [PMID: 37598530 PMCID: PMC10538389 DOI: 10.1016/j.cbpa.2023.102377] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
Living organisms have evolved various strategies to incorporate sulfur and selenium into bioactive natural products. These chalcogen-containing compounds serve important and diverse biological functions for their producers and many of them are essential medicines against infectious diseases and cancer. We review recent advances in the biosynthesis of some sulfur/selenium-containing natural products with a focus on the formation or cleavage of C-S/C-Se bonds. We highlight unusual enzymes that catalyze these transformations, describe their proposed mechanisms, and discuss how understanding these enzymes may facilitate the discovery and synthesis of novel natural products containing sulfur or selenium.
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Affiliation(s)
- Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Chemistry, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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44
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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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45
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Danelius E, Bu G, Wieske H, Gonen T. MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551405. [PMID: 37577574 PMCID: PMC10418104 DOI: 10.1101/2023.07.31.551405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles which have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material, and that different conformations of flexible compounds can be derived from the same experiment. These results will have impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- E Danelius
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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46
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Ayikpoe R, Zhu L, Chen JY, Ting CP, van der Donk WA. Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. ACS CENTRAL SCIENCE 2023; 9:1008-1018. [PMID: 37252350 PMCID: PMC10214503 DOI: 10.1021/acscentsci.3c00160] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 05/31/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of post-translational modification enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes, and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme complex catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethyl group. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent reaction catalyzed by a DUF692 enzyme complex, further expanding the repertoire of remarkable reactions catalyzed by these enzymes. Based on the three currently characterized DUF692 family members, we suggest the family be called multinuclear non-heme iron dependent oxidative enzymes (MNIOs).
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Affiliation(s)
- Richard
S. Ayikpoe
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Jeff Y. Chen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Chi P. Ting
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
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47
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Richards L, Flores MD, Millán C, Glynn C, Zee CT, Sawaya MR, Gallagher-Jones M, Borges RJ, Usón I, Rodriguez JA. Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED. ACS BIO & MED CHEM AU 2023; 3:201-210. [PMID: 37096030 PMCID: PMC10119933 DOI: 10.1021/acsbiomedchemau.2c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 04/26/2023]
Abstract
Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its de novo determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.
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Affiliation(s)
- Logan
S. Richards
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Maria D. Flores
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Claudia Millán
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Calina Glynn
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Chih-Te Zee
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Michael R. Sawaya
- Department
of Biological Chemistry and Department of Chemistry and Biochemistry, University of California Los Angeles (UCLA), Howard
Hughes Medical Institute (HHMI), UCLA-DOE Institute for Genomics and
Proteomics, Los Angeles, California 90095, United States
| | - Marcus Gallagher-Jones
- Correlated
Imaging, The Rosalind Franklin Institute, Harwell Science & Innovation
Campus, Rutherford Avenue, Harwell, Didcot OX11 0GD, United Kingdom
| | - Rafael J. Borges
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic
Methods, Institute of Molecular Biology
of Barcelona (IBMB−CSIC), Barcelona Science Park, Helix Building, Baldiri
Reixach 15, 08028 Barcelona, Spain
- ICREA,
Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department
of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and
Proteomics; STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, California 90095, United States
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48
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Danelius E, Patel K, Gonzalez B, Gonen T. MicroED in drug discovery. Curr Opin Struct Biol 2023; 79:102549. [PMID: 36821888 PMCID: PMC10023408 DOI: 10.1016/j.sbi.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was initially described in 2013 and has recently gained attention as an emerging technique for research in drug discovery. As compared to other methods in structural biology, MicroED provides many advantages deriving from the use of nanocrystalline material for the investigations. Here, we review the recent advancements in the field of MicroED and show important examples of small molecule, peptide and protein structures that has contributed to the current development of this method as an important tool for drug discovery.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Khushboo Patel
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brenda Gonzalez
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA.
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49
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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50
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. Nat Commun 2023; 14:1624. [PMID: 36959188 PMCID: PMC10036551 DOI: 10.1038/s41467-023-37287-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp)-modified C-terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C-terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C-terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shravan R Dommaraju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuwei Pan
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marko Nesic
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Sarlah
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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