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Li A, Wu L, Cui H, Song Y, Zhang X, Li X. Unlocking a Sustainable Future for Plastics: A Chemical-Enzymatic Pathway for Efficient Conversion of Mixed Waste to MHET and Energy-Saving PET Recycling. CHEMSUSCHEM 2024; 17:e202301612. [PMID: 38385577 DOI: 10.1002/cssc.202301612] [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: 01/04/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
The heterogeneous monomers obtained from plastic waste degradation are unfavorable for PET recondensation and high-value derivative synthesis. Herein, we developed an efficient chemical-enzymatic approach to convert mixed plastic wastes into homogeneous mono-2-hydroxyethyl terephthalate (MHET) without downstream purification, benefiting from three discovered BHETases (KbEst, KbHyd, and BrevEst) in nature. Towards the mixed plastic waste, integrating the chemical K2CO3-driven glycolysis process with the BHETase depolymerization technique resulted in an MHET yield of up to 98.26 % in 40 h. Remarkably, BrevEst accomplished the highest BHET hydrolysis (~87 % efficiency in 12 h) for yielding analytical-grade MHET compared to seven state-of-the-art PET hydrolases (18 %-40 %). In an investigation combining quantum theoretical computations and experimental validations, we established a MHET-initiated PET repolymerization pathway. This shortcut approach with MHET promises to strengthen the valorization of mixed plastics, offering a substantially more efficient and energy-saving route for PET recycling.
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Affiliation(s)
- Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Luxuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
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2
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de Crécy-Lagard V, Dias R, Friedberg I, Yuan Y, Swairjo MA. Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601547. [PMID: 39005379 PMCID: PMC11244979 DOI: 10.1101/2024.07.01.601547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Thirty to seventy percent of proteins in any given genome have no assigned function and have been labeled as the protein "unknownme". This large knowledge gap prevents the biological community from fully leveraging the plethora of genomic data that is now available. Machine-learning approaches are showing some promise in propagating functional knowledge from experimentally characterized proteins to the correct set of isofunctional orthologs. However, they largely fail to predict enzymatic functions unseen in the training set, as shown by dissecting the predictions made for 450 enzymes of unknown function from the model bacteria Escherichia coli using the DeepECTransformer platform. Lessons from these failures can help the community develop machine-learning methods that assist domain experts in making testable functional predictions for more members of the uncharacterized proteome.
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3
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Wang M, Li WW, Cao Z, Sun J, Xiong J, Tao SQ, Lv T, Gao K, Luo S, Dong SH. Genome mining of sulfonated lanthipeptides reveals unique cyclic peptide sulfotransferases. Acta Pharm Sin B 2024; 14:2773-2785. [PMID: 38828142 PMCID: PMC11143521 DOI: 10.1016/j.apsb.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 06/05/2024] Open
Abstract
Although sulfonation plays crucial roles in various biological processes and is frequently utilized in medicinal chemistry to improve water solubility and chemical diversity of drug leads, it is rare and underexplored in ribosomally synthesized and post-translationally modified peptides (RiPPs). Biosynthesis of RiPPs typically entails modification of hydrophilic residues, which substantially increases their chemical stability and bioactivity, albeit at the expense of reducing water solubility. To explore sulfonated RiPPs that may have improved solubility, we conducted co-occurrence analysis of RiPP class-defining enzymes and sulfotransferase (ST), and discovered two distinctive biosynthetic gene clusters (BGCs) encoding both lanthipeptide synthetase (LanM) and ST. Upon expressing these BGCs, we characterized the structures of novel sulfonated lanthipeptides and determined the catalytic details of LanM and ST. We demonstrate that SslST-catalyzed sulfonation is leader-independent but relies on the presence of A ring formed by LanM. Both LanM and ST are promiscuous towards residues in the A ring, but ST displays strict regioselectivity toward Tyr5. The recognition of cyclic peptide by ST was further discussed. Bioactivity evaluation underscores the significance of the ST-catalyzed sulfonation. This study sets up the starting point to engineering the novel lanthipeptide STs as biocatalysts for hydrophobic lanthipeptides improvement.
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Affiliation(s)
| | | | - Zhe Cao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianong Sun
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jiang Xiong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Si-Qin Tao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Tinghong Lv
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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4
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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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5
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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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6
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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7
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Zhang MM, Long Y, Li Y, Cui JJ, Lv T, Luo S, Gao K, Dong SH. Divergent Biosynthesis of Bridged Polycyclic Sesquiterpenoids by a Minimal Fungal Biosynthetic Gene Cluster. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38417166 DOI: 10.1021/acs.jnatprod.3c01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
The bridged polycyclic sesquiterpenoids derived from sativene, isosativene, and longifolene have unique structures, and many chemical synthesis approaches with at least 10 steps have been reported. However, their biosynthetic pathway remains undescribed. A minimal biosynthetic gene cluster (BGC), named bip, encoding a sesquiterpene cyclase (BipA) and a cytochrome P450 (BipB) is characterized to produce such complex sesquiterpenoids with multiple carbon skeletons based on enzymatic assays, heterologous expression, and precursor experiments. BipA is demonstrated as a versatile cyclase with (-)-sativene as the dominant product and (-)-isosativene and (-)-longifolene as minor ones. BipB is capable of hydroxylating different enantiomeric sesquiterpenes, such as (-)-longifolene and (+)-longifolene, at C-15 and C-14 in turn. The C-15- or both C-15- and C-14-hydroxylated products are then further oxidized by unclustered oxidases, resulting in a structurally diverse array of sesquiterpenoids. Bioinformatic analysis reveals the BipB homologues as a discrete clade of fungal sesquiterpene P450s. These findings elucidate the concise and divergent biosynthesis of such intricate bridged polycyclic sesquiterpenoids, offer valuable biocatalysts for biotransformation, and highlight the distinct biosynthetic strategy employed by nature compared to chemical synthesis.
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Affiliation(s)
- Meng-Meng Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yi Long
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yuxin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jiao-Jiao Cui
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Tinghong Lv
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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8
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Guo Y, Shen K, Zhang X, Huang H. In vitro characterization of alternative l-threonate and d-erythronate catabolic pathways. Biochem Biophys Res Commun 2024; 695:149440. [PMID: 38157628 DOI: 10.1016/j.bbrc.2023.149440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
l-threonate is the metabolite of vitamin C, while d-erythronate is the metabolite of N-acetyl-d-glucosamine, the nutritional supplement for joint health. They are widely distributed in the environment and human biofluids. Nevertheless, the catabolisms of l-threonate and d-erythronate are sparsely reported. Here we explored the functional diversity of an acid sugar kinase family (Pfam families PF07005-PF17042), and discovered a novel 2-oxo-tetronate kinase. The conserved genome neighborhood of the 2-oxo-tetronate kinase encodes members of class-II fructose-bisphosphate aldolase family (F_bP_aldolase, PF01116) and a dehydrogenase family (PF03446-PF14833). Instructed by this analysis, we experimentally verified that these enzymes are capable of degrading l-threonate into dihydroxyacetone phosphate (DHAP) in Arthrobacter sp. ZBG10, Clostridium scindens ATCC 35704, and Pseudonocardia dioxanivorans ATCC 55486. Meanwhile, a convergent catabolic pathway for d-erythronate was characterized in P. dioxanivorans ATCC 55486. Moreover, the phylogenetic distribution analysis indicates that the biological range of the identified l-threonate and d-erythronate catabolic pathways appears to extend mostly to members of the Actinomycetota, Cyanobacteriota, Bacillota, Pseudomonadota, and Bacteroidota phyla.
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Affiliation(s)
- Yibo Guo
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ke Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xinshuai Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Hua Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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9
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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: 0] [Impact Index Per Article: 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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10
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Pei ZF, Zhu L, Nair SK. Core-dependent post-translational modifications guide the biosynthesis of a new class of hypermodified peptides. Nat Commun 2023; 14:7734. [PMID: 38007494 PMCID: PMC10676384 DOI: 10.1038/s41467-023-43604-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPPs) class of natural products has undergone significant expansion due to the rapid growth in genome sequencing data. Using a bioinformatics approach, we identify the dehydrazoles, a novel class of hypermodified RiPPs that contain both side chain dehydration of Ser residues, and backbone heterocyclization at Ser, Thr, and Cys residues to the corresponding azol(in)es. Structure elucidation of the hypermodified peptide carnazolamide, a representative class member, shows that 18 post-translational modifications are installed by just five enzymes. Complete biosynthetic reconstitution demonstrates that dehydration is carried out by an unusual DUF4135 dehydration domain fused to a zinc-independent cyclase domain (CcaM). We demonstrate that CcaM only modifies Ser residues that precede an azole in the core peptide. As heterocyclization removes the carbonyl following the Ser residue, CcaM likely catalyzes dehydration without generating an enolate intermediate. Additionally, CcaM does not require the leader peptide, and this core-dependence effectively sets the order for the biosynthetic reactions. Biophysical studies demonstrate direct binding of azoles to CcaM consistent with this azole moiety-dependent dehydration. Bioinformatic analysis reveals more than 50 related biosynthetic gene clusters that contain additional catalysts that may produce structurally diverse scaffolds.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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11
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Guo MX, Zhang MM, Sun K, Cui JJ, Liu YC, Gao K, Dong SH, Luo S. Genome Mining of Linaridins Provides Insights into the Widely Distributed LinC Oxidoreductases. JOURNAL OF NATURAL PRODUCTS 2023; 86:2333-2341. [PMID: 37819880 DOI: 10.1021/acs.jnatprod.3c00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Linaridins are a family of underexplored ribosomally synthesized and post-translationally modified peptides despite the prevalence of their biosynthetic gene clusters (BGCs) in microbial genomes, as shown by bioinformatic studies. Our genome mining efforts reveal that 96 putative oxidoreductase genes, namely, LinC, are encoded in linaridin BGCs. We heterologously expressed two such LinC-containing linaridin BGCs, yan and ydn, from Streptomyces yunnanensis and obtained three new linaridins, named yunnanaridins A-C (1-3). Their structures are characterized by Z-configurations of the dehydrobutyrines and the presence of a variety of epimerized amino acid residues. Yunnanaridin A (1) is the sixth member of the family of type-B linaridins, whereas yunnanaridins B (2) and C (3) represent the first examples of expressed type-C linaridins. Interestingly, heterologous expression of the same BGCs with LinC in-frame knockouts produced the same compounds. This work expands the structural diversity of linaridins and provides evidence for the notion that the widespread LinCs may not be involved in linaridin biosynthesis.
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Affiliation(s)
- Meng-Xue Guo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Meng-Meng Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Ke Sun
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiao-Jiao Cui
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yi-Cheng Liu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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12
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Oberg N, Zallot R, Gerlt JA. EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. J Mol Biol 2023; 435:168018. [PMID: 37356897 PMCID: PMC10291204 DOI: 10.1016/j.jmb.2023.168018] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/04/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
The Enzyme Function Initiative (EFI) provides a web resource with "genomic enzymology" web tools to leverage the protein (UniProt) and genome (European Nucleotide Archive; ENA; https://www.ebi.ac.uk/ena/) databases to assist the assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized enzymes (https://efi.igb.illinois.edu/). The tools enable (1) exploration of sequence-function space in enzyme families using sequence similarity networks (SSNs; EFI-EST), (2) easy access to genome context for bacterial, archaeal, and fungal proteins in the SSN clusters so that isofunctional families can be identified and their functions inferred from genome context (EFI-GNT); and (3) determination of the abundance of SSN clusters in NIH Human Metagenome Project metagenomes using chemically guided functional profiling (EFI-CGFP). We describe enhancements that enable SSNs to be generated from taxonomy categories, allowing higher resolution analyses of sequence-function space; we provide examples of the generation of taxonomy category-specific SSNs.
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Affiliation(s)
- Nils Oberg
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States
| | - Rémi Zallot
- Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK; Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - John A Gerlt
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, United States.
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13
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Li A, Sheng Y, Cui H, Wang M, Wu L, Song Y, Yang R, Li X, Huang H. Discovery and mechanism-guided engineering of BHET hydrolases for improved PET recycling and upcycling. Nat Commun 2023; 14:4169. [PMID: 37443360 PMCID: PMC10344914 DOI: 10.1038/s41467-023-39929-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Although considerable research achievements have been made to address the plastic crisis using enzymes, their applications are limited due to incomplete degradation and low efficiency. Herein, we report the identification and subsequent engineering of BHETases, which have the potential to improve the efficiency of PET recycling and upcycling. Two BHETases (ChryBHETase and BsEst) are identified from the environment via enzyme mining. Subsequently, mechanism-guided barrier engineering is employed to yield two robust and thermostable ΔBHETases with up to 3.5-fold enhanced kcat/KM than wild-type, followed by atomic resolution understanding. Coupling ΔBHETase into a two-enzyme system overcomes the challenge of heterogeneous product formation and results in up to 7.0-fold improved TPA production than seven state-of-the-art PET hydrolases, under the conditions used here. Finally, we employ a ΔBHETase-joined tandem chemical-enzymatic approach to valorize 21 commercial post-consumed plastics into virgin PET and an example chemical (p-phthaloyl chloride) for achieving the closed-loop PET recycling and open-loop PET upcycling.
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Affiliation(s)
- Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Haiyang Cui
- RWTH Aachen University, Templergraben 55, Aachen, 52062, Germany
- University of Illinois at Urbana-Champaign, Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Minghui Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Luxuan Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Rongrong Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210009, People's Republic of China.
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14
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Liu J, Liu J, Li M, Zhou L, Kong W, Zhang H, Jin P, Lu F, Lin G, Shi L. Division of developmental phases of freshwater leech Whitmania pigra and key genes related to neurogenesis revealed by whole genome and transcriptome analysis. BMC Genomics 2023; 24:203. [PMID: 37069497 PMCID: PMC10111769 DOI: 10.1186/s12864-023-09286-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
The freshwater leech Whitmania pigra (W. pigra) Whitman (Annelida phylum) is a model organism for neurodevelopmental studies. However, molecular biology research on its embryonic development is still scarce. Here, we described a series of developmental stages of the W. pigra embryos and defined five broad stages of embryogenesis: cleavage stages, blastocyst stage, gastrula stage, organogenesis and refinement, juvenile. We obtained a total of 239.64 Gb transcriptome data of eight representative developmental phases of embryos (from blastocyst stage to maturity), which was then assembled into 21,482 unigenes according to our reference genome sequenced by single-molecule real-time (SMRT) long-read sequencing. We found 3114 genes differentially expressed during the eight phases with phase-specific expression pattern. Using a comprehensive transcriptome dataset, we demonstrated that 57, 49 and 77 DEGs were respectively related to morphogenesis, signal pathways and neurogenesis. 49 DEGs related to signal pathways included 30 wnt genes, 14 notch genes, and 5 hedgehog genes. In particular, we found a cluster consisting of 7 genes related to signal pathways as well as synapses, which were essential for regulating embryonic development. Eight genes cooperatively participated in regulating neurogenesis. Our results reveal the whole picture of W. pigra development mechanism from the perspective of transcriptome and provide new clues for organogenesis and neurodevelopmental studies of Annelida species.
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Affiliation(s)
- Jiali Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Jinxin Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Mingyue Li
- Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Lisi Zhou
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Weijun Kong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Hailin Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, 200065, China
| | - Panpan Jin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Fuhua Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China
| | - Gufa Lin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, 200065, China.
| | - Linchun Shi
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100193, China Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, 100193, China.
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15
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Zheng Y, Young ND, Song J, Chang BC, Gasser RB. An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus. Comput Struct Biotechnol J 2023; 21:2696-2704. [PMID: 37143762 PMCID: PMC10151223 DOI: 10.1016/j.csbj.2023.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
Major advances in genomic and associated technologies have demanded reliable bioinformatic tools and workflows for the annotation of genes and their products via comparative analyses using well-curated reference data sets, accessible in public repositories. However, the accurate in silico annotation of molecules (proteins) encoded in organisms (e.g., multicellular parasites) which are evolutionarily distant from those for which these extensive reference data sets are available, including invertebrate model organisms (e.g., Caenorhabditis elegans - free-living nematode, and Drosophila melanogaster - the vinegar fly) and vertebrate species (e.g., Homo sapiens and Mus musculus), remains a major challenge. Here, we constructed an informatic workflow for the enhanced annotation of biologically-important, excretory/secretory (ES) proteins ("secretome") encoded in the genome of a parasitic roundworm, called Haemonchus contortus (commonly known as the barber's pole worm). We critically evaluated the performance of five distinct methods, refined some of them, and then combined the use of all five methods to comprehensively annotate ES proteins, according to gene ontology, biological pathways and/or metabolic (enzymatic) processes. Then, using optimised parameter settings, we applied this workflow to comprehensively annotate 2591 of all 3353 proteins (77.3%) in the secretome of H. contortus. This result is a substantial improvement (10-25%) over previous annotations using individual, "off-the-shelf" algorithms and default settings, indicating the ready applicability of the present, refined workflow to gene/protein sequence data sets from a wide range of organisms in the Tree-of-Life.
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16
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Knox HL, Allen KN. Expanding the viewpoint: Leveraging sequence information in enzymology. Curr Opin Chem Biol 2023; 72:102246. [PMID: 36599282 PMCID: PMC10251232 DOI: 10.1016/j.cbpa.2022.102246] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 01/04/2023]
Abstract
The use of protein sequence to inform enzymology in terms of structure, mechanism, and function has burgeoned over the past two decades. Referred to as genomic enzymology, the utilization of bioinformatic tools such as sequence similarity networks and phylogenetic analyses has allowed the identification of new substrates and metabolites, novel pathways, and unexpected reaction mechanisms. The holistic examination of superfamilies can yield insight into the origins and paths of evolution of enzymes and the range of their substrates and mechanisms. Herein, we highlight advances in the use of genomic enzymology to address problems which the in-depth analyses of a single enzyme alone could not enable.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215-2521, USA
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215-2521, USA.
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17
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Amino acid (acyl carrier protein) ligase-associated biosynthetic gene clusters reveal unexplored biosynthetic potential. Mol Genet Genomics 2023; 298:49-65. [PMID: 36271918 DOI: 10.1007/s00438-022-01962-7] [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: 05/04/2022] [Accepted: 10/09/2022] [Indexed: 01/10/2023]
Abstract
This study aimed to evaluate the postulated cellular function of a novel family of amino acid (acyl carrier protein) ligases (AALs) in natural product biosynthesis. Here, we analyzed the manually curated, putative, aal-associated natural product biosynthetic gene clusters (NP BGCs) using two computational platforms for NP prediction, antiSMASH-BiG-SCAPE-CORASON and DeepBGC. The detected BGCs included a diversity of type I polyketide/nonribosomal peptide (PKS/NRPS) hybrid BGCs, exemplified by the guadinomine BGC, which suggested a dedicated function of AALs in the biosynthesis of rare (2S)-aminomalonyl-ACP extension units. Besides modular PKS/NRPSs and NRPSs, AAL-associated BGCs were predicted to assemble arylpolyenes, ladderane lipids, phosphonates, aminoglycosides, β-lactones, and thioamides of both nonribosomal and ribosomal origins. Additionally, we revealed a frequent association of AALs with putative, seldom observed transglutaminase-like and BtrH-like transferases of the cysteine protease superfamily, which may form larger families of ACP-dependent amide bond catalysts used in NP synthesis. Our results disclosed an exceptional chemical novelty and biosynthetic potential of the AAL-associated BGCs in NP biosynthesis. The presented in silico evidence supports the initial hypothesis and provides an important foundation for future experimental studies aimed at discovering novel pharmaceutically relevant active compounds.
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18
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YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Nat Chem Biol 2023; 19:111-119. [PMID: 36280794 DOI: 10.1038/s41589-022-01141-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022]
Abstract
YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.
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19
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Kennedy EN, Foster CA, Barr SA, Bourret RB. General strategies for using amino acid sequence data to guide biochemical investigation of protein function. Biochem Soc Trans 2022; 50:1847-1858. [PMID: 36416676 PMCID: PMC10257402 DOI: 10.1042/bst20220849] [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: 08/18/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to investigate general protein function. Studying individual members of a protein family is likely insufficient to provide a complete mechanistic understanding of family functions, especially for diverse families with thousands of known members. Strategies that exploit large amounts of available amino acid sequence data can inspire and guide biochemical experiments, generating broadly applicable insights into a given family. Here we review several methods that utilize abundant sequence data to focus experimental efforts and identify features truly representative of a protein family or domain. First, coevolutionary relationships between residues within primary sequences can be successfully exploited to identify structurally and/or functionally important positions for experimental investigation. Second, functionally important variable residue positions typically occupy a limited sequence space, a property useful for guiding biochemical characterization of the effects of the most physiologically and evolutionarily relevant amino acids. Third, amino acid sequence variation within domains shared between different protein families can be used to sort a particular domain into multiple subtypes, inspiring further experimental designs. Although generally applicable to any kind of protein domain because they depend solely on amino acid sequences, the second and third approaches are reviewed in detail because they appear to have been used infrequently and offer immediate opportunities for new advances. Finally, we speculate that future technologies capable of analyzing and manipulating conserved and variable aspects of the three-dimensional structures of a protein family could lead to broad insights not attainable by current methods.
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Affiliation(s)
- Emily N. Kennedy
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Clay A. Foster
- Department of Pediatrics, Section Hematology/Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Sarah A. Barr
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Robert B. Bourret
- Department of Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, United States of America
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20
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Flavonoids' Dual Benefits in Gastrointestinal Cancer and Diabetes: A Potential Treatment on the Horizon? Cancers (Basel) 2022; 14:cancers14246073. [PMID: 36551558 PMCID: PMC9776408 DOI: 10.3390/cancers14246073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Diabetes and gastrointestinal cancers (GI) are global health conditions with a massive burden on patients' lives worldwide. The development of both conditions is influenced by several factors, such as diet, genetics, environment, and infection, which shows a potential link between them. Flavonoids are naturally occurring phenolic compounds present in fruits and vegetables. Once ingested, unabsorbed flavonoids reaching the colon undergo enzymatic modification by the gut microbiome to facilitate absorption and produce ring fission products. The metabolized flavonoids exert antidiabetic and anti-GI cancer properties, targeting major impaired pathways such as apoptosis and cellular proliferation in both conditions, suggesting the potentially dual effects of flavonoids on diabetes and GI cancers. This review summarizes the current knowledge on the impact of flavonoids on diabetes and GI cancers in four significant pathways. It also addresses the synergistic effects of selected flavonoids on both conditions. While this is an intriguing approach, more studies are required to better understand the mechanism of how flavonoids can influence the same impaired pathways with different outcomes depending on the disease.
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21
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The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
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22
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Pei ZF, Zhu L, Sarksian R, van der Donk WA, Nair SK. Class V Lanthipeptide Cyclase Directs the Biosynthesis of a Stapled Peptide Natural Product. J Am Chem Soc 2022; 144:17549-17557. [PMID: 36107785 PMCID: PMC9621591 DOI: 10.1021/jacs.2c06808] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lanthipeptides are a class of cyclic peptides characterized by the presence of one or more lanthionine (Lan) or methyllanthionine (MeLan) thioether rings. These cross-links are produced by α,β-unsaturation of Ser or Thr residues in peptide substrates by dehydration, followed by a Michael-type conjugate addition of Cys residues onto the dehydroamino acids. Lanthipeptides may be broadly classified into at least five different classes, and the biosynthesis of classes I-IV lanthipeptides requires catalysis by LanC cyclases that control both the site-specificity and the stereochemistry of the conjugate addition. In contrast, there are no current examples of LanCs that occur in class V biosynthetic clusters, despite the presence of lanthionine rings in these compounds. In this work, bioinformatics-guided co-occurrence analysis identifies more than 240 putative class V lanthipeptide clusters that contain a LanC cyclase. Reconstitution studies demonstrate that the cyclase-catalyzed product is notably distinct from the product formed spontaneously. Stereochemical analysis shows that the cyclase diverts the final product to a configuration that is distinct from one that is energetically favored. Structural characterization of the final product by multi-dimensional NMR spectroscopy reveals that it forms a helical stapled peptide. Mutational analysis identified a plausible order for cyclization and suggests that enzymatic rerouting to the final structure is largely directed by the construction of the first lanthionine ring. These studies show that lanthipeptide cyclases are needed for the biosynthesis of some constrained peptides, the formations of which would otherwise be energetically unfavored.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, 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
| | - Raymond Sarksian
- 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
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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23
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Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
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Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- 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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24
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de Crécy-lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O’Donoghue S, Orengo C, O’Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. A roadmap for the functional annotation of protein families: a community perspective. Database (Oxford) 2022; 2022:6663924. [PMID: 35961013 PMCID: PMC9374478 DOI: 10.1093/database/baac062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/28/2022] [Accepted: 08/03/2022] [Indexed: 12/23/2022]
Abstract
Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.
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Affiliation(s)
- Valérie de Crécy-lagard
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | | | - Cecilia Arighi
- Department of Computer and Information Sciences, University of Delaware , Newark, DE 19713, USA
| | - Jill Babor
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD, UK
| | - Ian Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Crysten Blaby-Haas
- Biology Department, Brookhaven National Laboratory , Upton, NY 11973, USA
| | - Alan J Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , Geneva 4 CH-1211, Switzerland
| | - Stephen K Burley
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey , Piscataway, NJ 08854, USA
| | - Stacey Cleveland
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Lucy J Colwell
- Departmenf of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, UK
| | - Ana Conesa
- Spanish National Research Council, Institute for Integrative Systems Biology , Paterna, Valencia 46980, Spain
| | - Christian Dallago
- TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology , i12, Boltzmannstr. 3, Garching/Munich 85748, Germany
| | - Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong , 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China
| | - Anita de Waard
- Research Collaboration Unit, Elsevier , Jericho, VT 05465, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Raquel Dias
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida , Gainesville, FL 32610, USA
| | - Gang Fang
- NYU-Shanghai , Shanghai 200120, China
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University , Ames, IA 50011, USA
| | - John Gerlt
- Institute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign , Urbana, IL 61801, USA
| | - Joshua Goldford
- Physics of Living Systems, Massachusetts Institute of Technology , Cambridge, MA 02139, USA
| | - Mark Gorelik
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Benjamin M Gyori
- Laboratory of Systems Pharmacology, Harvard Medical School , Boston, MA 02115, USA
| | - Christopher Henry
- Mathematics and Computer Science Division, Argonne National Laboratory , Argonne, IL 60439, USA
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | - Peter D Karp
- Bioinformatics Research Group, SRI International , Menlo Park, CA 94025, USA
| | | | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus , Hinxton CB10 1SD, UK
| | - Claire McWhite
- Lewis-Sigler Institute for Integrative Genomics, Princeton University , Princeton, NJ 08540, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University , Ithaca, NY 14853, USA
| | - Paul Monaghan
- Department of Agricultural Education and Communication, University of Florida , Gainesville, FL 32611, USA
| | - Anne Morgat
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , Geneva 4 CH-1211, Switzerland
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Darren A Natale
- Georgetown University Medical Center , Washington, DC 20007, USA
| | - William C Nelson
- Biological Sciences Division, Pacific Northwest National Laboratories , Richland, WA 99354, USA
| | - Seán O’Donoghue
- School of Biotechnology and Biomolecular Sciences, University of NSW , Sydney, NSW 2052, Australia
| | - Christine Orengo
- Department of Structural and Molecular Biology, University College London , London WC1E 6BT, UK
| | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA
| | - Colbie Reed
- Department of Microbiology and Cell Sciences, University of Florida , Gainesville, FL 32611, USA
| | | | - Dmitri Rodionov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla, CA 92037, USA
| | - Irina A Rodionova
- Department of Bioengineering, Division of Engineering, University of California at San Diego , La Jolla, CA 92093-0412, USA
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida , Gainesville, FL 32611, USA
| | - Lana Saleh
- New England Biolabs , Ipswich, MA 01938, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia , Charlottesville, VA, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH) , 8600 Rockville Pike, Bethesda, MD 20817, USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033, USA
| | - Peter Uetz
- Center for Biological Data Science, Virginia Commonwealth University , Richmond, VA 23284, USA
| | - David Vallenet
- LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS , Evry 91057, France
| | - Erica Watson Carter
- Department of Plant Pathology, University of Florida Citrus Research and Education Center , 700 Experiment Station Rd., Lake Alfred, FL 33850, USA
| | | | - Valerie Wood
- Department of Biochemistry, University of Cambridge , Cambridge CB2 1GA, UK
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory , Berkeley, CA 94720, USA
| | - Jin Xu
- Department of Plant Pathology, University of Florida Citrus Research and Education Center , 700 Experiment Station Rd., Lake Alfred, FL 33850, USA
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25
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Nguyen NA, Cong Y, Hurrell RC, Arias N, Garg N, Puri AW, Schmidt EW, Agarwal V. A Silent Biosynthetic Gene Cluster from a Methanotrophic Bacterium Potentiates Discovery of a Substrate Promiscuous Proteusin Cyclodehydratase. ACS Chem Biol 2022; 17:1577-1585. [PMID: 35666841 PMCID: PMC9746716 DOI: 10.1021/acschembio.2c00251] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product-encoding biosynthetic gene clusters (BGCs) within microbial genomes far outnumber the known natural products; chemical products from such BGCs remain cryptic. These silent BGCs hold promise not only for the elaboration of new natural products but also for the discovery of useful biosynthetic enzymes. Here, we describe a genome mining strategy targeted toward the discovery of substrate promiscuous natural product biosynthetic enzymes. In the genome of the methanotrophic bacterium Methylovulum psychrotolerans Sph1T, we discover a transcriptionally silent natural product BGC that encoded numerous ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. These cryptic RiPP natural products were accessed using heterologous expression of the substrate peptide and biosynthetic enzyme-encoded genes. In line with our genome mining strategy, the RiPP biosynthetic enzymes in this BGC were found to be substrate promiscuous, which allowed us to use them in a combinatorial fashion with a similarly substrate-tolerant cyanobactin biosynthetic enzyme to introduce head-to-tail macrocyclization in the proteusin family of RiPP natural products.
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Affiliation(s)
- Nguyet A. Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Rachel C. Hurrell
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Natalie Arias
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Neha Garg
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332
| | - Aaron W. Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City UT, USA 84112
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City UT, USA 84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta GA, USA 30332,School of Biological Sciences, Georgia Institute of Technology, Atlanta GA, USA 30332,correspondence:
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26
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Zheng Y, Cong Y, Schmidt EW, Nair SK. Catalysts for the Enzymatic Lipidation of Peptides. Acc Chem Res 2022; 55:1313-1323. [PMID: 35442036 DOI: 10.1021/acs.accounts.2c00108] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biologically active peptides are a major growing class of drugs, but their therapeutic potential is constrained by several limitations including bioavailability and poor pharmacokinetics. The attachment of functional groups like lipids has proven to be a robust and effective strategy for improving their therapeutic potential. Biochemical and bioactivity-guided screening efforts have identified the cyanobactins as a large class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that are modified with lipids. These lipids are attached by the F superfamily of peptide prenyltransferase enzymes that utilize 5-carbon (prenylation) or 10-carbon (geranylation) donors. The chemical structures of various cyanobactins initially showed isoprenoid attachments on Ser, Thr, or Tyr. Biochemical characterization of the F prenyltransferases from the corresponding clusters shows that the different enzymes have different acceptor residue specificities but are otherwise remarkably sequence tolerant. Hence, these enzymes are well suited for biotechnological applications. The crystal structure of the Tyr O-prenyltransferase PagF reveals that the F enzyme shares a domain architecture reminiscent of a canonical ABBA prenyltransferase fold but lacks secondary structural elements necessary to form an enclosed active site. Binding of either cyclic or linear peptides is sufficient to close the active site to allow for productive catalysis, explaining why these enzymes cannot use isolated amino acids as substrates.Almost all characterized isoprenylated cyanobactins are modified with 5-carbon isoprenoids. However, chemical characterization demonstrates that the piricyclamides are modified with a 10-carbon geranyl moiety, and in vitro reconstitution of the corresponding PirF shows that the enzyme is a geranyltransferase. Structural analysis of PirF shows an active site nearly identical with that of the PagF prenyltransferase but with a single amino acid substitution. Of note, mutation at this residue in PagF or PirF can completely switch the isoprenoid donor specificity of these enzymes. Recent efforts have resulted in significant expansion of the F family with enzymes identified that can carry out C-prenylations of Trp, N-prenylations of Trp, and bis-N-prenylations of Arg. Additional genome-guided efforts based on the sequence of F enzymes identify linear cyanobactins that are α-N-prenylated and α-C-methylated by a bifunctional prenyltransferase/methyltransferase fusion and a bis-α-N- and α-C-prenylated linear peptide. The discovery of these different classes of prenyltransferases with diverse acceptor residue specificities expands the biosynthetic toolkit for enzymatic prenylation of peptide substrates.In this Account, we review the current knowledge scope of the F family of peptide prenyltransferases, focusing on the biochemical, structure-function, and chemical characterization studies that have been carried out in our laboratories. These enzymes are easily amenable for diversity-oriented synthetic efforts as they can accommodate substrate peptides of diverse sequences and are thus attractive catalysts for use in synthetic biology approaches to generate high-value peptidic therapeutics.
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Affiliation(s)
- Yiwu Zheng
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- 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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Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes. Appl Microbiol Biotechnol 2022; 106:2993-3007. [PMID: 35435459 PMCID: PMC9064869 DOI: 10.1007/s00253-022-11923-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/13/2023]
Abstract
Abstract Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network. Sequences from one of these clades clearly diverged from all others, having on average the lower isoelectric points and hydropathy indices, the highest number of N-glycosylation sites, and N-terminal sequence peptides for secretion. Putative proteins from this clade are absent from brown-rot and ectomycorrhizal species that have lost the capability of degrading lignin enzymatically. They are almost exclusively present in white-rot and other saprotrophic Basidiomycota that digest lignin enzymatically, thus lending support for a specific role of DyPs from this clade in biochemical lignin modification. Additional nearly full-length fungal DyP genes were isolated from the environment by sequence capture by hybridization; they all belonged to the clade of the presumably secreted DyPs and to another related clade. We suggest focusing our attention on the presumably intracellular DyPs from the other clades, which have not been characterized thus far and could represent enzyme proteins with novel catalytic properties. Key points • A fungal DyP phylogeny delineates seven main sequence clades. • Putative extracellular DyPs form a single clade of Basidiomycota sequences. • Extracellular DyPs are associated to white-rot fungi. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11923-0.
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28
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Oberg N, Precord TW, Mitchell DA, Gerlt JA. RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry. ACS BIO & MED CHEM AU 2022; 2:22-35. [PMID: 36119373 PMCID: PMC9477430 DOI: 10.1021/acsbiomedchemau.1c00048] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The radical SAM superfamily (RSS), arguably the most functionally diverse enzyme superfamily, is also one of the largest with ~700K members currently in the UniProt database. The vast majority of the members have uncharacterized enzymatic activities and metabolic functions. In this Perspective, we describe RadicalSAM.org, a new web-based resource that enables a user-friendly genomic enzymology strategy to explore sequence-function space in the RSS. The resource attempts to enable identification of isofunctional groups of radical SAM enzymes using sequence similarity networks (SSNs) and the genome context of the bacterial, archaeal, and fungal members provided by genome neighborhood diagrams (GNDs). Enzymatic activities and in vivo functions frequently can be inferred from genome context given the tendency for genes of related function to be clustered. We invite the scientific community to use RadicalSAM.org to (i) guide their experimental studies to discover new enzymatic activities and metabolic functions, (ii) contribute experimentally verified annotations to RadicalSAM.org to enhance the ability to predict novel activities and functions, and (iii) provide suggestions for improving this resource.
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Affiliation(s)
- Nils Oberg
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Timothy W. Precord
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States,Department of Chemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States,Department of Chemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States,Department of Microbiology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - John A. Gerlt
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States,Department of Chemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States,Department of Biochemistry, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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29
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Lin YT, Ali HS, de Visser S. Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues. Chemistry 2021; 28:e202103982. [PMID: 34911156 DOI: 10.1002/chem.202103982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.
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Affiliation(s)
- Yen-Ting Lin
- UoM: The University of Manchester, Chemical Engineering and Analytical Science, UNITED KINGDOM
| | - Hafiz S Ali
- UoM: The University of Manchester, Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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30
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Allen KN, Whitman CP. The Birth of Genomic Enzymology: Discovery of the Mechanistically Diverse Enolase Superfamily. Biochemistry 2021; 60:3515-3528. [PMID: 34664940 DOI: 10.1021/acs.biochem.1c00494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Enzymes are categorized into superfamilies by sequence, structural, and mechanistic similarities. The evolutionary implications can be profound. Until the mid-1990s, the approach was fragmented largely due to limited sequence and structural data. However, in 1996, Babbitt et al. published a paper in Biochemistry that demonstrated the potential power of mechanistically diverse superfamilies to identify common ancestry, predict function, and, in some cases, predict specificity. This Perspective describes the findings of the original work and reviews the current understanding of structure and mechanism in the founding family members. The outcomes of the genomic enzymology approach have reached far beyond the functional assignment of members of the enolase superfamily, inspiring the study of superfamilies and the adoption of sequence similarity networks and genome context and yielding fundamental insights into enzyme evolution.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Christian P Whitman
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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31
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Rid7C, a member of the YjgF/YER057c/UK114 (Rid) protein family, is a novel endoribonuclease that regulates the expression of a specialist RNA polymerase involved in differentiation in Nonomuraea gerenzanensis. J Bacteriol 2021; 204:e0046221. [PMID: 34694905 DOI: 10.1128/jb.00462-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The YjgF/YER057c/UK114 (Rid) is a protein family breadth conserved in all domains of life and includes the widely distributed archetypal RidA (YjgF) subfamily and seven other subfamilies (Rid1 to Rid7). Among these subfamilies, RidA is the only family to have been biochemically well characterized and is involved in the deamination of the reactive enamine/imine intermediates. In this study, we have characterized a protein of the Rid7 subfamily, named Rid7C, in Nonomuraea gerenzanensis, an actinomycete that is characterized by the presence of two types of RNA polymerases. This is due to the co-existence in its genome of two RNAP β chain-encoding genes: rpoB(S) (the wild-type rpoB gene) and rpoB(R) (a specialist, mutant-type rpoB gene) that controls A40926 antibiotic production and a wide range of metabolic adaptive behaviors. Here, we found that expression of rpoB(R) is regulated post-transcriptionally by RNA processing in the 5'-UTR of rpoB(R) mRNA, and that the endoribonuclease activity of Rid7C is responsible for mRNA processing thereby overseeing several tracts of morphological and biochemical differentiation. We also provide evidence that Rid7C may be associated with ribonuclease P M1 RNA, although M1 RNA is not required for rpoB(R) mRNA processing in vitro, and that Rid7C endoribonuclease activity is inhibited by A40926 suggesting the existence of a negative feedback loop on A40926 production, and a role of the endogenous synthesis of A40926 in the modulation of biochemical differentiation in this microorganism. Importance The YjgF/YER057c/UK114 family includes many proteins with diverse functions involved in detoxification, RNA maturation, and control of mRNA translation. We found that Rid7C is an endoribonuclease that is involved in processing of rpoB(R) mRNA, coding for a specialized RNA polymerase beta subunit that oversees morphological differentiation and A40926 antibiotic production in Nonomuraea gerenzanensis. Rid7C-mediated processing promotes rpoB(R) mRNA translation and antibiotic production, while Rid7C endoribonuclease activity is inhibited by A40926 suggesting a role of the endogenous synthesis of A40926 in modulation of biochemical differentiation in this microorganism. Finally, we show that recombinant Rid7C co-purified with M1 RNA (the RNA subunit of ribonuclease P) from Escherichia coli extract, suggesting a functional interaction between Rid7C and M1 RNA activities.
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32
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Pereira J, Alva V. How do I get the most out of my protein sequence using bioinformatics tools? Acta Crystallogr D Struct Biol 2021; 77:1116-1126. [PMID: 34473083 PMCID: PMC8411974 DOI: 10.1107/s2059798321007907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on.
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Affiliation(s)
- Joana Pereira
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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33
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Discovery and mining of enzymes from the human gut microbiome. Trends Biotechnol 2021; 40:240-254. [PMID: 34304905 DOI: 10.1016/j.tibtech.2021.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022]
Abstract
Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.
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34
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Gerlt JA. Evolution of Enzyme Function and the Development of Catalytic Efficiency: Triosephosphate Isomerase, Jeremy R. Knowles, and W. John Albery. Biochemistry 2021; 60:3529-3538. [PMID: 34015914 DOI: 10.1021/acs.biochem.1c00211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Every reader knows that an enzyme accelerates a reaction by reducing the activation-energy barrier. However, understanding how this is achieved by the structure of the enzyme and its interactions with stable complexes and transition states and, then, using this to (re)design enzymes to catalyze novel reactions remain the "holy grail" of mechanistic enzymology. The necessary foundation is the free-energy profile that specifies the energies of the bound substate, product, and intervening intermediates as well as the transition states by which they are interconverted. When this free-energy profile is compared to that for the uncatalyzed reaction, strategies for establishing and enhancing catalysis can be identified. This Perspective reminds readers that the first free-energy profile determined for an enzyme-catalyzed reaction, that for triosephosphate isomerase, was published in Biochemistry in 1976 by Jeremy R. Knowles, W. John Albery, and co-workers. They used the profile to propose three steps of increasing "subtlety" that can be influenced by evolutionary pressure to increase the flux through the reaction coordinate: (1) "uniform binding" of the substrate, product, and intermediates; (2) "differential binding" of complexes so that these are isoenergetic (to minimize the energy of the intervening transition states); and (3) "catalysis of an elementary step" in which the transition state for the kinetically significant chemical step is stabilized so that flux can be determined by the rate of substrate binding or product dissociation. These papers continue to guide mechanistic studies of enzyme-catalyzed reactions and provide principles for the (re)design of novel enzymes.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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