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Pierre HC, Amrine CSM, Doyle MG, Salvi A, Raja HA, Chekan JR, Huntsman AC, Fuchs JR, Liu K, Burdette JE, Pearce CJ, Oberlies NH. Verticillins: fungal epipolythiodioxopiperazine alkaloids with chemotherapeutic potential. Nat Prod Rep 2024. [PMID: 38629495 DOI: 10.1039/d3np00068k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Covering: 1970 through June of 2023Verticillins are epipolythiodioxopiperazine (ETP) alkaloids, many of which possess potent, nanomolar-level cytotoxicity against a variety of cancer cell lines. Over the last decade, their in vivo activity and mode of action have been explored in detail. Notably, recent studies have indicated that these compounds may be selective inhibitors of histone methyltransferases (HMTases) that alter the epigenome and modify targets that play a crucial role in apoptosis, altering immune cell recognition, and generating reactive oxygen species. Verticillin A (1) was the first of 27 analogues reported from fungal cultures since 1970. Subsequent genome sequencing identified the biosynthetic gene cluster responsible for producing verticillins, allowing a putative pathway to be proposed. Further, molecular sequencing played a pivotal role in clarifying the taxonomic characterization of verticillin-producing fungi, suggesting that most producing strains belong to the genus Clonostachys (i.e., Bionectria), Bionectriaceae. Recent studies have explored the total synthesis of these molecules and the generation of analogues via both semisynthetic and precursor-directed biosynthetic approaches. In addition, nanoparticles have been used to deliver these molecules, which, like many natural products, possess challenging solubility profiles. This review summarizes over 50 years of chemical and biological research on this class of fungal metabolites and offers insights and suggestions on future opportunities to push these compounds into pre-clinical and clinical development.
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Affiliation(s)
- Herma C Pierre
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Chiraz Soumia M Amrine
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
- Department of Physical and Earth Sciences. Arkansas Tech University, 1701 N. Boulder Ave., Russellville, Arkansas 72801, USA
| | - Michael G Doyle
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Amrita Salvi
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave (M/C 870), Chicago, Illinois 60607, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Andrew C Huntsman
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, 500 W. 12th Ave., Columbus, Ohio 43210, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, 500 W. 12th Ave., Columbus, Ohio 43210, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology and the Georgia Cancer Center, Medical College of Georgia, Augusta, GA 30912, USA
- Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30904, USA
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave (M/C 870), Chicago, Illinois 60607, USA
| | | | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
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2
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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024. [PMID: 38411572 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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3
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Cordoza J, Chen PYT, Blaustein LR, Lima ST, Fiore MF, Chekan JR, Moore BS, McKinnie SMK. Mechanistic and Structural Insights into a Divergent PLP-Dependent l-Enduracididine Cyclase from a Toxic Cyanobacterium. ACS Catal 2023; 13:9817-9828. [PMID: 37497377 PMCID: PMC10367076 DOI: 10.1021/acscatal.3c01294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/21/2023] [Indexed: 07/28/2023]
Abstract
Cyclic arginine noncanonical amino acids (ncAAs) are found in several actinobacterial peptide natural products with therapeutically useful antibacterial properties. The preparation of ncAAs like enduracididine and capreomycidine currently takes multiple biosynthetic or chemosynthetic steps, thus limiting the commercial availability and applicability of these cyclic guanidine-containing amino acids. We recently discovered and characterized the biosynthetic pathway of guanitoxin, a potent freshwater cyanobacterial neurotoxin, that contains an arginine-derived cyclic guanidine phosphate within its highly polar structure. The ncAA l-enduracididine is an early intermediate in guanitoxin biosynthesis and is produced by GntC, a unique pyridoxal-5'-phosphate (PLP)-dependent enzyme. GntC catalyzes a cyclodehydration from a stereoselectively γ-hydroxylated l-arginine precursor via a reaction that functionally and mechanistically diverges from previously established actinobacterial cyclic arginine ncAA pathways. Herein, we interrogate l-enduracididine biosynthesis from the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024 using spectroscopy, stable isotope labeling techniques, and X-ray crystallography structure-guided site-directed mutagenesis. GntC initially facilitates the reversible deprotonations of the α- and β-positions of its substrate before catalyzing an irreversible diastereoselective dehydration and subsequent intramolecular cyclization. The comparison of holo- and substrate-bound GntC structures and activity assays on site-specific mutants further identified amino acid residues that contribute to the overall catalytic mechanism. These interdisciplinary efforts at structurally and functionally characterizing GntC enable an improved understanding of how nature divergently produces cyclic arginine ncAAs and generate additional tools for their biocatalytic production and downstream biological applications.
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Affiliation(s)
- Jennifer
L. Cordoza
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Percival Yang-Ting Chen
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
| | - Linnea R. Blaustein
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Stella T. Lima
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
- Center
for Nuclear Energy in Agriculture, University
of São Paulo, Piracicaba, São Paulo 13416-000, Brazil
| | - Marli F. Fiore
- Center
for Nuclear Energy in Agriculture, University
of São Paulo, Piracicaba, São Paulo 13416-000, Brazil
| | - Jonathan R. Chekan
- Center
for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Bradley S. Moore
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92903, United States
| | - Shaun M. K. McKinnie
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
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4
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Cordoza JL, Chen PYT, Blaustein LR, Lima ST, Fiore MF, Chekan JR, Moore BS, McKinnie SMK. Mechanistic and structural insights into a divergent PLP-dependent L-enduracididine cyclase from a toxic cyanobacterium. bioRxiv 2023:2023.03.21.533663. [PMID: 36993528 PMCID: PMC10055224 DOI: 10.1101/2023.03.21.533663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cyclic arginine noncanonical amino acids (ncAAs) are found in several actinobacterial peptide natural products with therapeutically useful antibacterial properties. The preparation of ncAAs like enduracididine and capreomycidine currently takes multiple biosynthetic or chemosynthetic steps, thus limiting the commercial availability and applicability of these cyclic guanidine-containing amino acids. We recently discovered and characterized the biosynthetic pathway of guanitoxin, a potent freshwater cya-nobacterial neurotoxin, that contains an arginine-derived cyclic guanidine phosphate within its highly polar structure. The ncAA L-enduracididine is an early intermediate in guanitoxin biosynthesis and is produced by GntC, a unique pyridoxal-5'-phosphate (PLP)-dependent enzyme. GntC catalyzes a cyclodehydration from a stereoselectively γ-hydroxylated L-arginine precursor via a reaction that functionally and mechanistically diverges from previously established actinobacterial cyclic arginine ncAA pathways. Herein, we interrogate L-enduracididine biosynthesis from the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024 using spectroscopic, stable isotope labeling techniques, and X-ray crystal structure-guided site-directed mutagenesis. GntC initially facilitates the reversible deprotonations of the α- and β-positions of its substrate prior to catalyzing an irreversible diastereoselective dehydration and subsequent intramolecular cyclization. The comparison of holo- and substrate bound GntC structures and activity assays on sitespecific mutants further identified amino acid residues that contribute to the overall catalytic mechanism. These interdisciplinary efforts at structurally and functionally characterizing GntC enables an improved understanding of how Nature divergently produces cyclic arginine ncAAs and generates additional tools for their biocatalytic production and downstream biological applications.
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5
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Lima ST, Ampolini BG, Underwood EB, Graf TN, Earp CE, Khedi IC, Pasquale MA, Chekan JR. A Widely Distributed Biosynthetic Cassette Is Responsible for Diverse Plant Side Chain Cross-Linked Cyclopeptides. Angew Chem Int Ed Engl 2023; 62:e202218082. [PMID: 36529706 PMCID: PMC10107690 DOI: 10.1002/anie.202218082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Cyclopeptide alkaloids are an abundant class of plant cyclopeptides with over 200 analogs described and bioactivities ranging from analgesic to antiviral. While these natural products have been known for decades, their biosynthetic basis remains unclear. Using a transcriptome-mining approach, we link the cyclopeptide alkaloids from Ceanothus americanus to dedicated RiPP precursor peptides and identify new, widely distributed split BURP peptide cyclase containing gene clusters. Guided by our bioinformatic analysis, we identify and isolate new cyclopeptides from Coffea arabica, which we named arabipeptins. Reconstitution of the enzyme activity for the BURP found in the biosynthesis of arabipeptin A validates the activity of the newly discovered split BURP peptide cyclases. These results expand our understanding of the biosynthetic pathways responsible for diverse cyclic plant peptides and suggest that these side chain cross-link modifications are widely distributed in eudicots.
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Affiliation(s)
- Stella T Lima
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Brigitte G Ampolini
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Ethan B Underwood
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Tyler N Graf
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Cody E Earp
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Imani C Khedi
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
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6
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Lima ST, Ampolini BG, Underwood EB, Graf TN, Earp CE, Khedi IC, Pasquale MA, Chekan JR. A Widely Distributed Biosynthetic Cassette Is Responsible for Diverse Plant Side Chain Cross‐Linked Cyclopeptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202218082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Stella T. Lima
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Brigitte G. Ampolini
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Ethan B. Underwood
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Tyler N. Graf
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Cody E. Earp
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Imani C. Khedi
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Michael A. Pasquale
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Jonathan R. Chekan
- University of North Carolina at Greensboro Chemistry and Biochemistry 301 McIver St409 Sullivan Building 27412 Greensboro UNITED STATES
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7
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Kandy SK, Chekan JR. Biosynthesis of the Plant‐Produced Toxin Strychnine Elucidated. Angew Chem Int Ed Engl 2022; 61:e202212301. [DOI: 10.1002/anie.202212301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Sanath K. Kandy
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Jonathan R. Chekan
- University of North Carolina at Greensboro Chemistry and Biochemistry 301 McIver St409 Sullivan Building 27412 Greensboro UNITED STATES
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8
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Kandy SK, Chekan JR. Biosynthesis of the Plant‐Produced Toxin Strychnine Elucidated. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202212301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sanath K. Kandy
- University of North Carolina at Greensboro Chemistry and Biochemistry UNITED STATES
| | - Jonathan R. Chekan
- University of North Carolina at Greensboro Chemistry and Biochemistry 301 McIver St409 Sullivan Building 27412 Greensboro UNITED STATES
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9
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Chen PYT, Adak S, Chekan JR, Liscombe DK, Miyanaga A, Bernhardt P, Diethelm S, Fielding EN, George JH, Miles ZD, Murray LAM, Steele TS, Winter JM, Noel JP, Moore BS. Structural Basis of Stereospecific Vanadium-Dependent Haloperoxidase Family Enzymes in Napyradiomycin Biosynthesis. Biochemistry 2022; 61:1844-1852. [PMID: 35985031 PMCID: PMC10978243 DOI: 10.1021/acs.biochem.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vanadium-dependent haloperoxidases (VHPOs) from Streptomyces bacteria differ from their counterparts in fungi, macroalgae, and other bacteria by catalyzing organohalogenating reactions with strict regiochemical and stereochemical control. While this group of enzymes collectively uses hydrogen peroxide to oxidize halides for incorporation into electron-rich organic molecules, the mechanism for the controlled transfer of highly reactive chloronium ions in the biosynthesis of napyradiomycin and merochlorin antibiotics sets the Streptomyces vanadium-dependent chloroperoxidases apart. Here we report high-resolution crystal structures of two homologous VHPO family members associated with napyradiomycin biosynthesis, NapH1 and NapH3, that catalyze distinctive chemical reactions in the construction of meroterpenoid natural products. The structures, combined with site-directed mutagenesis and intact protein mass spectrometry studies, afforded a mechanistic model for the asymmetric alkene and arene chlorination reactions catalyzed by NapH1 and the isomerase activity catalyzed by NapH3. A key lysine residue in NapH1 situated between the coordinated vanadate and the putative substrate binding pocket was shown to be essential for catalysis. This observation suggested the involvement of the ε-NH2, possibly through formation of a transient chloramine, as the chlorinating species much as proposed in structurally distinct flavin-dependent halogenases. Unexpectedly, NapH3 is modified post-translationally by phosphorylation of an active site His (τ-pHis) consistent with its repurposed halogenation-independent, α-hydroxyketone isomerase activity. These structural studies deepen our understanding of the mechanistic underpinnings of VHPO enzymes and their evolution as enantioselective biocatalysts.
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Affiliation(s)
- Percival Yang-Ting Chen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Sanjoy Adak
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - David K Liscombe
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Akimasa Miyanaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Peter Bernhardt
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Stefan Diethelm
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Elisha N Fielding
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jonathan H George
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Zachary D Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Lauren A M Murray
- Department of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Taylor S Steele
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jaclyn M Winter
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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10
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Lima ST, Fallon TR, Cordoza JL, Chekan JR, Delbaje E, Hopiavuori AR, Alvarenga DO, Wood SM, Luhavaya H, Baumgartner JT, Dörr FA, Etchegaray A, Pinto E, McKinnie SMK, Fiore MF, Moore BS. Biosynthesis of Guanitoxin Enables Global Environmental Detection in Freshwater Cyanobacteria. J Am Chem Soc 2022; 144:9372-9379. [PMID: 35583956 DOI: 10.1021/jacs.2c01424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Harmful cyanobacterial blooms (cyanoHABs) cause recurrent toxic events in global watersheds. Although public health agencies monitor the causal toxins of most cyanoHABs and scientists in the field continue developing precise detection and prediction tools, the potent anticholinesterase neurotoxin, guanitoxin, is not presently environmentally monitored. This is largely due to its incompatibility with widely employed analytical methods and instability in the environment, despite guanitoxin being among the most lethal cyanotoxins. Here, we describe the guanitoxin biosynthesis gene cluster and its rigorously characterized nine-step metabolic pathway from l-arginine in the cyanobacterium Sphaerospermopsis torques-reginae ITEP-024. Through environmental sequencing data sets, guanitoxin (gnt) biosynthetic genes are repeatedly detected and expressed in municipal freshwater bodies that have undergone past toxic events. Knowledge of the genetic basis of guanitoxin biosynthesis now allows for environmental, biosynthetic gene monitoring to establish the global scope of this neurotoxic organophosphate.
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Affiliation(s)
- Stella T Lima
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Timothy R Fallon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jennifer L Cordoza
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Austin R Hopiavuori
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Danillo O Alvarenga
- Department of Biology, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Steffaney M Wood
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Jackson T Baumgartner
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Felipe A Dörr
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Ribeirao Preto, Sao Paulo 05508-000, Brazil
| | - Augusto Etchegaray
- Center for Life Sciences, Graduate Program in Health Sciences, Pontifical Catholic University of Campinas (PUC-Campinas), Campinas, Sao Paulo 13087-571, Brazil
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Shaun M K McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
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Abstract
Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Keelie S Butler
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, 27402, USA.
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12
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Griffin SL, Chekan JR, Lira JM, Robinson AE, Yerkes CN, Siehl DL, Wright TR, Nair SK, Cicchillo RM. Characterization of a Glyphosate-Tolerant Enzyme from Streptomyces svecius: A Distinct Class of 5-Enolpyruvylshikimate-3-phosphate Synthases. J Agric Food Chem 2021; 69:5096-5104. [PMID: 33826316 DOI: 10.1021/acs.jafc.1c00439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Natural and modified versions of the 5-enolpyruvylshikimate-3-phosphate synthase (epsps) gene have been used to confer tolerance to the broad-spectrum herbicide glyphosate in a variety of commercial crops. The most widely utilized trait was obtained from the Agrobacterium tumefaciens strain CP4 and has been commercialized in several glyphosate-tolerant crops. The EPSPS gene products are enzymes that have been divided into three classes based on sequence similarity, sensitivity to glyphosate, and steady-state catalytic parameters. Herein, we describe the informatics-guided identification and biochemical and structural characterization of a novel EPSPS from Streptomyces sviceus (DGT-28 EPSPS). The data suggest DGT-28 EPSPS and other closely related homologues exemplify a distinct new class (Class IV) of EPSPS enzymes that display intrinsic tolerance to high concentrations of glyphosate (Ki ≥ 5000 μM). We further demonstrate that dgt-28 epsps, when transformed into stable plants, provides robust (≥4× field rates) vegetative/reproductive herbicide tolerance and has utility in weed-control systems comparable to that of commercialized events.
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Affiliation(s)
- Samantha L Griffin
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Jonathan R Chekan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina 27412, United States
| | - Justin M Lira
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Andrew E Robinson
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Carla N Yerkes
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Daniel L Siehl
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Terry R Wright
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert M Cicchillo
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
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13
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Fiore MF, de Lima ST, Carmichael WW, McKinnie SMK, Chekan JR, Moore BS. Guanitoxin, re-naming a cyanobacterial organophosphate toxin. Harmful Algae 2020; 92:101737. [PMID: 32113603 DOI: 10.1016/j.hal.2019.101737] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/26/2019] [Accepted: 12/28/2019] [Indexed: 05/06/2023]
Abstract
Anatoxin-a(S) is the most potent natural neurotoxin produced by fresh water cyanobacteria. It is also the least understood and monitored. Although this potent cholinesterase inhibitor was first reported in the 1970s and connected with animal poisonings, the lack of chemical standards and identified biosynthetic genes together with limited diagnostics and acute reactivity of this naturally-occurring organophosphate have limited our understanding of its environmental breadth and human health implications. Anatoxin-a(S) irreversibly inhibits acetylcholinesterase much like other organophosphate agents like paraoxon. It is however often confused with the similarly named anatoxin-a that has a completely different chemical structure, mechanism of action, and biosynthesis. Herein we propose renaming of anatoxin-a(S) to clarify its distinct structure and mechanism and to draw renewed attention to this potent natural poison. We propose the new name guanitoxin (GNT) to emphasize its distinctive guanidino organophosphate chemical structure.
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Affiliation(s)
- Marli Fátima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Stella Thomaz de Lima
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Wayne W Carmichael
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | | | - Jonathan R Chekan
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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14
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Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM, Rajakovich LJ, Krebs C, Cicchillo RM, Nair SK. Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc Natl Acad Sci U S A 2019; 116:13299-13304. [PMID: 31209034 PMCID: PMC6613135 DOI: 10.1073/pnas.1900711116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
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Affiliation(s)
- Jonathan R Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | | | - Terry R Wright
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN 46268
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Robert M Cicchillo
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN 46268
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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15
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Chekan JR, Lee GY, El Gamal A, Purdy TN, Houk KN, Moore BS. Bacterial Tetrabromopyrrole Debrominase Shares a Reductive Dehalogenation Strategy with Human Thyroid Deiodinase. Biochemistry 2019; 58:5329-5338. [PMID: 31117392 DOI: 10.1021/acs.biochem.9b00318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enzymatic dehalogenation is an important and well-studied biological process in both the detoxification and catabolism of small molecules, many of which are anthropogenic in origin. However, dedicated dehalogenation reactions that replace a halogen atom with a hydrogen are rare in the biosynthesis of natural products. In fact, the debrominase Bmp8 is the only known example. It catalyzes the reductive debromination of the coral settlement cue and the potential human toxin 2,3,4,5-tetrabromopyrrole as part of the biosynthesis of the antibiotic pentabromopseudilin. Using a combination of protein crystallography, mutagenesis, and computational modeling, we propose a catalytic mechanism for Bmp8 that is reminiscent of that catalyzed by human deiodinases in the maintenance of thyroid hormones. The identification of the key catalytic residues enabled us to recognize divergent functional homologues of Bmp8. Characterization of one of these homologues demonstrated its debromination activity even though it is found in a completely distinct genomic context. This observation suggests that additional enzymes outside those associated with the tetrabromopyrrole biosynthetic pathway may be able to alter the lifetime of this compound in the environment.
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Affiliation(s)
- Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Ga Young Lee
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Abrahim El Gamal
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - Trevor N Purdy
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography , University of California San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
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16
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Luhavaya H, Sigrist R, Chekan JR, McKinnie SMK, Moore BS. Biosynthesis of l-4-Chlorokynurenine, an Antidepressant Prodrug and a Non-Proteinogenic Amino Acid Found in Lipopeptide Antibiotics. Angew Chem Int Ed Engl 2019; 58:8394-8399. [PMID: 30963655 DOI: 10.1002/anie.201901571] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/06/2019] [Indexed: 12/18/2022]
Abstract
l-4-Chlorokynurenine (l-4-Cl-Kyn) is a neuropharmaceutical drug candidate that is in development for the treatment of major depressive disorder. Recently, this amino acid was naturally found as a residue in the lipopeptide antibiotic taromycin. Herein, we report the unprecedented conversion of l-tryptophan into l-4-Cl-Kyn catalyzed by four enzymes in the taromycin biosynthetic pathway from the marine bacterium Saccharomonospora sp. CNQ-490. We used genetic, biochemical, structural, and analytical techniques to establish l-4-Cl-Kyn biosynthesis, which is initiated by the flavin-dependent tryptophan chlorinase Tar14 and its flavin reductase partner Tar15. This work revealed the first tryptophan 2,3-dioxygenase (Tar13) and kynurenine formamidase (Tar16) enzymes that are selective for chlorinated substrates. The substrate scope of Tar13, Tar14, and Tar16 was examined and revealed intriguing promiscuity, thereby opening doors for the targeted engineering of these enzymes as useful biocatalysts.
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Affiliation(s)
- Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Renata Sigrist
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Department of Organic Chemistry, University of Campinas UNICAMP, Cidade Universitária Zeferino Vaz s/n, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaun M K McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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17
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Luhavaya H, Sigrist R, Chekan JR, McKinnie SMK, Moore BS. Biosynthesis of
l
‐4‐Chlorokynurenine, an Antidepressant Prodrug and a Non‐Proteinogenic Amino Acid Found in Lipopeptide Antibiotics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hanna Luhavaya
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Renata Sigrist
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Department of Organic ChemistryUniversity of Campinas UNICAMPCidade Universitária Zeferino Vaz s/n P.O. Box 6154 13083-970 Campinas SP Brazil
| | - Jonathan R. Chekan
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San Diego La Jolla CA 92093 USA
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18
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Chekan JR, McKinnie SMK, Moore ML, Poplawski SG, Michael TP, Moore BS. Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid. Angew Chem Int Ed Engl 2019; 58:8454-8457. [PMID: 30995339 DOI: 10.1002/anie.201902910] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/10/2019] [Indexed: 11/08/2022]
Abstract
Kainic acid, the flagship member of the kainoid family of natural neurochemicals, is a widely used neuropharmacological agent that helped unravel the key role of ionotropic glutamate receptors, including the kainate receptor, in the central nervous system. Worldwide shortages of this seaweed natural product in the year 2000 prompted numerous chemical syntheses, including scalable preparations with as few as six-steps. Herein we report the discovery and characterization of the concise two-enzyme biosynthetic pathway to kainic acid from l-glutamic acid and dimethylallyl pyrophosphate in red macroalgae and show that the biosynthetic genes are co-clustered in genomes of Digenea simplex and Palmaria palmata. Moreover, we applied a key biosynthetic α-ketoglutarate-dependent dioxygenase enzyme in a biotransformation methodology to efficiently construct kainic acid on the gram scale. This study establishes both the feasibility of mining seaweed genomes for their biotechnological prowess.
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Affiliation(s)
- Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaun M K McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Malia L Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | | | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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19
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Chekan JR, McKinnie SMK, Moore ML, Poplawski SG, Michael TP, Moore BS. Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan R. Chekan
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Shaun M. K. McKinnie
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | - Malia L. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
| | | | | | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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20
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Brunson JK, McKinnie SMK, Chekan JR, McCrow JP, Miles ZD, Bertrand EM, Bielinski VA, Luhavaya H, Oborník M, Smith GJ, Hutchins DA, Allen AE, Moore BS. Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom. Science 2018; 361:1356-1358. [PMID: 30262498 PMCID: PMC6276376 DOI: 10.1126/science.aau0382] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/15/2018] [Indexed: 01/26/2023]
Abstract
Oceanic harmful algal blooms of Pseudo-nitzschia diatoms produce the potent mammalian neurotoxin domoic acid (DA). Despite decades of research, the molecular basis for its biosynthesis is not known. By using growth conditions known to induce DA production in Pseudo-nitzschia multiseries, we implemented transcriptome sequencing in order to identify DA biosynthesis genes that colocalize in a genomic four-gene cluster. We biochemically investigated the recombinant DA biosynthetic enzymes and linked their mechanisms to the construction of DA's diagnostic pyrrolidine skeleton, establishing a model for DA biosynthesis. Knowledge of the genetic basis for toxin production provides an orthogonal approach to bloom monitoring and enables study of environmental factors that drive oceanic DA production.
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Affiliation(s)
- John K Brunson
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Shaun M K McKinnie
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan R Chekan
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - John P McCrow
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Zachary D Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erin M Bertrand
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Hanna Luhavaya
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Miroslav Oborník
- Institute of Parasitology, University of South Bohemia and Biology Center CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - G Jason Smith
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing, CA 95039, USA
| | - David A Hutchins
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew E Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA 92037, USA.
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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21
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Abstract
While halogenases have been studied for decades, the first natural product dehalogenase was only recently described. This bacterial enzyme, Bmp8, catalyzes the reductive debromination of 2,3,4,5-tetrabromopyrrole to form 2,3,4-tribromopyrrole as part of the biosynthesis of pentabromopseudilin, a marine natural product. Bmp8 is hypothesized to utilize a catalytic mechanism analogous to the important human thyroid hormone deiodinase enzyme family, potentially enabling Bmp8 to serve as model system to study this conserved mechanism. Herein, we describe a method for the soluble expression and purification of Bmp8. Furthermore, we detail activity assay protocols to quantify both consumption of the tetrabromopyrrole substrate and formation of the tribromopyrrole product. These methods will enable further study of this unusual enzyme and its catalytic mechanism.
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Affiliation(s)
- Jonathan R Chekan
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, United States.
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22
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Affiliation(s)
- Jonathan R Chekan
- Scripps Institution of Oceanography and ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , La Jolla, California 92093, United States
| | - Bradley S Moore
- Scripps Institution of Oceanography and ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , La Jolla, California 92093, United States
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23
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Olivares P, Ulrich EC, Chekan JR, van der Donk WA, Nair SK. Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads. ACS Chem Biol 2017; 12:456-463. [PMID: 27977135 DOI: 10.1021/acschembio.6b00939] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The broad-spectrum phosphonate antibiotic fosfomycin is currently in use for clinical treatment of infections caused by both Gram-positive and Gram-negative uropathogens. The antibiotic is biosynthesized by various streptomycetes, as well as by pseudomonads. Notably, the biosynthetic strategies used by the two genera share only two steps: the first step in which primary metabolite phosphoenolpyruvate (PEP) is converted to phosphonopyruvate (PnPy) and the terminal step in which 2-hydroxypropylphosphonate (2-HPP) is converted to fosfomycin. Otherwise, distinct enzymatic paths are employed. Here, we biochemically confirm the last two steps in the fosfomycin biosynthetic pathway of Pseudomonas syringae PB-5123, showing that Psf3 performs the reduction of 2-oxopropylphosphonate (2-OPP) to (S)-2-HPP, followed by the Psf4-catalyzed epoxidation of (S)-2-HPP to fosfomycin. Psf4 can also accept (R)-2-HPP as a substrate but instead performs an oxidation to make 2-OPP. We show that the combined activities of Psf3 and Psf4 can be used to convert racemic 2-HPP to fosfomycin in an enantioconvergent process. X-ray structures of each enzyme with bound substrates provide insights into the stereospecificity of each conversion. These studies shed light on the reaction mechanisms of the two terminal enzymes in a distinct pathway employed by pseudomonads for the production of a potent antimicrobial agent.
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Affiliation(s)
- Philip Olivares
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emily C. Ulrich
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan R. Chekan
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, ‡Department of Chemistry, §Carl R. Woese Institute for Genomic
Biology, ∥Howard Hughes Medical Institute, and ⊥Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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24
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Abstract
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Lanthipeptides
are ribosomally synthesized and post-translationally
modified peptides (RiPPs) that display a wide variety of biological
activities, from antimicrobial to antiallodynic. Lanthipeptides that
display antimicrobial activity are called lantibiotics. The post-translational
modification reactions of lanthipeptides include dehydration of Ser
and Thr residues to dehydroalanine and dehydrobutyrine, a transformation
that is carried out in three unique ways in different classes of lanthipeptides.
In a cyclization process, Cys residues then attack the dehydrated
residues to generate the lanthionine and methyllanthionine thioether
cross-linked amino acids from which lanthipeptides derive their name.
The resulting polycyclic peptides have constrained conformations that
confer their biological activities. After installation of the characteristic
thioether cross-links, tailoring enzymes introduce additional post-translational
modifications that are unique to each lanthipeptide and that fine-tune
their activities and/or stability. This review focuses on studies
published over the past decade that have provided much insight into
the mechanisms of the enzymes that carry out the post-translational
modifications.
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Affiliation(s)
- Lindsay M Repka
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan R Chekan
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Satish K Nair
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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25
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Chekan JR, Koos JD, Zong C, Maksimov MO, Link AJ, Nair SK. Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. J Am Chem Soc 2016; 138:16452-16458. [PMID: 27998080 DOI: 10.1021/jacs.6b10389] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lasso peptides are a class of bioactive ribosomally synthesized and post-translationally modified peptides (RiPPs), with a threaded knot structure that is formed by an isopeptide bond attaching the N-terminus of the peptide to a side chain carboxylate. Some lasso peptide biosynthetic clusters harbor an enzyme that specifically hydrolyzes the isopeptide bond to yield the linear peptide. We describe here the 2.4 Å resolution structure of a lasso peptide isopeptidase revealing a topologically novel didomain architecture consisting of an open β-propeller appended to an α/β hydrolase domain. The 2.2 Å resolution cocrystal structure of an inactive variant in complex with a lasso peptide reveals deformation of the substrate, and reorganization of the enzyme active site, which exposes and orients the isopeptide bond for hydrolysis. Structure-based mutational analysis reveals how this enzyme recognizes the lasso peptide substrate by shape complementarity rather than through sequence specificity. The isopeptidase gene can be used to facilitate genome mining, as a network-based mining strategy queried with this sequence identified 87 putative lasso peptide biosynthetic clusters, 65 of which have not been previously described. Lastly, we validate this mining approach by heterologous expression of two clusters encoded within the genome of Asticcaucalis benevestitus, and demonstrate that both clusters produce lasso peptides.
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Affiliation(s)
- Jonathan R Chekan
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
| | - Joseph D Koos
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
| | - Chuhan Zong
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
| | - Mikhail O Maksimov
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
| | - A James Link
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
| | - Satish K Nair
- Department of Biochemistry, ‡Institute for Genomic Biology and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States and.,Departments of Chemical and Biological Engineering, ⊥Molecular Biology, and #Chemistry Princeton University , Princeton, New Jersey 08544, United States
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26
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Abstract
Research in recent years have illuminated data on the mechanisms and targets of phosphonic acid antibiotics and herbicides, including fosfomycin, glyphosate, fosmidomycin and FR900098. Here we review the current state of knowledge of the structural and biochemical characterization of resistance mechanisms against these bioactive natural products. Advances in the understanding of these resistance determinants have spurred knowledge-based campaigns aimed towards the design of derivatives that retain biological activity but are less prone to tolerance.
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Affiliation(s)
- Jonathan R. Chekan
- Department of Biochemistry, University of Illinois at Urbana Champaign, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, USA
| | - Dillon P. Cogan
- Department of Biochemistry, University of Illinois at Urbana Champaign, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana Champaign, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, USA
- Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA
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27
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Peck SC, Chekan JR, Ulrich EC, Nair SK, van der Donk WA. A common late-stage intermediate in catalysis by 2-hydroxyethyl-phosphonate dioxygenase and methylphosphonate synthase. J Am Chem Soc 2015; 137:3217-20. [PMID: 25699631 DOI: 10.1021/jacs.5b00282] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
2-Hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are nonheme iron oxygenases that both catalyze the carbon-carbon bond cleavage of 2-hydroxyethylphosphonate but generate different products. Substrate labeling experiments led to a mechanistic hypothesis in which the fate of a common intermediate determined product identity. We report here the generation of a bifunctional mutant of HEPD (E176H) that exhibits the activity of both HEPD and MPnS. The product distribution of the mutant is sensitive to a substrate isotope effect, consistent with an isotope-sensitive branching mechanism involving a common intermediate. The X-ray structure of the mutant was determined and suggested that the introduced histidine does not coordinate the active site metal, unlike the iron-binding glutamate it replaced.
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Affiliation(s)
- Spencer C Peck
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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28
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Chekan JR, Kwon IH, Agarwal V, Dodd D, Revindran V, Mackie RI, Cann I, Nair SK. Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17. J Biol Chem 2014; 289:34965-77. [PMID: 25342756 DOI: 10.1074/jbc.m114.579904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hemicelluloses, the polysaccharide component of plant cell walls, represent one of the most abundant biopolymers in nature. The most common hemicellulosic constituents of softwoods, such as conifers and cycads, are mannans consisting of a 1,4-linked β-mannopyranosyl main chain with branch decorations. Efforts toward the utilization of hemicellulose for bioconversion into cellulosic biofuels have resulted in the identification of several families of glycoside hydrolases that can degrade mannan. However, effective biofermentation of manno-oligosaccharides is limited by a lack of appropriate uptake route in ethanologenic organisms. Here, we used transcriptome sequencing to gain insights into mannan degradation by the thermophilic anaerobic bacterium Caldanaerobius polysaccharolyticus. The most highly up-regulated genes during mannan fermentation occur in a cluster containing several genes encoding enzymes for efficient mannan hydrolysis as well as a solute-binding protein (CpMnBP1) that exhibits specificity for short mannose polymers but exhibited the flexibility to accommodate branched polysaccharide decorations. Co-crystal structures of CpMnBP1 in complex with mannobiose (1.4-Å resolution) and mannotriose (2.2-Å resolution) revealed the molecular rationale for chain length and oligosaccharide specificity. Calorimetric analysis of several active site variants confirmed the roles of residues critical to the function of CpMnBP1. This work represents the first biochemical characterization of a mannose-specific solute-binding protein and provides a framework for engineering mannan utilization capabilities for microbial fermentation.
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Affiliation(s)
| | | | | | - Dylan Dodd
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology
| | - Vanessa Revindran
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Isaac Cann
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology,
| | - Satish K Nair
- From the Departments of Biochemistry, Institute for Genomic Biology, Center for Biophysics and Computational Biology, and
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29
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Dunbar KL, Chekan JR, Cox CL, Burkhart BJ, Nair SK, Mitchell DA. Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis. Nat Chem Biol 2014; 10:823-9. [PMID: 25129028 PMCID: PMC4167974 DOI: 10.1038/nchembio.1608] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 06/19/2014] [Indexed: 11/24/2022]
Abstract
Despite intensive research, the cyclodehydratase responsible for azoline biogenesis in thiazole/oxazole-modified microcin (TOMM) natural products remains enigmatic. The collaboration of two proteins, C and D, is required for cyclodehydration. The C protein is homologous to E1 ubiquitin-activating enzymes, while the D protein is within the YcaO superfamily. Recent studies have demonstrated that TOMM YcaOs phosphorylate amide carbonyl oxygens to facilitate azoline formation. Here we report the X-ray crystal structure of an uncharacterized YcaO from Escherichia coli (Ec-YcaO). Ec-YcaO harbors an unprecedented fold and ATP-binding motif. This motif is conserved among TOMM YcaOs and is required for cyclodehydration. Furthermore, we demonstrate that the C protein regulates substrate binding and catalysis and that the proline-rich C-terminus of the D protein is involved in C protein recognition and catalysis. This study identifies the YcaO active site and paves the way for the characterization of the numerous YcaO domains not associated with TOMM biosynthesis.
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Affiliation(s)
- Kyle L Dunbar
- 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3]
| | - Jonathan R Chekan
- 1] Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2]
| | - Courtney L Cox
- 1] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brandon J Burkhart
- 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Satish K Nair
- 1] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A Mitchell
- 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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30
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Hung JE, Fogle EJ, Garg N, Chekan JR, Nair SK, van der Donk WA. Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase. PLoS One 2014; 9:e87134. [PMID: 24498026 PMCID: PMC3909101 DOI: 10.1371/journal.pone.0087134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 12/19/2013] [Indexed: 12/11/2022] Open
Abstract
Phosphite dehydrogenase (PTDH) catalyzes the NAD(+)-dependent oxidation of phosphite to phosphate. This reaction requires the deprotonation of a water nucleophile for attack on phosphite. A crystal structure was recently solved that identified Arg301 as a potential base given its proximity and orientation to the substrates and a water molecule within the active site. Mutants of this residue showed its importance for efficient catalysis, with about a 100-fold loss in k cat and substantially increased K m,phosphite for the Ala mutant (R301A). The 2.35 Å resolution crystal structure of the R301A mutant with NAD(+) bound shows that removal of the guanidine group renders the active site solvent exposed, suggesting the possibility of chemical rescue of activity. We show that the catalytic activity of this mutant is restored to near wild-type levels by the addition of exogenous guanidinium analogues; Brønsted analysis of the rates of chemical rescue suggests that protonation of the rescue reagent is complete in the transition state of the rate-limiting step. Kinetic isotope effects on the reaction in the presence of rescue agents show that hydride transfer remains at least partially rate-limiting, and inhibition experiments show that K i of sulfite with R301A is ∼400-fold increased compared to the parent enzyme, similar to the increase in K m for phosphite in this mutant. The results of our experiments indicate that Arg301 plays an important role in phosphite binding as well as catalysis, but that it is not likely to act as an active site base.
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Affiliation(s)
- John E. Hung
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Emily J. Fogle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Neha Garg
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jonathan R. Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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31
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Agarwal V, Peck SC, Chen JH, Borisova SA, Chekan JR, van der Donk WA, Nair SK. Structure and function of phosphonoacetaldehyde dehydrogenase: the missing link in phosphonoacetate formation. ACTA ACUST UNITED AC 2013; 21:125-35. [PMID: 24361046 DOI: 10.1016/j.chembiol.2013.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/06/2013] [Accepted: 11/14/2013] [Indexed: 10/25/2022]
Abstract
Phosphonates (C-PO₃²⁻) have applications as antibiotics, herbicides, and detergents. In some environments, these molecules represent the predominant source of phosphorus, and several microbes have evolved dedicated enzymatic machineries for phosphonate degradation. For example, most common naturally occurring phosphonates can be catabolized to either phosphonoacetaldehyde or phosphonoacetate, which can then be hydrolyzed to generate inorganic phosphate and acetaldehyde or acetate, respectively. The phosphonoacetaldehyde oxidase gene (phnY) links these two hydrolytic processes and provides a previously unknown catabolic mechanism for phosphonoacetate production in the microbial metabolome. Here, we present biochemical characterization of PhnY and high-resolution crystal structures of the apo state, as well as complexes with substrate, cofactor, and product. Kinetic analysis of active site mutants demonstrates how a highly conserved aldehyde dehydrogenase active site has been modified in nature to generate activity with a phosphonate substrate.
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Affiliation(s)
- Vinayak Agarwal
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Spencer C Peck
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jui-Hui Chen
- 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
| | - Svetlana A Borisova
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jonathan R Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; 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; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Satish K Nair
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; 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.
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