1
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Cui JJ, Zhang Y, Ju KS. Phosphonoalamides Reveal the Biosynthetic Origin of Phosphonoalanine Natural Products and a Convergent Pathway for Their Diversification. Angew Chem Int Ed Engl 2024; 63:e202405052. [PMID: 38780891 DOI: 10.1002/anie.202405052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
Phosphonate natural products, with their potent inhibitory activity, have found widespread use across multiple industries. Their success has inspired development of genome mining approaches that continue to reveal previously unknown bioactive scaffolds and biosynthetic insights. However, a greater understanding of phosphonate metabolism is required to enable prediction of compounds and their bioactivities from sequence information alone. Here, we expand our knowledge of this natural product class by reporting the complete biosynthesis of the phosphonoalamides, antimicrobial tripeptides with a conserved N-terminal l-phosphonoalanine (PnAla) residue produced by Streptomyces. The phosphonoalamides result from the convergence of PnAla biosynthesis and peptide ligation pathways. We elucidate the biochemistry underlying the transamination of phosphonopyruvate to PnAla, a new early branchpoint in phosphonate biosynthesis catalyzed by an aminotransferase with evolved specificity for phosphonate metabolism. Peptide formation is catalyzed by two ATP-grasp ligases, the first of which produces dipeptides, and a second which ligates dipeptides to PnAla to produce phosphonoalamides. Substrate specificity profiling revealed a dramatic expansion of dipeptide and tripeptide products, while finding PnaC to be the most promiscuous dipeptide ligase reported thus far. Our findings highlight previously unknown transformations in natural product biosynthesis, promising enzyme biocatalysts, and unveil insights into the diversity of phosphonopeptide natural products.
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Affiliation(s)
- Jerry J Cui
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
| | - Yeying Zhang
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
- Division of Medicinal Chemistry and Pharmacognosy, Center for Applied Plant Sciences, Infectious Disease Institute, The Ohio State University, 318W. 12th Ave, Columbus, OH-43210, USA
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2
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Cui J, Ju KS. Biosynthesis of Bacillus Phosphonoalamides Reveals Highly Specific Amino Acid Ligation. ACS Chem Biol 2024; 19:1506-1514. [PMID: 38885091 PMCID: PMC11259534 DOI: 10.1021/acschembio.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Phosphonate natural products have a history of commercial success across numerous industries due to their potent inhibition of metabolic processes. Over the past decade, genome mining approaches have successfully led to the discovery of numerous bioactive phosphonates. However, continued success is dependent upon a greater understanding of phosphonate metabolism, which will enable the prioritization and prediction of biosynthetic gene clusters for targeted isolation. Here, we report the complete biosynthetic pathway for phosphonoalamides E and F, antimicrobial phosphonopeptides with a conserved C-terminal l-phosphonoalanine (PnAla) residue. These peptides, produced by Bacillus, are the direct result of PnAla biosynthesis and serial ligation by two ATP-grasp ligases. A critical step of this pathway was the reversible transamination of phosphonopyruvate to PnAla by a dedicated transaminase with preference for the forward reaction. The dipeptide ligase PnfA was shown to ligate alanine to PnAla to afford phosphonoalamide E, which was subsequently ligated to alanine by PnfB to form phosphonoalamide F. Specificity profiling of both ligases found each to be highly specific, although the limited acceptance of noncanonical substrates by PnfA allowed for in vitro formation of products incorporating alternative pharmacophores. Our findings further establish the transaminative branch of phosphonate metabolism, unveil insights into the specificity of ATP-grasp ligation, and highlight the biocatalytic potential of biosynthetic enzymes.
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Affiliation(s)
- Jerry Cui
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, United States
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio 43210, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, United States
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3
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The functional importance of bacterial oxidative phosphonate pathways. Biochem Soc Trans 2023; 51:487-499. [PMID: 36892197 DOI: 10.1042/bst20220479] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Organophosphonates (Pns) are a unique class of natural products characterized by a highly stable C-P bond. Pns exhibit a wide array of interesting structures as well as useful bioactivities ranging from antibacterial to herbicidal. More structurally simple Pns are scavenged and catabolized by bacteria as a source of phosphorus. Despite their environmental and industrial importance, the pathways involved in the metabolism of Pns are far from being fully elucidated. Pathways that have been characterized often reveal unusual chemical transformations and new enzyme mechanisms. Among these, oxidative enzymes play an outstanding role during the biosynthesis and degradation of Pns. They are to a high extent responsible for the structural diversity of Pn secondary metabolites and for the break-down of both man-made and biogenic Pns. Here, we review our current understanding of the importance of oxidative enzymes for microbial Pn metabolism, discuss the underlying mechanistic principles, similarities, and differences between pathways. This review illustrates Pn biochemistry to involve a mix of classical redox biochemistry and unique oxidative reactions, including ring formations, rearrangements, and desaturations. Many of these reactions are mediated by specialized iron-dependent oxygenases and oxidases. Such enzymes are the key to both early pathway diversification and late-stage functionalization of complex Pns.
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4
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Ju KS, Nair SK. Convergent and divergent biosynthetic strategies towards phosphonic acid natural products. Curr Opin Chem Biol 2022; 71:102214. [PMID: 36202046 PMCID: PMC9722595 DOI: 10.1016/j.cbpa.2022.102214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 01/27/2023]
Abstract
The phosphonate class of natural products have received significant interests in the post-genomic era due to the relative ease with which their biosynthetic genes may be identified and the resultant final products be characterized. Recent large-scale studies of the elucidation and distributions of phosphonate pathways have provided a robust landscape for deciphering the underlying biosynthetic logic. A recurrent theme in phosphonate biosynthetic pathways is the interweaving of enzymatic reactions across different routes, which enables diversification to elaborate chemically novel scaffolds. Here, we provide a few vignettes of how Nature has utilized both convergent and divergent biosynthetic strategies to compile pathways for production of novel phosphonates. These examples illustrate how common intermediates may either be generated or intercepted to diversify chemical scaffolds and provides a starting point for both biotechnological and synthetic biological applications towards new phosphonates by similar combinatorial approaches.
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Affiliation(s)
- Kou-San Ju
- Department of Microbiology, The Ohio State University, Columbus OH 43210,Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, Columbus OH 43210,Infectious Diseases Institute. The Ohio State University, Columbus OH 43210,Corresponding authors: Kou-San Ju () and Satish K. Nair ()
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois, Urbana, IL 61801,Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801,Carl Woese Institute for Genomic Biology. University of Illinois, Urbana, IL 61801,Corresponding authors: Kou-San Ju () and Satish K. Nair ()
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5
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Shen BR, Annamalai P, Bai R, Badsara SS, Lee CF. Blue LED-Mediated Syntheses of Arylazo Phosphine Oxides and Phosphonates via N-P Bond Formation. Org Lett 2022; 24:5988-5993. [PMID: 35926085 DOI: 10.1021/acs.orglett.2c02251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The synthesis of (E)-diphenyl(aryldiazenyl)phosphine oxides and dialkyl (E)-(aryldiazenyl)phosphonates via visible light-mediated N-P bond formation between diazo species and phosphine oxides and phosphite derivatives, respectively, is described. The diazo species were generated via the reaction of aniline with isoamyl nitrite, which upon reaction with phosphorus surrogates generated arylazophosphine oxides and arylazo phosphonates in good to excellent yields. This sustainable chemical process offers a broad substrate scope and reasonably viable product formation.
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Affiliation(s)
- Bo-Ru Shen
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | | | - Rekha Bai
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Satpal Singh Badsara
- MFOS Laboratory, Department of Chemistry, University of Rajasthan, JLN, Marg, Jaipur, Rajasthan 302004, India
| | - Chin-Fa Lee
- Department of Chemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC.,i-Center for Advanced Science and Technology (iCAST), National Chung Hsing University, Taichung 402, Taiwan, ROC.,Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung 402, Taiwan, ROC
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6
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Abstract
Microbial phosphonate biosynthetic machinery has been identified in ~5 % of bacterial genomes and encodes natural products like fosfomycin as well as cell surface decorations. Almost all biological phosphonates originate from the rearrangement of phosphoenolpyruvate (PEP) to phosphonopyruvate (PnPy) catalysed by PEP mutase (Ppm), and PnPy is often converted to phosphonoacetaldehyde (PnAA) by PnPy decarboxylase (Ppd). Seven enzymes are known or likely to act on either PnPy or PnAA as early branch points en route to diverse biosynthetic outcomes, and these enzymes may be broadly classified into three reaction types: hydride transfer, aminotransfer, and carbon-carbon bond formation. However, the relative abundance of these branch points in microbial phosphonate biosynthesis is unknown. Also unknown is the proportion of ppm-containing gene neighbourhoods encoding new branch point enzymes and potentially novel phosphonates. In this study we computationally sorted 434 ppm-containing gene neighbourhoods based on these seven branch point enzymes. Unsurprisingly, the majority (56 %) of these pathways encode for production of the common naturally occurring compound 2-aminoethylphosphonate (AEP) or a hydroxylated derivative. The next most abundant genetically encoded intermediates were phosphonoalanine (PnAla, 9.2 %), 2-hydroxyethylphosphonate (HEP, 8.5 %), and phosphonoacetate (PnAc, 6 %). Significantly, about 13 % of the gene neighbourhoods could not be assigned to any of the seven branch points and may encode novel phosphonates. Sequence similarity network analysis revealed families of unusual gene neighbourhoods including possible production of phosphonoacrylate and phosphonofructose, the apparent biosynthetic use of the C-P lyase operon, and a virus-encoded phosphonate. Overall, these results highlight the utility of branch point inventories to identify novel gene neighbourhoods and guide future phosphonate discovery efforts.
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Affiliation(s)
- Siwei Li
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
| | - Geoff P. Horsman
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
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7
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Valentino H, Sobrado P. Characterization of a Nitro-Forming Enzyme Involved in Fosfazinomycin Biosynthesis. Biochemistry 2021; 60:2851-2864. [PMID: 34516102 DOI: 10.1021/acs.biochem.1c00512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-hydroxylating monooxygenases (NMOs) are a subclass of flavin-dependent enzymes that hydroxylate nitrogen atoms. Recently, unique NMOs that perform multiple reactions on one substrate molecule have been identified. Fosfazinomycin M (FzmM) is one such NMO, forming nitrosuccinate from aspartate (Asp) in the fosfazinomycin biosynthetic pathway in some Streptomyces sp. This work details the biochemical and kinetic analysis of FzmM. Steady-state kinetic investigation shows that FzmM performs a coupled reaction with Asp (kcat, 3.0 ± 0.01 s-1) forming nitrosuccinate, which can be converted to fumarate and nitrite by the action of FzmL. FzmM displays a 70-fold higher kcat/KM value for NADPH compared to NADH and has a narrow optimal pH range (7.5-8.0). Contrary to other NMOs where the kred is rate-limiting, FzmM exhibits a very fast kred (50 ± 0.01 s-1 at 4 °C) with NADPH. NADPH binds at a KD value of ∼400 μM, and hydride transfer occurs with pro-R stereochemistry. Oxidation of FzmM in the absence of Asp exhibits a spectrum with a shoulder at ∼370 nm, consistent with the formation of a C(4a)-hydroperoxyflavin intermediate, which decays into oxidized flavin and hydrogen peroxide at a rate 100-fold slower than the kcat. This reaction is enhanced in the presence of Asp with a slightly faster kox than the kcat, suggesting that flavin dehydration or Asp oxidation is partially rate limiting. Multiple sequence analyses of FzmM to NMOs identified conserved residues involved in flavin binding but not for NADPH. Additional sequence analysis to related monooxygenases suggests that FzmM shares sequence motifs absent in other NMOs.
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Affiliation(s)
- Hannah Valentino
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.,Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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8
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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9
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Wojdyla Z, Borowski T. Enzyme Multifunctionality by Control of Substrate Positioning Within the Catalytic Cycle—A QM/MM Study of Clavaminic Acid Synthase. Chemistry 2020; 27:2196-2211. [DOI: 10.1002/chem.202004426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
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10
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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11
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Petkowski JJ, Bains W, Seager S. Natural Products Containing 'Rare' Organophosphorus Functional Groups. Molecules 2019; 24:E866. [PMID: 30823503 PMCID: PMC6429109 DOI: 10.3390/molecules24050866] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/13/2019] [Accepted: 02/22/2019] [Indexed: 12/25/2022] Open
Abstract
Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P⁻N (phosphoramidate), P⁻S (phosphorothioate), and P⁻C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P⁻N, P⁻S, and P⁻C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P⁻S) and phosphoramidate (P⁻N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. We postulate that the extent of utilization of some phosphorus groups by life, especially those containing P⁻N bonds, is likely severely underestimated and has been largely overlooked, mainly due to the technological limitations in their detection and analysis.
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Affiliation(s)
- Janusz J Petkowski
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
| | - William Bains
- Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK.
| | - Sara Seager
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
- Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA.
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12
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Wang KKA, Ng TL, Wang P, Huang Z, Balskus EP, van der Donk WA. Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. Nat Commun 2018; 9:3687. [PMID: 30206228 PMCID: PMC6133997 DOI: 10.1038/s41467-018-06083-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/14/2018] [Indexed: 01/03/2023] Open
Abstract
Fosfazinomycin and kinamycin are natural products that contain nitrogen-nitrogen (N-N) bonds but that are otherwise structurally unrelated. Despite their considerable structural differences, their biosynthetic gene clusters share a set of genes predicted to facilitate N-N bond formation. In this study, we show that for both compounds, one of the nitrogen atoms in the N-N bond originates from nitrous acid. Furthermore, we show that for both compounds, an acetylhydrazine biosynthetic synthon is generated first and then funneled via a glutamyl carrier into the respective biosynthetic pathways. Therefore, unlike other pathways to N-N bond-containing natural products wherein the N-N bond is formed directly on a biosynthetic intermediate, during the biosyntheses of fosfazinomycin, kinamycin, and related compounds, the N-N bond is made in an independent pathway that forms a branch of a convergent route to structurally complex natural products.
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Affiliation(s)
- Kwo-Kwang A Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Tai L Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Zedu Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Chemistry, Fudan University, Shanghai, 200438-6789, China
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, MA, USA.
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Howard Hughes Medical Institute, Chevy Chase, 20815, MD, USA.
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13
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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14
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Matsuda K, Tomita T, Shin-ya K, Wakimoto T, Kuzuyama T, Nishiyama M. Discovery of Unprecedented Hydrazine-Forming Machinery in Bacteria. J Am Chem Soc 2018; 140:9083-9086. [DOI: 10.1021/jacs.8b05354] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kenichi Matsuda
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazuo Shin-ya
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
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15
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Waldman AJ, Balskus EP. Discovery of a Diazo-Forming Enzyme in Cremeomycin Biosynthesis. J Org Chem 2018; 83:7539-7546. [PMID: 29771512 DOI: 10.1021/acs.joc.8b00367] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The molecular architectures and potent bioactivities of diazo-containing natural products have attracted the interest of synthetic and biological chemists. Despite this attention, the biosynthetic enzymes involved in diazo group construction have not been identified. Here, we show that the ATP-dependent enzyme CreM installs the diazo group in cremeomycin via late-stage N-N bond formation using nitrite. This finding should inspire efforts to use diazo-forming enzymes in biocatalysis and synthetic biology as well as enable genome-based discovery of new diazo-containing metabolites.
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Affiliation(s)
- Abraham J Waldman
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford St , Cambridge , Massachusetts 02138 , United States
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford St , Cambridge , Massachusetts 02138 , United States
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16
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Herr CQ, Hausinger RP. Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases. Trends Biochem Sci 2018; 43:517-532. [PMID: 29709390 DOI: 10.1016/j.tibs.2018.04.002] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/21/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
Since their discovery in the 1960s, the family of Fe(II)/2-oxoglutarate-dependent oxygenases has undergone a tremendous expansion to include enzymes catalyzing a vast diversity of biologically important reactions. Recent examples highlight roles in controlling chromatin modification, transcription, mRNA demethylation, and mRNA splicing. Others generate modifications in tRNA, translation factors, ribosomes, and other proteins. Thus, oxygenases affect all components of molecular biology's central dogma, in which information flows from DNA to RNA to proteins. These enzymes also function in biosynthesis and catabolism of cellular metabolites, including antibiotics and signaling molecules. Due to their critical importance, ongoing efforts have targeted family members for the development of specific therapeutics. This review provides a general overview of recently characterized oxygenase reactions and their key biological roles.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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17
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Waldman AJ, Ng TL, Wang P, Balskus EP. Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5784-5863. [PMID: 28375000 PMCID: PMC5534343 DOI: 10.1021/acs.chemrev.6b00621] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.
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Affiliation(s)
- Abraham J. Waldman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Tai L. Ng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Peng Wang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
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Bai J, Yan D, Zhang T, Guo Y, Liu Y, Zou Y, Tang M, Liu B, Wu Q, Yu S, Tang Y, Hu Y. A Cascade of Redox Reactions Generates Complexity in the Biosynthesis of the Protein Phosphatase-2 Inhibitor Rubratoxin A. Angew Chem Int Ed Engl 2017; 56:4782-4786. [DOI: 10.1002/anie.201701547] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Tao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yongzhi Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yunbao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Zou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Qiong Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Shishan Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
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19
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Bai J, Yan D, Zhang T, Guo Y, Liu Y, Zou Y, Tang M, Liu B, Wu Q, Yu S, Tang Y, Hu Y. A Cascade of Redox Reactions Generates Complexity in the Biosynthesis of the Protein Phosphatase-2 Inhibitor Rubratoxin A. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Tao Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yongzhi Guo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yunbao Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Zou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Mancheng Tang
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Qiong Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Shishan Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
| | - Yi Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
- Department of Chemical and Biomolecular Engineering; Department of Chemistry and Biochemistry; University of California; Los Angeles CA 90095 USA
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing 100050 China
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20
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Freestone TS, Ju KS, Wang B, Zhao H. Discovery of a Phosphonoacetic Acid Derived Natural Product by Pathway Refactoring. ACS Synth Biol 2017; 6:217-223. [PMID: 28103011 DOI: 10.1021/acssynbio.6b00299] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The activation of silent natural product gene clusters is a synthetic biology problem of great interest. As the rate at which gene clusters are identified outpaces the discovery rate of new molecules, this unknown chemical space is rapidly growing, as too are the rewards for developing technologies to exploit it. One class of natural products that has been underrepresented is phosphonic acids, which have important medical and agricultural uses. Hundreds of phosphonic acid biosynthetic gene clusters have been identified encoding for unknown molecules. Although methods exist to elicit secondary metabolite gene clusters in native hosts, they require the strain to be amenable to genetic manipulation. One method to circumvent this is pathway refactoring, which we implemented in an effort to discover new phosphonic acids from a gene cluster from Streptomyces sp. strain NRRL F-525. By reengineering this cluster for expression in the production host Streptomyces lividans, utility of refactoring is demonstrated with the isolation of a novel phosphonic acid, O-phosphonoacetic acid serine, and the characterization of its biosynthesis. In addition, a new biosynthetic branch point is identified with a phosphonoacetaldehyde dehydrogenase, which was used to identify additional phosphonic acid gene clusters that share phosphonoacetic acid as an intermediate.
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Affiliation(s)
- Todd S. Freestone
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, §Departments of Biochemistry, Bioengineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kou-San Ju
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, §Departments of Biochemistry, Bioengineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Bin Wang
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, §Departments of Biochemistry, Bioengineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, ‡Carl R. Woese Institute for Genomic
Biology, §Departments of Biochemistry, Bioengineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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21
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Abstract
Organophosphonic acids are unique as natural products in terms of stability and mimicry. The C-P bond that defines these compounds resists hydrolytic cleavage, while the phosphonyl group is a versatile mimic of transition-states, intermediates, and primary metabolites. This versatility may explain why a variety of organisms have extensively explored the use organophosphonic acids as bioactive secondary metabolites. Several of these compounds, such as fosfomycin and bialaphos, figure prominently in human health and agriculture. The enzyme reactions that create these molecules are an interesting mix of chemistry that has been adopted from primary metabolism as well as those with no chemical precedent. Additionally, the phosphonate moiety represents a source of inorganic phosphate to microorganisms that live in environments that lack this nutrient; thus, unusual enzyme reactions have also evolved to cleave the C-P bond. This review is a comprehensive summary of the occurrence and function of organophosphonic acids natural products along with the mechanisms of the enzymes that synthesize and catabolize these molecules.
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Affiliation(s)
- Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University , Waterloo, Ontario N2L 3C5, Canada
| | - David L Zechel
- Department of Chemistry, Queen's University , Kingston, Ontario K7L 3N6, Canada
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22
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Abstract
The biosynthetic origin of a unique hydrazide moiety in the phosphonate natural product fosfazinomycin is investigated.
The biosynthetic origin of a unique hydrazide moiety in the phosphonate natural product fosfazinomycin is unknown. This study presents the activities of five proteins encoded in its gene cluster. The flavin-dependent oxygenase FzmM catalyses the oxidation of l-Asp to N-hydroxy-Asp. When FzmL is added, fumarate is produced in addition to nitrous acid. The adenylosuccinate lyase homolog FzmR eliminates acetylhydrazine from N-acetyl-hydrazinosuccinate, which in turn is the product of FzmQ-catalysed acetylation of hydrazinosuccinate. Collectively, these findings suggest a path to N-acetylhydrazine from l-Asp. The incorporation of nitrogen from l-Asp into fosfazinomycin was confirmed by isotope labelling studies. Installation of the N-terminal Val of fosfazinomycin is catalysed by FzmI in a Val-tRNA dependent process.
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Affiliation(s)
- Zedu Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801
| | - Kwo-Kwang Abraham Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801
| | - Wilfred A van der Donk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801
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23
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Wu LF, Meng S, Tang GL. Ferrous iron and α-ketoglutarate-dependent dioxygenases in the biosynthesis of microbial natural products. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:453-70. [DOI: 10.1016/j.bbapap.2016.01.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/22/2016] [Accepted: 01/29/2016] [Indexed: 01/29/2023]
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24
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Chin JP, McGrath JW, Quinn JP. Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling. Curr Opin Chem Biol 2016; 31:50-7. [DOI: 10.1016/j.cbpa.2016.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/24/2022]
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25
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Battula S, Kumar A, Ahmed QN. Metal-free oxidative cleavage of the C-C bond in α-hydroxy-β-oxophosphonates. Org Biomol Chem 2015; 13:9953-6. [PMID: 26365809 DOI: 10.1039/c5ob01615k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The potential of TBHP to promote oxidative hydroxylation of α-hydroxy-β-oxophosphonates (HOPs) through C(CO)-C bond cleavage is described. This cleavage, as depicted in the mechanism is expected through an isomer of HOP that reacts with TBHP to generate acids.
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Affiliation(s)
- Satyanarayana Battula
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (IIIM), Jammu, 180001, India
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26
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Battula S, Battini N, Singh D, Ahmed QN. 2-Oxo promoted hydrophosphonylation & aerobic intramolecular nucleophilic displacement reaction. Org Biomol Chem 2015. [DOI: 10.1039/c5ob01310k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly efficient catalyst free methods for the synthesis of α-hydroxy-β-oxo phosphonates (HOP) and α-oxoesters (OE) have been described for the first time. The existence of a 2-oxo group in α-oxoaldehydes (OA) was a key factor in promoting the reaction of the tervalent phosphite form towards activated aldehydes (OA) in the synthesis of HOP.
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Affiliation(s)
- Satyanarayana Battula
- Medicinal Chemistry Division
- Indian Institute of Integrative Medicine (IIIM)
- Jammu
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Narsaiah Battini
- Medicinal Chemistry Division
- Indian Institute of Integrative Medicine (IIIM)
- Jammu
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Deepika Singh
- Quality Control and Quality Assurance (QC & QA)
- IIIM
- Jammu
- India
| | - Qazi Naveed Ahmed
- Medicinal Chemistry Division
- Indian Institute of Integrative Medicine (IIIM)
- Jammu
- India
- Academy of Scientific and Innovative Research (AcSIR)
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27
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2015. [DOI: 10.1039/c5np90013a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 33 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as artesin A from Artemisia sieversiana.
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