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Epiktetov DO, Sviridov AV, Tarlachkov SV, Shushkova TV, Toropygin IY, Leontievsky AA. Glyphosate-Induced Phosphonatase Operons in Soil Bacteria of the Genus Achromobacter. Int J Mol Sci 2024; 25:6409. [PMID: 38928116 PMCID: PMC11203657 DOI: 10.3390/ijms25126409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Achromobacter insolitus and Achromobacter aegrifaciens, bacterial degraders of the herbicide glyphosate, were found to induce phosphonatase (phosphonoacetaldehyde hydrolase, EC 3.11.1.1) when grown on minimal media with glyphosate as the sole source of phosphorus. The phosphonatases of the strains were purified to an electrophoretically homogeneous state and characterized. The enzymes differed in their kinetic characteristics and some other parameters from the previously described phosphonatases. The phosphonatase of A. insolitus was first revealed to separate into two stable forms, which had similar kinetic characteristics but interacted differently with affinity and ion-exchange resins. The genomes of the investigated bacteria were sequenced. The phosphonatase genes were identified, and their context was determined: the bacteria were shown to have gene clusters, which, besides the phosphonatase operon, included genes for LysR-type transcription activator (substrate sensor) and putative iron-containing oxygenase PhnHD homologous to monooxygenases PhnY and TmpB of marine organophosphonate degraders. Genes of 2-aminoethylphosphonate aminotransferase (PhnW, EC 2.6.1.37) were absent in the achromobacterial phosphonatase operons; instead, we revealed the presence of genes encoding the putative flavin oxidase HpnW. In silico simulation showed 1-hydroxy-2-aminoethylphosphonate to be the most likely substrate of the new monooxygenase, and a number of glycine derivatives structurally similar to glyphosate to be substrates of flavin oxidase.
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Affiliation(s)
- Dmitry O. Epiktetov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Alexey V. Sviridov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Sergey V. Tarlachkov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
- Branch of Shemyakin—Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Puschino, 142290 Moscow, Russia
| | - Tatyana V. Shushkova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
| | - Ilya Yu. Toropygin
- V.N. Orekhovich Research Institute of Biomedical Chemistry, Bld. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia;
| | - Alexey A. Leontievsky
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Russian Academy of Sciences, 5 Prosp. Nauki, 142290 Pushchino, Russia; (D.O.E.); (S.V.T.); (T.V.S.); (A.A.L.)
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2
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Jodts RJ, Ho MB, Reyes RM, Park YJ, Doan PE, Rosenzweig AC, Hoffman BM. Initial Steps in Methanobactin Biosynthesis: Substrate Binding by the Mixed-Valent Diiron Enzyme MbnBC. Biochemistry 2024; 63:1170-1177. [PMID: 38587906 DOI: 10.1021/acs.biochem.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The MbnBC enzyme complex converts cysteine residues in a peptide substrate, MbnA, to oxazolone/thioamide groups during the biosynthesis of copper chelator methanobactin (Mbn). MbnBC belongs to the mixed-valent diiron oxygenase (MVDO) family, of which members use an Fe(II)Fe(III) cofactor to react with dioxygen for substrate modification. Several crystal structures of the inactive Fe(III)Fe(III) form of MbnBC alone and in complex with MbnA have been reported, but a mechanistic understanding requires determination of the oxidation states of the crystallographically observed Fe ions in the catalytically active Fe(II)Fe(III) state, along with the site of MbnA binding. Here, we have used electron nuclear double resonance (ENDOR) spectroscopy to determine such structural and electronic properties of the active site, in particular, the mode of substrate binding to the MV state, information not accessible by X-ray crystallography alone. The oxidation states of the two Fe ions were determined by 15N ENDOR analysis. The presence and locations of both bridging and terminal exogenous solvent ligands were determined using 1H and 2H ENDOR. In addition, 2H ENDOR using an isotopically labeled MbnA substrate indicates that MbnA binds to the Fe(III) ion of the cluster via the sulfur atom of its N-terminal modifiable cysteine residue, with displacement of a coordinated solvent ligand as shown by complementary 1H ENDOR. These results, which underscore the utility of ENDOR in studying MVDOs, provide a molecular picture of the initial steps in Mbn biosynthesis.
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3
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Lidbury IDEA, Hitchcock A, Groenhof SRM, Connolly AN, Moushtaq L. New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria. Adv Microb Physiol 2024; 84:1-49. [PMID: 38821631 DOI: 10.1016/bs.ampbs.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.
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Affiliation(s)
- Ian D E A Lidbury
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
| | - Andrew Hitchcock
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Plants, Photosynthesis, and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Sophie R M Groenhof
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Alex N Connolly
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Laila Moushtaq
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
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4
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Furtak A, Szafranek-Nakonieczna A, Furtak K, Pytlak A. A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120453. [PMID: 38430886 DOI: 10.1016/j.jenvman.2024.120453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.
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Affiliation(s)
- Adam Furtak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland
| | - Anna Szafranek-Nakonieczna
- Department of Biology and Biotechnology of Microorganisms, Institute of Medical Sciences, The John Paul II Catholic University of Lublin, Konstantynów 1 I, 20-708, Lublin, Poland
| | - Karolina Furtak
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Krańcowa 8, INCBR Centre, 24-100, Puławy, Poland
| | - Anna Pytlak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
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5
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Zangelmi E, Ruffolo F, Dinhof T, Gerdol M, Malatesta M, Chin JP, Rivetti C, Secchi A, Pallitsch K, Peracchi A. Deciphering the role of recurrent FAD-dependent enzymes in bacterial phosphonate catabolism. iScience 2023; 26:108108. [PMID: 37876809 PMCID: PMC10590968 DOI: 10.1016/j.isci.2023.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/30/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Phosphonates-compounds containing a direct C-P bond-represent an important source of phosphorus in some environments. The most common natural phosphonate is 2-aminoethylphosphonate (AEP). Many bacteria can break AEP down through specialized "hydrolytic" pathways, which start with the conversion of AEP into phosphonoacetaldehyde (PAA), catalyzed by the transaminase PhnW. However, the substrate scope of these pathways is very narrow, as PhnW cannot process other common AEP-related phosphonates, notably N-methyl AEP (M1AEP). Here, we describe a heterogeneous group of FAD-dependent oxidoreductases that efficiently oxidize M1AEP to directly generate PAA, thus expanding the versatility and usefulness of the hydrolytic AEP degradation pathways. Furthermore, some of these enzymes can also efficiently oxidize plain AEP. By doing so, they surrogate the role of PhnW in organisms that do not possess the transaminase and create novel versions of the AEP degradation pathways in which PAA is generated solely by oxidative deamination.
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Affiliation(s)
- Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, 1090 Vienna, Austria
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, UK
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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6
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Ruffolo F, Dinhof T, Murray L, Zangelmi E, Chin JP, Pallitsch K, Peracchi A. The Microbial Degradation of Natural and Anthropogenic Phosphonates. Molecules 2023; 28:6863. [PMID: 37836707 PMCID: PMC10574752 DOI: 10.3390/molecules28196863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Phosphonates are compounds containing a direct carbon-phosphorus (C-P) bond, which is particularly resistant to chemical and enzymatic degradation. They are environmentally ubiquitous: some of them are produced by microorganisms and invertebrates, whereas others derive from anthropogenic activities. Because of their chemical stability and potential toxicity, man-made phosphonates pose pollution problems, and many studies have tried to identify biocompatible systems for their elimination. On the other hand, phosphonates are a resource for microorganisms living in environments where the availability of phosphate is limited; thus, bacteria in particular have evolved systems to uptake and catabolize phosphonates. Such systems can be either selective for a narrow subset of compounds or show a broader specificity. The role, distribution, and evolution of microbial genes and enzymes dedicated to phosphonate degradation, as well as their regulation, have been the subjects of substantial studies. At least three enzyme systems have been identified so far, schematically distinguished based on the mechanism by which the C-P bond is ultimately cleaved-i.e., through either a hydrolytic, radical, or oxidative reaction. This review summarizes our current understanding of the molecular systems and pathways that serve to catabolize phosphonates, as well as the regulatory mechanisms that govern their activity.
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Affiliation(s)
- Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, A-1090 Vienna, Austria
| | - Leanne Murray
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, UK
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, A-1090 Vienna, Austria;
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, I-43124 Parma, Italy (E.Z.)
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7
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Ayikpoe R, Zhu L, Chen JY, Ting CP, van der Donk WA. Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. ACS CENTRAL SCIENCE 2023; 9:1008-1018. [PMID: 37252350 PMCID: PMC10214503 DOI: 10.1021/acscentsci.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 05/31/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of post-translational modification enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes, and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme complex catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethyl group. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent reaction catalyzed by a DUF692 enzyme complex, further expanding the repertoire of remarkable reactions catalyzed by these enzymes. Based on the three currently characterized DUF692 family members, we suggest the family be called multinuclear non-heme iron dependent oxidative enzymes (MNIOs).
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Affiliation(s)
- Richard
S. Ayikpoe
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Jeff Y. Chen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Chi P. Ting
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
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8
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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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9
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Ayikpoe RS, Zhu L, Chen JY, Ting CP, van der Donk WA. A remarkable transformation catalyzed by a domain-of-unknown-function 692 during the biosynthesis of a new RiPP natural product. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527370. [PMID: 36798408 PMCID: PMC9934569 DOI: 10.1101/2023.02.06.527370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of posttranslational modification enzymes involved in the biosynthesis of ribosomally-synthesized and posttranslationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is ubiquitously encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethylation. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent DUF692 enzyme, further expanding the repertoire of remarkable reactions catalyzed by these enzymes.
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Affiliation(s)
- Richard S. Ayikpoe
- 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
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Jeff Y. Chen
- 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
| | - Chi P. Ting
- 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
| | - 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 at the University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
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10
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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Albert T, Moënne-Loccoz P. Spectroscopic Characterization of a Diferric Mycobacterial Hemerythrin-Like Protein with Unprecedented Reactivity toward Nitric Oxide. J Am Chem Soc 2022; 144:17611-17621. [PMID: 36099449 DOI: 10.1021/jacs.2c07113] [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
Hemerythrin-like proteins (HLPs) are broadly distributed across taxonomic groups and appear to play highly diverse functional roles in prokaryotes. Mycobacterial HLPs contribute to the survival of these pathogenic bacteria in mammalian macrophages, but their modes of action remain unclear. A recent crystallographic characterization of Mycobacterium kansasii HLP (Mka-HLP) revealed the unexpected presence of a tyrosine sidechain (Tyr54) near the coordination sphere of one of the two iron centers. Here, we show that Tyr54 is a true ligand to the Fe2(III) ion which, in conjunction with the presence of a μ-oxo group bridging the two iron(III), brings unique reactivity toward nitric oxide (NO). Monitoring the titration of Mka-HLP with NO by Fourier-transform infrared and electron paramagnetic resonance spectroscopies shows that both diferric and diferrous forms of Mka-HLP accumulate an uncoupled high-spin and low-spin {FeNO}7 pair. We assign the reactivity of the diferric protein to an initial radical reaction between NO and the μ-oxo bridge to form nitrite and a mixed-valent diiron center that can react further with NO. Amperometric measurements of NO consumption by Mka-HLP confirm that this reactivity can proceed at low micromolar concentrations of NO, before additional NO consumption, supporting a NO scavenging role for mycobacterial HLPs.
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Affiliation(s)
- Therese Albert
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Pierre Moënne-Loccoz
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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12
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β-Hydroxylation of α-amino-β-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin. Commun Chem 2022; 5:87. [PMID: 36697788 PMCID: PMC9814697 DOI: 10.1038/s42004-022-00703-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/13/2022] [Indexed: 01/28/2023] Open
Abstract
Caprazamycin is a nucleoside antibiotic that inhibits phospho-N-acetylmuramyl-pentapeptide translocase (MraY). The biosynthesis of nucleoside antibiotics has been studied but is still far from completion. The present study characterized enzymes Cpz10, Cpz15, Cpz27, Mur17, Mur23 out of caprazamycin/muraymycin biosynthetic gene cluster, particularly the nonheme αKG-dependent enzyme Cpz10. Cpz15 is a β-hydroxylase converting uridine mono-phosphate to uridine 5' aldehyde, then incorporating with threonine by Mur17 (Cpz14) to form 5'-C-glycyluridine. Cpz10 hydroxylates synthetic 11 to 12 in vitro. Major product 13 derived from mutant Δcpz10 is phosphorylated by Cpz27. β-Hydroxylation of 11 by Cpz10 permits the maturation of caprazamycin, but decarboxylation of 11 by Mur23 oriented to muraymycin formation. Cpz10 recruits two iron atoms to activate dioxygen with regio-/stereo-specificity and commit electron/charge transfer, respectively. The chemo-physical interrogations should greatly advance our understanding of caprazamycin biosynthesis, which is conducive to pathway/protein engineering for developing more effective nucleoside antibiotics.
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13
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Parkinson EI, Lakkis HG, Alwali AA, Metcalf MEM, Modi R, Metcalf WW. An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2-Oxoglutarate-Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin. Angew Chem Int Ed Engl 2022; 61:e202206173. [PMID: 35588368 PMCID: PMC9296572 DOI: 10.1002/anie.202206173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/20/2022]
Abstract
The biosynthesis of the natural product dehydrofosmidomycin involves an unusual transformation in which 2-(trimethylamino)ethylphosphonate is rearranged, desaturated and demethylated by the enzyme DfmD, a divergent member of the 2-oxoglutarate-dependent dioxygenase superfamily. Although other members of this enzyme family catalyze superficially similar transformations, the combination of all three reactions in a single enzyme has not previously been observed. By characterizing the products of in vitro reactions with labeled and unlabeled substrates, we show that DfmD performs this transformation in two steps, with the first involving desaturation of the substrate to form 2-(trimethylamino)vinylphosphonate, and the second involving rearrangement and demethylation to form methyldehydrofosmidomycin. These data reveal significant differences from the desaturation and rearrangement reactions catalyzed by other family members.
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Affiliation(s)
- Elizabeth I. Parkinson
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Hani G. Lakkis
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Amir A. Alwali
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Mary Elizabeth M. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
| | - Ramya Modi
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - William W. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
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14
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Langton M, Appell M, Koob J, Pandelia ME. Domain Fusion of Two Oxygenases Affords Organophosphonate Degradation in Pathogenic Fungi. Biochemistry 2022; 61:956-962. [PMID: 35506879 PMCID: PMC9177745 DOI: 10.1021/acs.biochem.2c00163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Proteins of the HD-domain superfamily employ a conserved histidine-aspartate (HD) dyad to coordinate diverse metallocofactors. While most known HD-domain proteins are phosphohydrolases, new additions to this superfamily have emerged such as oxygenases and lyases, expanding their functional repertoire. To date, three HD-domain oxygenases have been identified, all of which employ a mixed-valent FeIIFeIII cofactor to activate their substrates and utilize molecular oxygen to afford cleavage of C-C or C-P bonds via a diferric superoxo intermediate. Phylogenetic analysis reveals an uncharacterized multidomain protein in the pathogenic soil fungus Fonsecaea multimorphosa, herein designated PhoF. PhoF consists of an N-terminal FeII/α-ketoglutarate-dependent domain resembling that of PhnY and a C-terminal HD-domain like that of PhnZ. PhnY and PhnZ are part of an organophosphonate degradation pathway in which PhnY hydroxylates 2-aminoethylphosphonic acid, and PhnZ cleaves the C-P bond of the hydroxylated product yielding phosphate and glycine. Employing electron paramagnetic resonance and Mössbauer spectroscopies in tandem with activity assays, we determined that PhoF carries out the O2-dependent degradation of two aminophosphonates, demonstrating an expanded catalytic efficiency with respect to the individual, but mechanistically coupled PhnY and PhnZ. Our results recognize PhoF as a new example of an HD-domain oxygenase and show that domain fusion of an organophosphonate degradation pathway may be a strategy for disease-causing fungi to acquire increased functional versatility, potentially important for their survival.
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Affiliation(s)
- Michelle Langton
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Matthew Appell
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Jeremy Koob
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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15
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Parkinson EI, Lakkis HG, Alwali AA, Metcalf MEM, Modi R, Metcalf WW. An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2‐Oxoglutarate‐Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202206173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | - Ramya Modi
- Purdue University Chemistry UNITED STATES
| | - William W. Metcalf
- University of Illinois Urbana-Champaign Microbiology 601 S. GoodwinB103 CLSL 61801 Urbana UNITED STATES
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16
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Li X, Xue S, Guo Y, Chang WC. Mechanism of Methyldehydrofosmidomycin Maturation: Use Olefination to Enable Chain Elongation. J Am Chem Soc 2022; 144:8257-8266. [PMID: 35482829 DOI: 10.1021/jacs.2c01924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Utilization of mononuclear iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to enable C-H bond functionalization is a widely used strategy to diversify the structural complexity of natural products. Besides those well-studied reactions including hydroxylation, epoxidation, and halogenation, in the biosynthetic pathway of dehydrofosmidomycin, an Fe/2OG enzyme is reported to catalyze desaturation, alkyl chain elongation, along with demethylation in which trimethyl-2-aminoethylphosphonate is converted into methyldehydrofosmidomycin. How this transformation takes place is largely unknown. Herein, we characterized the reactive species, revealed the structure of the reaction intermediate, and used mechanistic probes to investigate the reaction pathway and mechanism. These results led to the elucidation of a two-step process in which the first reaction employs a long-lived Fe(IV)-oxo species to trigger C═C bond installation. During the second reaction, the olefin installed in situ enables C-C bond formation that is accompanied with a C-N bond cleavage and hydroxylation to furnish the alkyl chain elongation and demethylation. This work expands the reaction repertoire of Fe/2OG enzymes by introducing a new pathway to the known C-C bond formation mechanisms utilized by metalloenzymes.
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Affiliation(s)
- Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shan Xue
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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17
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A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2123566119. [PMID: 35320042 PMCID: PMC9060507 DOI: 10.1073/pnas.2123566119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanobactins (Mbns), copper-binding peptidic compounds produced by some bacteria, are candidate therapeutics for human diseases of copper overload. The paired oxazolone-thioamide bidentate ligands of methanobactins are generated from cysteine residues in a precursor peptide, MbnA, by the MbnBC enzyme complex. MbnBC activity depends on the presence of iron and oxygen, but the catalytically active form has not been identified. Here, we provide evidence that a dinuclear Fe(II)Fe(III) center in MbnB, which is the only representative of a >13,000-member protein family to be characterized, is responsible for this reaction. These findings expand the known roles of diiron enzymes in biology and set the stage for mechanistic understanding, and ultimately engineering, of the MbnBC biosynthetic complex. The iron-containing heterodimeric MbnBC enzyme complex plays a central role in the biosynthesis of methanobactins (Mbns), ribosomally synthesized, posttranslationally modified natural products that bind copper with high affinity. MbnBC catalyzes a four-electron oxidation of a cysteine residue in its precursor-peptide substrate, MbnA, to an oxazolone ring and an adjacent thioamide group. Initial studies of MbnBC indicated the presence of both diiron and triiron species, complicating identification of the catalytically active species. Here, we present evidence through activity assays combined with electron paramagnetic resonance (EPR) and Mössbauer spectroscopic analysis that the active species is a mixed-valent, antiferromagnetically coupled Fe(II)Fe(III) center. Consistent with this assignment, heterologous expression of the MbnBC complex in culture medium containing less iron yielded purified protein with less bound iron but greater activity in vitro. The maximally activated MbnBC prepared in this manner could modify both cysteine residues in MbnA, in contrast to prior findings that only the first cysteine could be processed. Site-directed mutagenesis and multiple crystal structures clearly identify the two essential Fe ions in the active cluster as well as the location of the previously detected third Fe site. Moreover, structural modeling indicates a role for MbnC in recognition of the MbnA leader peptide. These results add a biosynthetic oxidative rearrangement reaction to the repertoire of nonheme diiron enzymes and provide a foundation for elucidating the MbnBC mechanism.
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18
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Song X, Liu J, Wang B. Emergence of Function from Nonheme Diiron Oxygenases: A Quantum Mechanical/Molecular Mechanical Study of Oxygen Activation and Organophosphonate Catabolism Mechanisms by PhnZ. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xitong Song
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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19
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de Visser SP, Mukherjee G, Ali HS, Sastri CV. Local Charge Distributions, Electric Dipole Moments, and Local Electric Fields Influence Reactivity Patterns and Guide Regioselectivities in α-Ketoglutarate-Dependent Non-heme Iron Dioxygenases. Acc Chem Res 2022; 55:65-74. [PMID: 34915695 DOI: 10.1021/acs.accounts.1c00538] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Non-heme iron dioxygenases catalyze vital processes for human health related to the biosynthesis of essential products and the biodegradation of toxic metabolites. Often the natural product biosyntheses by these non-heme iron dioxygenases is highly regio- and chemoselective, which are commonly assigned to tight substrate-binding and positioning. However, recent high-level computational modeling has shown that substrate-binding and positioning is only part of the story and long-range electrostatic interactions can play a major additional role.In this Account, we review and summarize computational viewpoints on the high regio- and chemoselectivity of α-ketoglutarate-dependent non-heme iron dioxygenases and how external perturbations affect the catalysis. In particular, studies from our groups have shown that often a regioselectivity in enzymes can be accomplished by stabilization of the rate-determining transition state for the reaction through external charges, electric dipole moments, or local electric field effects. Furthermore, bond dissociation energies in molecules are shown to be influenced by an electric field effect, and through targeting a specific bond in an electric field, this can lead to an unusually specific reaction. For instance, in the carbon-induced starvation protein, we studied two substrate-bound conformations and showed that regardless of what C-H bond of the substrate is closest to the iron(IV)-oxo oxidant, the lowest hydrogen atom abstraction barrier is always for the pro-S C2-H abstraction due to an induced dipole moment of the protein that weakens this bond. In another example of the hygromycin biosynthesis enzyme, an oxidative ring-closure reaction in the substrate forms an ortho-δ-ester ring. Calculations on this enzyme show that the selectivity is guided by a protonated lysine residue in the active site that, through its positive charge, triggers a low energy hydrogen atom abstraction barrier. A final set of examples in this Account discuss the viomycin biosynthesis enzyme and the 2-(trimethylammonio)ethylphosphonate dioxygenase (TmpA) enzyme. Both of these enzymes are shown to possess a significant local dipole moment and local electric field effect due to charged residues surrounding the substrate and oxidant binding pockets. The protein dipole moment and local electric field strength changes the C-H bond strengths of the substrate as compared to the gas-phase triggers the regioselectivity of substrate activation. In particular, we show that in the gas phase and in a protein environment C-H bond strengths are different due to local electric dipole moments and electric field strengths. These examples show that enzymes have an intricately designed structure that enables a chemical reaction under ambient conditions through the positioning of positively and negatively charged residues that influence and enhance reaction mechanisms. These computational insights create huge possibilities in bioengineering to apply local electric field and dipole moments in proteins to achieve an unusual selectivity and specificity and trigger a fit-for-purpose biocatalyst for unique biotransformations.
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Affiliation(s)
- Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
| | - Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
| | - Hafiz Saqib Ali
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
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20
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Murphy ARJ, Scanlan DJ, Chen Y, Adams NBP, Cadman WA, Bottrill A, Bending G, Hammond JP, Hitchcock A, Wellington EMH, Lidbury IDEA. Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle. Nat Commun 2021; 12:4554. [PMID: 34315891 PMCID: PMC8316502 DOI: 10.1038/s41467-021-24646-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
The planktonic synthesis of reduced organophosphorus molecules, such as alkylphosphonates and aminophosphonates, represents one half of a vast global oceanic phosphorus redox cycle. Whilst alkylphosphonates tend to accumulate in recalcitrant dissolved organic matter, aminophosphonates do not. Here, we identify three bacterial 2-aminoethylphosphonate (2AEP) transporters, named AepXVW, AepP and AepSTU, whose synthesis is independent of phosphate concentrations (phosphate-insensitive). AepXVW is found in diverse marine heterotrophs and is ubiquitously distributed in mesopelagic and epipelagic waters. Unlike the archetypal phosphonate binding protein, PhnD, AepX has high affinity and high specificity for 2AEP (Stappia stellulata AepX Kd 23 ± 4 nM; methylphosphonate Kd 3.4 ± 0.3 mM). In the global ocean, aepX is heavily transcribed (~100-fold>phnD) independently of phosphate and nitrogen concentrations. Collectively, our data identifies a mechanism responsible for a major oxidation process in the marine phosphorus redox cycle and suggests 2AEP may be an important source of regenerated phosphate and ammonium, which are required for oceanic primary production.
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Affiliation(s)
- Andrew R J Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Nathan B P Adams
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
- Nanotemper Technologies GmbH, Flößergasse 4, Munich, Germany
| | - William A Cadman
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Andrew Bottrill
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - Gary Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, UK
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, UK
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | | | - Ian D E A Lidbury
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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21
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Simon MA, Ongpipattanakul C, Nair SK, van der Donk WA. Biosynthesis of fosfomycin in pseudomonads reveals an unexpected enzymatic activity in the metallohydrolase superfamily. Proc Natl Acad Sci U S A 2021; 118:e2019863118. [PMID: 34074759 PMCID: PMC8201877 DOI: 10.1073/pnas.2019863118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The epoxide-containing phosphonate natural product fosfomycin is a broad-spectrum antibiotic used in the treatment of cystitis. Fosfomycin is produced by both the plant pathogen Pseudomonas syringae and soil-dwelling streptomycetes. While the streptomycete pathway has recently been fully elucidated, the pseudomonad pathway is still mostly elusive. Through a systematic evaluation of heterologous expression of putative biosynthetic enzymes, we identified the central enzyme responsible for completing the biosynthetic pathway in pseudomonads. The missing transformation involves the oxidative decarboxylation of the intermediate 2-phosphonomethylmalate to a new intermediate, 3-oxo-4-phosphonobutanoate, by PsfC. Crystallographic studies reveal that PsfC unexpectedly belongs to a new class of diiron metalloenzymes that are part of the polymerase and histidinol phosphatase superfamily.
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Affiliation(s)
- Max A Simon
- Department of Bioengineering, 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
| | - Chayanid Ongpipattanakul
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Satish K Nair
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Wilfred A van der Donk
- Department of Bioengineering, 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
- HHMI, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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22
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Lin YT, Ali HS, de Visser SP. Electrostatic Perturbations from the Protein Affect C-H Bond Strengths of the Substrate and Enable Negative Catalysis in the TmpA Biosynthesis Enzyme. Chemistry 2021; 27:8851-8864. [PMID: 33978257 DOI: 10.1002/chem.202100791] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/08/2022]
Abstract
The nonheme iron dioxygenase 2-(trimethylammonio)-ethylphosphonate dioxygenase (TmpA) is an enzyme involved in the regio- and chemoselective hydroxylation at the C1 -position of the substrate as part of the biosynthesis of glycine betaine in bacteria and carnitine in humans. To understand how the enzyme avoids breaking the weak C2 -H bond in favor of C1 -hydroxylation, we set up a cluster model of 242 atoms representing the first and second coordination sphere of the metal center and substrate binding pocket, and investigated possible reaction mechanisms of substrate activation by an iron(IV)-oxo species by density functional theory methods. In agreement with experimental product distributions, the calculations predict a favorable C1 -hydroxylation pathway. The calculations show that the selectivity is guided through electrostatic perturbations inside the protein from charged residues, external electric fields and electric dipole moments. In particular, charged residues influence and perturb the homolytic bond strength of the C1 -H and C2 -H bonds of the substrate, and strongly strengthens the C2 -H bond in the substrate-bound orientation.
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Affiliation(s)
- Yen-Ting Lin
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Hafiz Saqib Ali
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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23
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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24
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Langton M, Sun S, Ueda C, Markey M, Chen J, Paddy I, Jiang P, Chin N, Milne A, Pandelia ME. The HD-Domain Metalloprotein Superfamily: An Apparent Common Protein Scaffold with Diverse Chemistries. Catalysts 2020; 10:1191. [PMID: 34094591 PMCID: PMC8177086 DOI: 10.3390/catal10101191] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The histidine-aspartate (HD)-domain protein superfamily contains metalloproteins that share common structural features but catalyze vastly different reactions ranging from oxygenation to hydrolysis. This chemical diversion is afforded by (i) their ability to coordinate most biologically relevant transition metals in mono-, di-, and trinuclear configurations, (ii) sequence insertions or the addition of supernumerary ligands to their active sites, (iii) auxiliary substrate specificity residues vicinal to the catalytic site, (iv) additional protein domains that allosterically regulate their activities or have catalytic and sensory roles, and (v) their ability to work with protein partners. More than 500 structures of HD-domain proteins are available to date that lay out unique structural features which may be indicative of function. In this respect, we describe the three known classes of HD-domain proteins (hydrolases, oxygenases, and lyases) and identify their apparent traits with the aim to portray differences in the molecular details responsible for their functional divergence and reconcile existing notions that will help assign functions to yet-to-be characterized proteins. The present review collects data that exemplify how nature tinkers with the HD-domain scaffold to afford different chemistries and provides insight into the factors that can selectively modulate catalysis.
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Affiliation(s)
- Michelle Langton
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Sining Sun
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Chie Ueda
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Max Markey
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jiahua Chen
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Isaac Paddy
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Paul Jiang
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Natalie Chin
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Amy Milne
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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25
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Sun S, Pandelia ME. HD-[HD-GYP] Phosphodiesterases: Activities and Evolutionary Diversification within the HD-GYP Family. Biochemistry 2020; 59:2340-2350. [PMID: 32496757 DOI: 10.1021/acs.biochem.0c00257] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic dinucleotides are signaling molecules that modulate many processes, including immune response and virulence factor production. Their cellular levels in bacteria are fine-tuned by metal-dependent phosphodiesterases, namely, the EAL and HD-GYP proteins, with HD-GYPs belonging to the larger HD domain superfamily. In this study, we first focus on the catalytic properties and the range of metal ions and substrates of the HD-[HD-GYP] subfamily, consisting of two HD domains. We identified SO3491 as a homologue of VCA0681 and the second example of an HD-[HD-GYP]. Both proteins hydrolyze c-di-GMP and 3'3'c-GAMP and coordinate various metal ions, but only Fe and to a lesser extent Co support hydrolysis. The proteins are active only in the diferrous form and not in the one-electron more oxidized FeIIFeIII state. Although the C-terminal HD-GYP domain is essential for activity, the role of the N-terminal HD domain remains unknown. We show that the N-terminal site is important for protein stability, influences the individual apparent kcat and KM (but not kcat/KM), and cannot bind c-di-GMP, thus precluding its involvement in cyclic dinucleotide sensing. We proceeded to perform phylogenetic analyses to examine the distribution and functional relationships of the HD-[HD-GYP]s to the rest of the HD-GYPs. The phylogeny provides a correlation map that draws a link between the evolutionary and functional diversification of HD-GYPs, serving as a template for predicting the chemical nature of the metallocofactor, level of activity, and reaction outcome.
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Affiliation(s)
- Sining Sun
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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Gama SR, Lo BSY, Séguin J, Pallitsch K, Hammerschmidt F, Zechel DL. C-H Bond Cleavage Is Rate-Limiting for Oxidative C-P Bond Cleavage by the Mixed Valence Diiron-Dependent Oxygenase PhnZ. Biochemistry 2019; 58:5271-5280. [PMID: 31046250 DOI: 10.1021/acs.biochem.9b00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PhnZ utilizes a mixed valence diiron(II/III) cofactor and O2 to oxidatively cleave the carbon-phosphorus bond of (R)-2-amino-1-hydroxyethylphosphonic acid to form glycine and orthophosphate. The active site residues Y24 and E27 are proposed to mediate induced-fit recognition of the substrate and access of O2 to one of the active site Fe ions. H62 is proposed to deprotonate the C1-hydroxyl of the substrate during catalysis. Kinetic isotope effects (KIEs), pH-rate dependence, and site-directed mutagenesis were used to probe the rate-determining transition state and the roles of these three active site residues. Primary deuterium KIE values of 5.5 ± 0.3 for D(V) and 2.2 ± 0.4 for D(V/K) were measured with (R)-2-amino[1-2H1]-1-hydroxyethylphosphonic acid, indicating that cleavage of the C1-H bond of the substrate is rate-limiting. This step is also rate-limiting for PhnZ Y24F, as shown by a significant deuterium KIE value of 2.3 ± 0.1 for D(V). In contrast, a different reaction step appears to be rate-limiting for the PhnZ E27A and H62A variants, which exhibited D(V) values near unity. A solvent KIE of 2.2 ± 0.3 for D2O(V) is observed for PhnZ. Significant solvent KIE values are also observed for the PhnZ Y24F and E27A variants. In contrast, the PhnZ H62A variant does not show a significant solvent KIE, suggesting that H62 is mediating proton transfer in the transition state. A proton inventory study with PhnZ indicates that 1.5 ± 0.6 protons are in flight in the rate-determining step. Overall, the rate-determining transition state for oxidative C-P bond cleavage by PhnZ is proposed to involve C-H bond cleavage that is coupled to deprotonation of the substrate C1-hydroxyl by H62.
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Affiliation(s)
- Simanga R Gama
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Becky Suet Yan Lo
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Jacqueline Séguin
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
| | - Katharina Pallitsch
- Institute of Organic Chemistry , University of Vienna , 1090 Vienna , Austria
| | | | - David L Zechel
- Department of Chemistry , Queen's University , Kingston , Ontario , Canada K7L 3N6
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