1
|
Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
Collapse
Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
| |
Collapse
|
2
|
Kaushik S, Yadav J, Das S, Singh S, Jyoti A, Srivastava VK, Sharma V, Kumar S, Kumar S. Deciphering the Role of S-adenosyl Homocysteine Nucleosidase in Quorum
Sensing Mediated Biofilm Formation. Curr Protein Pept Sci 2022; 23:211-225. [DOI: 10.2174/1389203723666220519152507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/21/2022] [Accepted: 03/11/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
S-adenosylhomocysteine nucleosidase (MTAN) is a protein that plays a crucial role in several
pathways of bacteria that are essential for its survival and pathogenesis. In addition to the role of
MTAN in methyl-transfer reactions, methionine biosynthesis, and polyamine synthesis, MTAN is also
involved in bacterial quorum sensing (QS). In QS, chemical signaling autoinducer (AI) secreted by
bacteria assists cell to cell communication and is regulated in a cell density-dependent manner. They
play a significant role in the formation of bacterial biofilm. MTAN plays a major role in the synthesis
of these autoinducers. Signaling molecules secreted by bacteria, i.e., AI-1 are recognized as acylated
homoserine lactones (AHL) that function as signaling molecules within bacteria. QS enables bacteria
to establish physical interactions leading to biofilm formation. The formation of biofilm is a primary
reason for the development of multidrug-resistant properties in pathogenic bacteria like Enterococcus
faecalis (E. faecalis). In this regard, inhibition of E. faecalis MTAN (EfMTAN) will block the QS and
alter the bacterial biofilm formation. In addition to this, it will also block methionine biosynthesis and
many other critical metabolic processes. It should also be noted that inhibition of EfMTAN will not
have any effect on human beings as this enzyme is not present in humans. This review provides a comprehensive
overview of the structural-functional relationship of MTAN. We have also highlighted the
current status, enigmas that warrant further studies, and the prospects for identifying potential inhibitors
of EfMTAN for the treatment of E. faecalis infections. In addition to this, we have also reported
structural studies of EfMTAN using homology modeling and highlighted the putative binding sites of
the protein.
Collapse
Affiliation(s)
- Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Structural Biology Lab, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Suraj Singh
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, India
| | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT University, Vellore-632014, Tamil Nadu, India
| | - Sujeet Kumar
- Centre for Proteomics and Drug Discovery, Amity Institute of Biotechnology, Amity University, Maharashtra, India
| |
Collapse
|
3
|
Sadler JC, Wallace S. Microbial synthesis of vanillin from waste poly(ethylene terephthalate). GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2021; 23:4665-4672. [PMID: 34276250 PMCID: PMC8256426 DOI: 10.1039/d1gc00931a] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
Poly(ethylene terephthalate) (PET) is an abundant and extremely useful material, with widespread applications across society. However, there is an urgent need to develop technologies to valorise post-consumer PET waste to tackle plastic pollution and move towards a circular economy. Whilst PET degradation and recycling technologies have been reported, examples focus on repurposing the resultant monomers to produce more PET or other second-generation materials. Herein, we report a novel pathway in engineered Escherichia coli for the direct upcycling of PET derived monomer terephthalic acid into the value-added small molecule vanillin, a flavour compound ubiquitous in the food and cosmetic industries, and an important bulk chemical. After process optimisation, 79% conversion to vanillin from TA was achieved, a 157-fold improvement over our initial conditions. Parameters such as temperature, cell permeabilisation and in situ product removal were key to maximising vanillin titres. Finally, we demonstrate the conversion of post-consumer PET from a plastic bottle into vanillin by coupling the pathway with enzyme-catalysed PET hydrolysis. This work demonstrates the first biological upcycling of post-consumer plastic waste into vanillin using an engineered microorganism.
Collapse
Affiliation(s)
- Joanna C Sadler
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
| | - Stephen Wallace
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh Roger Land Building Alexander Crum Brown Road King's Buildings Edinburgh EH9 3FF UK
| |
Collapse
|
4
|
Zhong A, Lee YH, Liu YN, Liu HW. Biosynthesis of Oxetanocin-A Includes a B 12-Dependent Radical SAM Enzyme That Can Catalyze both Oxidative Ring Contraction and the Demethylation of SAM. Biochemistry 2021; 60:537-546. [PMID: 33560833 PMCID: PMC7904626 DOI: 10.1021/acs.biochem.0c00915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxetanocin-A is an antitumor, antiviral, and antibacterial nucleoside. It is biosynthesized via the oxidative ring contraction of a purine nucleoside co-opted from primary metabolism. This reaction is catalyzed by a B12-dependent radical S-adenosyl-l-methionine (SAM) enzyme, OxsB, and a phosphohydrolase, OxsA. Previous experiments showed that the product of the OxsB/OxsA-catalyzed reaction is an oxetane aldehyde produced alongside an uncharacterized byproduct. Experiments reported herein reveal that OxsB/OxsA complex formation is crucial for the ring contraction reaction and that reduction of the aldehyde intermediate is catalyzed by a nonspecific dehydrogenase from the general cellular pool. In addition, the byproduct is identified as a 1,3-thiazinane adduct between the aldehyde and l-homocysteine. While homocysteine was never included in the OxsB/OxsA assays, the data suggest that it can be generated from SAM via S-adenosyl-l-homocysteine (SAH). Further study revealed that conversion of SAM to SAH is facilitated by OxsB; however, the subsequent conversion of SAH to homocysteine is due to protein contaminants that co-purify with OxsA. Nevertheless, the observed demethylation of SAM to SAH suggests possible methyltransferase activity of OxsB, and substrate methylation was indeed detected in the OxsB-catalyzed reaction. This work is significant because it not only completes the description of the oxetanocin-A biosynthetic pathway but also suggests that OxsB may be capable of methyltransferase activity.
Collapse
Affiliation(s)
- Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yung-nan Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
5
|
North JA, Wildenthal JA, Erb TJ, Evans BS, Byerly KM, Gerlt JA, Tabita FR. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol Microbiol 2020; 113:923-937. [PMID: 31950558 DOI: 10.1111/mmi.14459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 01/19/2023]
Abstract
S-adenosyl-l-methionine (SAM) is a necessary cosubstrate for numerous essential enzymatic reactions including protein and nucleotide methylations, secondary metabolite synthesis and radical-mediated processes. Radical SAM enzymes produce 5'-deoxyadenosine, and SAM-dependent enzymes for polyamine, neurotransmitter and quorum sensing compound synthesis produce 5'-methylthioadenosine as by-products. Both are inhibitory and must be addressed by all cells. This work establishes a bifunctional oxygen-independent salvage pathway for 5'-deoxyadenosine and 5'-methylthioadenosine in both Rhodospirillum rubrum and Extraintestinal Pathogenic Escherichia coli. Homologous genes for this pathway are widespread in bacteria, notably pathogenic strains within several families. A phosphorylase (Rhodospirillum rubrum) or separate nucleoside and kinase (Escherichia coli) followed by an isomerase and aldolase sequentially function to salvage these two wasteful and inhibitory compounds into adenine, dihydroxyacetone phosphate and acetaldehyde or (2-methylthio)acetaldehyde during both aerobic and anaerobic growth. Both SAM by-products are metabolized with equal affinity during aerobic and anaerobic growth conditions, suggesting that the dual-purpose salvage pathway plays a central role in numerous environments, notably the human body during infection. Our newly discovered bifunctional oxygen-independent pathway, widespread in bacteria, salvages at least two by-products of SAM-dependent enzymes for carbon and sulfur salvage, contributing to cell growth.
Collapse
Affiliation(s)
- Justin A North
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - John A Wildenthal
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Bradley S Evans
- The Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Kathryn M Byerly
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - John A Gerlt
- Department of Biochemistry, The Institute for Genomic Biology, Champaign, IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Fred R Tabita
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
6
|
Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
Collapse
Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| |
Collapse
|
7
|
Sadler JC, Humphreys LD, Snajdrova R, Burley GA. A Tandem Enzymatic sp 2 -C-Methylation Process: Coupling in Situ S-Adenosyl-l-Methionine Formation with Methyl Transfer. Chembiochem 2017; 18:992-995. [PMID: 28371017 DOI: 10.1002/cbic.201700115] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Indexed: 01/07/2023]
Abstract
A one-pot, two-step biocatalytic platform for the regiospecfic C-methylation and C-ethylation of aromatic substrates is described. The tandem process utilises SalL (Salinospora tropica) for in situ synthesis of S-adenosyl-l-methionine (SAM), followed by alkylation of aromatic substrates by the C-methyltransferase NovO (Streptomyces spheroides). The application of this methodology is demonstrated for the regiospecific labelling of aromatic substrates by the transfer of methyl, ethyl and isotopically labelled 13 CH3,13 CD3 and CD3 groups from their corresponding SAM analogues formed in situ.
Collapse
Affiliation(s)
- Joanna C Sadler
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Luke D Humphreys
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK.,Present address: Gilead Alberta ULC, 1021 Hayter Road NW, Edmonton, AB, T6S 1A1, Canada
| | - Radka Snajdrova
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Glenn A Burley
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| |
Collapse
|
8
|
Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states. Proc Natl Acad Sci U S A 2016; 113:13756-13761. [PMID: 27856757 DOI: 10.1073/pnas.1609718113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic mechanism requires multiple proton-transfer events. Of particular interest is the protonation state of residue D198, which possesses a pKa above 8 and functions as a general acid to initiate the enzymatic reaction. In this study we present three corefined neutron/X-ray crystal structures of wild-type HpMTAN cocrystallized with S-adenosylhomocysteine (SAH), Formycin A (FMA), and (3R,4S)-4-(4-Chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine (p-ClPh-Thio-DADMe-ImmA) as well as one neutron/X-ray crystal structure of an inactive variant (HpMTAN-D198N) cocrystallized with SAH. These results support a mechanism of D198 pKa elevation through the unexpected sharing of a proton with atom N7 of the adenine moiety possessing unconventional hydrogen-bond geometry. Additionally, the neutron structures also highlight active site features that promote the stabilization of the transition state and slight variations in these interactions that result in 100-fold difference in binding affinities between the DADMe-ImmA and ImmA analogs.
Collapse
|
9
|
Shin D, Frane ND, Brecht RM, Keeler J, Nagarajan R. A Comparative Analysis of Acyl-Homoserine Lactone Synthase Assays. Chembiochem 2015; 16:2651-9. [PMID: 26456773 DOI: 10.1002/cbic.201500387] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 11/10/2022]
Abstract
Quorum sensing is cell-to-cell communication that allows bacteria to coordinate attacks on their hosts by inducing virulent gene expression, biofilm production, and other cellular functions, including antibiotic resistance. AHL synthase enzymes synthesize N-acyl-l-homoserine lactones, commonly referred to as autoinducers, to facilitate quorum sensing in Gram-negative bacteria. Studying the synthases, however, has proven to be a difficult road. Two assays, including a radiolabeled assay and a colorimetric (DCPIP) assay are well-documented in literature to study AHL synthases. In this paper, we describe additional methods that include an HPLC-based, C-S bond cleavage and coupled assays to investigate this class of enzymes. In addition, we compare and contrast each assay for both acyl-CoA- and acyl-ACP-utilizing synthases. The expanded toolkit described in this study should facilitate mechanistic studies on quorum sensing signal synthases and expedite discovery of antivirulent compounds.
Collapse
Affiliation(s)
- Daniel Shin
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Nicole D Frane
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA
| | - Ryan M Brecht
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, PO Box 208114, New Haven, CT, 06520-8114, USA
| | - Jesse Keeler
- Department of Chemistry, Northwest Nazarene University, Nampa, ID, 83686, USA.,Loma Linda School of Medicine, Coleman Pavilion, 11175 Campus Street, Loma Linda, CA, 92350, USA
| | - Rajesh Nagarajan
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Drive, Boise, ID, 83725, USA.
| |
Collapse
|
10
|
Abstract
This review focuses on the steps unique to methionine biosynthesis, namely the conversion of homoserine to methionine. The past decade has provided a wealth of information concerning the details of methionine metabolism and the review focuses on providing a comprehensive overview of the field, emphasizing more recent findings. Details of methionine biosynthesis are addressed along with key cellular aspects, including regulation, uptake, utilization, AdoMet, the methyl cycle, and growing evidence that inhibition of methionine biosynthesis occurs under stressful cellular conditions. The first unique step in methionine biosynthesis is catalyzed by the metA gene product, homoserine transsuccinylase (HTS, or homoserine O-succinyltransferase). Recent experiments suggest that transcription of these genes is indeed regulated by MetJ, although the repressor-binding sites have not yet been verified. Methionine also serves as the precursor of S-adenosylmethionine, which is an essential molecule employed in numerous biological processes. S-adenosylhomocysteine is produced as a consequence of the numerous AdoMet-dependent methyl transfer reactions that occur within the cell. In E. coli and Salmonella, this molecule is recycled in two discrete steps to complete the methyl cycle. Cultures challenged by oxidative stress appear to experience a growth limitation that depends on methionine levels. E. coli that are deficient for the manganese and iron superoxide dismutases (the sodA and sodB gene products, respectively) require the addition of methionine or cysteine for aerobic growth. Modulation of methionine levels in response to stressful conditions further increases the complexity of its regulation.
Collapse
|
11
|
Barta ML, Thomas K, Yuan H, Lovell S, Battaile KP, Schramm VL, Hefty PS. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J Biol Chem 2014; 289:32214-32229. [PMID: 25253688 DOI: 10.1074/jbc.m114.594325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The obligate intracellular human pathogen Chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. Genomic sequencing of Chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. In order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). The sources or biosynthetic pathways required to obtain these electron carriers within C. trachomatis are poorly understood. The 1.58Å crystal structure of C. trachomatis hypothetical protein CT263 presented here supports a role in quinone biosynthesis. Although CT263 lacks sequence-based functional annotation, the crystal structure of CT263 displays striking structural similarity to 5'-methylthioadenosine nucleosidase (MTAN) enzymes. Although CT263 lacks the active site-associated dimer interface found in prototypical MTANs, co-crystal structures with product (adenine) or substrate (5'-methylthioadenosine) indicate that the canonical active site residues are conserved. Enzymatic characterization of CT263 indicates that the futalosine pathway intermediate 6-amino-6-deoxyfutalosine (kcat/Km = 1.8 × 10(3) M(-1) s(-1)), but not the prototypical MTAN substrates (e.g. S-adenosylhomocysteine and 5'-methylthioadenosine), is hydrolyzed. Bioinformatic analyses of the chlamydial proteome also support the futalosine pathway toward the synthesis of menaquinone in Chlamydiaceae. This report provides the first experimental support for quinone synthesis in Chlamydia. Menaquinone synthesis provides another target for agents to combat C. trachomatis infection.
Collapse
Affiliation(s)
- Michael L Barta
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Keisha Thomas
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Hongling Yuan
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, Kansas 66047, and
| | - Kevin P Battaile
- Industrial Macromolecular Crystallography Association-Collaborative Access Team, Hauptman-Woodward Medical Research Institute, Argonne, Illinois 60439
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - P Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045,.
| |
Collapse
|
12
|
Methylthioadenosine/S-adenosylhomocysteine nucleosidase (Pfs) of Staphylococcus aureus is essential for the virulence independent of LuxS/AI-2 system. Int J Med Microbiol 2013; 303:190-200. [PMID: 23611628 DOI: 10.1016/j.ijmm.2013.03.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/22/2013] [Accepted: 03/24/2013] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus aureus is a major cause of infectious morbidity and mortality in both community and hospital settings. The bacterium continues to cause diverse invasive, life-threatening infections, such as pneumonia, endocarditis, and septicemia. Methylthioadenosine/S-adenosylhomocysteine nucleosidase (Pfs) is predicted to be an important enzyme involved in methylation reactions, polyamine synthesis, vitamin synthesis, and quorum sensing pathways. For the first time, we demonstrate that Pfs is essential for the virulence of S. aureus. The pfs mutant strain, as compared to the isogenic wild type, displayed a decreased production of extracellular proteases, which was correlated with a dramatic decrease in the expression of the sspABC operon and a moderate decrease of aur expression. The mouse model of sepsis and subcutaneous abscesses indicated that the pfs mutant strain displayed highly impaired virulence compared to the isogenic wild type. The decreased virulence of the pfs mutant strain is in correspondence with its decreased proliferation in vivo, indicated with a real-time analysis in the transparent system of zebrafish embryos. These phenotypes of the pfs mutant strain are LuxS/AI-2 independent despite the essential role pfs plays in AI-2 production. Our data suggest that Pfs is a potential novel target for anti-infection therapy.
Collapse
|
13
|
Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chem Biol 2013; 8:189-99. [PMID: 23082955 DOI: 10.1021/cb300477w] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The discrepancy between the pace of sequencing and functional characterization of genomes is a major challenge in understanding complex microbial metabolic processes and metabolic interactions in the environment. Here, we identified and validated genes related to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Untargeted mass spectrometry based metabolomics was used to identify metabolites utilized by Escherichia coli and Shewanella oneidensis MR-1. Targeted high-throughput metabolite profiling of spent media of 8042 individual mutant strains was performed to link utilization to specific genes. Using this approach we identified genes of known function as well as novel transport proteins and enzymes required for the utilization of tested metabolites. Specific examples include two subunits of a predicted ABC transporter encoded by the genes SO1043 and SO1044 required for the utilization of citrulline and a predicted histidase encoded by the gene SO3057 required for the utilization of ergothioneine by S. oneidensis. In vitro assays with purified proteins showed substrate specificity of SO3057 toward ergothioneine and histidine betaine in contrast to substrate specificity of a paralogous histidase SO0098 toward histidine. This generally applicable, high-throughput workflow has the potential both to discover novel metabolic capabilities of microorganisms and to identify the corresponding genes.
Collapse
Affiliation(s)
- Richard Baran
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| | - Benjamin P. Bowen
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| | - Morgan N. Price
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| | - Adam P. Arkin
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| | - Adam M. Deutschbauer
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| | - Trent R. Northen
- Life
Sciences Division and ‡Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Rd., Berkeley, California 94720, United States
| |
Collapse
|
14
|
Mishra V, Ronning DR. Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5'-alkylthio binding subsite. Biochemistry 2012; 51:9763-72. [PMID: 23148563 DOI: 10.1021/bi301221k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzyme is a multifunctional enzyme that catalyzes the hydrolysis of the N-ribosidic bond of at least four different adenosine-based metabolites: S-adenosylhomocysteine (SAH), 5'-methylthioadenosine (MTA), 5'-deoxyadenosine (5'-DOA), and 6-amino-6-deoxyfutalosine. These activities place the enzyme at the hub of seven fundamental bacterial metabolic pathways: S-adenosylmethionine (SAM) utilization, polyamine biosynthesis, the purine salvage pathway, the methionine salvage pathway, the SAM radical pathways, autoinducer-2 biosynthesis, and menaquinone biosynthesis. The last pathway makes MTAN essential for Helicobacter pylori viability. Although structures of various bacterial and plant MTANs have been described, the interactions between the homocysteine moiety of SAH and the 5'-alkylthiol binding site of MTAN have never been resolved. We have determined crystal structures of an inactive mutant form of H. pylori MTAN bound to MTA and SAH to 1.63 and 1.20 Å, respectively. The active form of MTAN was also crystallized in the presence of SAH, allowing the determination of the structure of a ternary enzyme-product complex resolved at 1.50 Å. These structures identify interactions between the homocysteine moiety and the 5'-alkylthiol binding site of the enzyme. This information can be leveraged for the development of species-specific MTAN inhibitors that prevent the growth of H. pylori.
Collapse
Affiliation(s)
- Vidhi Mishra
- Department of Chemistry, University of Toledo, Toledo, OH 43606, USA
| | | |
Collapse
|
15
|
Clinch K, Evans GB, Fröhlich RFG, Gulab SA, Gutierrez JA, Mason JM, Schramm VL, Tyler PC, Woolhouse AD. Transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase incorporating acyclic ribooxacarbenium ion mimics. Bioorg Med Chem 2012; 20:5181-7. [PMID: 22854195 DOI: 10.1016/j.bmc.2012.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/28/2012] [Accepted: 07/04/2012] [Indexed: 11/24/2022]
Abstract
Several acyclic hydroxy-methylthio-amines with 3-5 carbon atoms were prepared and coupled via a methylene link to 9-deazaadenine. The products were tested for inhibition against human MTAP and Escherichia coli and Neisseria meningitidis MTANs and gave K(i) values as low as 0.23 nM. These results were compared to those obtained with 1st and 2nd generation inhibitors (1S)-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino-5-methylthio-D-ribitol (MT-Immucillin-A, 3) and (3R,4S)-1-[9-deazaadenin-9-yl)methyl]3-hydroxy-4-methylthiomethylpyrrolidine (MT-DADMe-Immucillin-A, 4). The best inhibitors were found to exhibit binding affinities of approximately 2- to 4-fold those of 3 but were significantly weaker than 4. Cleavage of the 2,3 carbon-carbon bond in MT-Immucillin-A (3) gave an acyclic product (79) with a 21,500 fold loss of activity against E. coli MTAN. In another case, N-methylation of a side chain secondary amine resulted in a 250-fold loss of activity against the same enzyme [(±)-65 vs (±)-68]. The inhibition results were also contrasted with those acyclic derivatives previously prepared as inhibitors for a related enzyme, purine nucleoside phosphorylase (PNP), where some inhibitors in the latter case were found to be more potent than their cyclic counterparts.
Collapse
Affiliation(s)
- Keith Clinch
- Carbohydrate Chemistry, Industrial Research Limited, PO Box 31310, Lower Hutt 5040, New Zealand.
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Natural and synthetic small boron-containing molecules as potential inhibitors of bacterial and fungal quorum sensing. Chem Rev 2010; 111:209-37. [PMID: 21171664 DOI: 10.1021/cr100093b] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
17
|
Parveen N, Cornell KA. Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism. Mol Microbiol 2010; 79:7-20. [PMID: 21166890 DOI: 10.1111/j.1365-2958.2010.07455.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The importance of methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase in bacteria has started to be appreciated only in the past decade. A comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through S-adenosylmethionine (SAM)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (AI-2). SAM is also essential for synthesis of polyamines, N-acylhomoserine lactone (autoinducer-1), and production of vitamins and other biomolecules formed by SAM radical reactions. MTA, SAH and 5'-deoxyadenosine (5'dADO) are product inhibitors of these reactions, and are substrates of MTA/SAH nucleosidase, underscoring its importance in a wide array of metabolic reactions. Inhibition of this enzyme by certain substrate analogues also limits synthesis of autoinducers and hence causes reduction in biofilm formation and may attenuate virulence. Interestingly, the inhibitors of MTA/SAH nucleosidase are very effective against the Lyme disease causing spirochaete, Borrelia burgdorferi, which uniquely expresses three homologous functional enzymes. These results indicate that inhibition of this enzyme can affect growth of different bacteria by affecting different mechanisms. Therefore, new inhibitors are currently being explored for development of potential novel broad-spectrum antimicrobials.
Collapse
Affiliation(s)
- Nikhat Parveen
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, 225 Warren Street, Newark, NJ 07103-3535, USA.
| | | |
Collapse
|
18
|
Siu KKW, Asmus K, Zhang AN, Horvatin C, Li S, Liu T, Moffatt B, Woods VL, Howell PL. Mechanism of substrate specificity in 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. J Struct Biol 2010; 173:86-98. [PMID: 20554051 DOI: 10.1016/j.jsb.2010.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 06/02/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]
Abstract
5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN) plays a key role in the methionine-recycling pathway of bacteria and plants. Despite extensive structural and biochemical studies, the molecular mechanism of substrate specificity for MTAN remains an outstanding question. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while the plant enzymes select preferentially for MTA, with either no or significantly reduced activity towards SAH. Bacterial and plant MTANs show significant conservation in the overall structure, and the adenine- and ribose-binding sites. The observation of a more constricted 5'-alkylthio binding site in Arabidopsis thalianaAtMTAN1 and AtMTAN2, two plant MTAN homologues, led to the hypothesis that steric hindrance may play a role in substrate selection in plant MTANs. We show using isothermal titration calorimetry that SAH binds to both Escherichia coli MTAN (EcMTAN) and AtMTAN1 with comparable micromolar affinity. To understand why AtMTAN1 can bind but not hydrolyze SAH, we determined the structure of the protein-SAH complex at 2.2Å resolution. The lack of catalytic activity appears to be related to the enzyme's inability to bind the substrate in a catalytically competent manner. The role of dynamics in substrate selection was also examined by probing the amide proton exchange rates of EcMTAN and AtMTAN1 via deuterium-hydrogen exchange coupled mass spectrometry. These results correlate with the B factors of available structures and the thermodynamic parameters associated with substrate binding, and suggest a higher level of conformational flexibility in the active site of EcMTAN. Our results implicate dynamics as an important factor in substrate selection in MTAN.
Collapse
Affiliation(s)
- Karen K W Siu
- Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Dalhoff C, Hüben M, Lenz T, Poot P, Nordhoff E, Köster H, Weinhold E. Synthesis of S-Adenosyl-L-homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases. Chembiochem 2010; 11:256-65. [DOI: 10.1002/cbic.200900349] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
20
|
Albers E. Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5â²-methylthioadenosine. IUBMB Life 2009; 61:1132-42. [DOI: 10.1002/iub.278] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
21
|
Product inhibition in the radical S-adenosylmethionine family. FEBS Lett 2009; 583:1358-62. [PMID: 19328201 DOI: 10.1016/j.febslet.2009.03.044] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 03/20/2009] [Accepted: 03/22/2009] [Indexed: 11/22/2022]
Abstract
Members of the radical S-adenosylmethionine (AdoMet) superfamily reductively cleave AdoMet to generate the highly reactive 5'-deoxyadenosyl radical (DOA()) which initiates biological transformations by abstraction of a hydrogen atom. We demonstrate that three members of the family: biotin synthase (BioB), lipoyl synthase (LipA) and tyrosine lyase (ThiH) are inhibited in vitro by a combination of the products 5'-deoxyadenosine (DOA) and methionine. These results suggest the observed inhibition is a common feature of the radical AdoMet proteins that form DOA and methionine as products. Addition of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) to BioB, LipA or ThiH activity assays removed the product inhibition by catalysing the hydrolysis of DOA and gave an increase in activity.
Collapse
|
22
|
Towards area-based in vitro metabolic engineering: Assembly of Pfs enzyme onto patterned microfabricated chips. Biotechnol Prog 2008; 24:1042-51. [DOI: 10.1002/btpr.44] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
23
|
Luo X, Larios Berlin D, Buckhout-White S, Bentley WE, Payne GF, Ghodssi R, Rubloff GW. Design optimization for bioMEMS studies of enzyme-controlled metabolic pathways. Biomed Microdevices 2008; 10:899-908. [DOI: 10.1007/s10544-008-9204-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
24
|
Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell 2008; 29:691-702. [PMID: 18374645 DOI: 10.1016/j.molcel.2008.01.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2007] [Revised: 10/02/2007] [Accepted: 01/09/2008] [Indexed: 12/16/2022]
Abstract
We have identified a highly conserved RNA motif that occurs upstream of genes involved in S-adenosyl-L-methionine (SAM) recycling in many Gram-positive and Gram-negative species of bacteria. The phylogenetic distribution and the conserved structural features of representatives of this motif are indicative of riboswitch function. Riboswitches are widespread metabolite-sensing gene control elements that are typically found in the 5' untranslated regions (UTRs) of bacterial mRNAs. We experimentally verified that examples of this RNA motif specifically recognize S-adenosylhomocysteine (SAH) in protein-free in vitro assays, and confirmed that these RNAs strongly discriminate against SAM and other closely related analogs. A representative SAH motif was found to activate expression of a downstream gene in vivo when the metabolite is bound. These observations confirm that SAH motif RNAs are distinct ligand-binding aptamers for a riboswitch class that selectively binds SAH and controls genes essential for recycling expended SAM coenzymes.
Collapse
Affiliation(s)
- Joy Xin Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | | | | | | |
Collapse
|
25
|
Luo X, Lewandowski AT, Yi H, Payne GF, Ghodssi R, Bentley WE, Rubloff GW. Programmable assembly of a metabolic pathway enzyme in a pre-packaged reusable bioMEMS device. LAB ON A CHIP 2008; 8:420-30. [PMID: 18305860 DOI: 10.1039/b713756g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We report a biofunctionalization strategy for the assembly of catalytically active enzymes within a completely packaged bioMEMS device, through the programmed generation of electrical signals at spatially and temporally defined sites. The enzyme of a bacterial metabolic pathway, S-adenosylhomocysteine nucleosidase (Pfs), is genetically fused with a pentatyrosine "pro-tag" at its C-terminus. Signal responsive assembly is based on covalent conjugation of Pfs to the aminopolysaccharide, chitosan, upon biochemical activation of the pro-tag, followed by electrodeposition of the enzyme-chitosan conjugate onto readily addressable sites in microfluidic channels. Compared to traditional physical entrapment and surface immobilization approaches in microfluidic environments, our signal-guided electrochemical assembly is unique in that the enzymes are assembled under mild aqueous conditions with spatial and temporal programmability and orientational control. Significantly, the chitosan-mediated enzyme assembly can be reversed, making the bioMEMS reusable for repeated assembly and catalytic activity. Additionally, the assembled enzymes retain catalytic activity over multiple days, demonstrating enhanced enzyme stability. We envision that this assembly strategy can be applied to rebuild metabolic pathways in microfluidic environments for antimicrobial drug discovery.
Collapse
Affiliation(s)
- Xiaolong Luo
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Siu KKW, Lee JE, Sufrin JR, Moffatt BA, McMillan M, Cornell KA, Isom C, Howell PL. Molecular determinants of substrate specificity in plant 5'-methylthioadenosine nucleosidases. J Mol Biol 2008; 378:112-28. [PMID: 18342331 DOI: 10.1016/j.jmb.2008.01.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/28/2008] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
Abstract
5'-Methylthioadenosine (MTA)/S-adenosylhomocysteine (SAH) nucleosidase (MTAN) is essential for cellular metabolism and development in many bacterial species. While the enzyme is found in plants, plant MTANs appear to select for MTA preferentially, with little or no affinity for SAH. To understand what determines substrate specificity in this enzyme, MTAN homologues from Arabidopsis thaliana (AtMTAN1 and AtMTAN2, which are referred to as AtMTN1 and AtMTN2 in the plant literature) have been characterized kinetically. While both homologues hydrolyze MTA with comparable kinetic parameters, only AtMTAN2 shows activity towards SAH. AtMTAN2 also has higher catalytic activity towards other substrate analogues with longer 5'-substituents. The structures of apo AtMTAN1 and its complexes with the substrate- and transition-state-analogues, 5'-methylthiotubercidin and formycin A, respectively, have been determined at 2.0-1.8 A resolution. A homology model of AtMTAN2 was generated using the AtMTAN1 structures. Comparison of the AtMTAN1 and AtMTAN2 structures reveals that only three residues in the active site differ between the two enzymes. Our analysis suggests that two of these residues, Leu181/Met168 and Phe148/Leu135 in AtMTAN1/AtMTAN2, likely account for the divergence in specificity of the enzymes. Comparison of the AtMTAN1 and available Escherichia coli MTAN (EcMTAN) structures suggests that a combination of differences in the 5'-alkylthio binding region and reduced conformational flexibility in the AtMTAN1 active site likely contribute to its reduced efficiency in binding substrate analogues with longer 5'-substituents. In addition, in contrast to EcMTAN, the active site of AtMTAN1 remains solvated in its ligand-bound forms. As the apparent pK(a) of an amino acid depends on its local environment, the putative catalytic acid Asp225 in AtMTAN1 may not be protonated at physiological pH and this suggests the transition state of AtMTAN1, like human MTA phosphorylase and Streptococcus pneumoniae MTAN, may be different from that found in EcMTAN.
Collapse
Affiliation(s)
- Karen K W Siu
- Program in Molecular Structure and Function, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Rezanka T, Sigler K. Biologically active compounds of semi-metals. PHYTOCHEMISTRY 2008; 69:585-606. [PMID: 17991498 DOI: 10.1016/j.phytochem.2007.09.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 09/25/2007] [Accepted: 09/25/2007] [Indexed: 05/25/2023]
Abstract
Semi-metals (boron, silicon, arsenic and selenium) form organo-metal compounds, some of which are found in nature and affect the physiology of living organisms. They include, e.g., the boron-containing antibiotics aplasmomycin, borophycin, boromycin, and tartrolon or the silicon compounds present in "silicate" bacteria, relatives of the genus Bacillus, which release silicon from aluminosilicates through the secretion of organic acids. Arsenic is incorporated into arsenosugars and arsenobetaines by marine algae and invertebrates, and fungi and bacteria can produce volatile methylated arsenic compounds. Some prokaryotes can use arsenate as a terminal electron acceptor while others can utilize arsenite as an electron donor to generate energy. Selenium is incorporated into selenocysteine that is found in some proteins. Biomethylation of selenide produces methylselenide and dimethylselenide. Selenium analogues of amino acids, antitumor, antibacterial, antifungal, antiviral, anti-infective drugs are often used as analogues of important pharmacological sulfur compounds. Other metalloids, i.e. the rare and toxic tellurium and the radioactive short-lived astatine, have no biological significance.
Collapse
Affiliation(s)
- Tomás Rezanka
- Institute of Microbiology, Vídenská 1083, Prague 142 20, Czech Republic.
| | | |
Collapse
|
28
|
Řezanka T, Sigler K. Biologically Active Compounds Of Semi-Metals. BIOACTIVE NATURAL PRODUCTS (PART O) 2008. [DOI: 10.1016/s1572-5995(08)80018-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
29
|
Singh V, Luo M, Brown RL, Norris GE, Schramm VL. Transition-state structure of neisseria meningitides 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. J Am Chem Soc 2007; 129:13831-3. [PMID: 17956098 PMCID: PMC2527693 DOI: 10.1021/ja0754204] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vipender Singh
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Minkui Luo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Rosemary L. Brown
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Gillian E. Norris
- Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461,
| |
Collapse
|
30
|
Singh V, Schramm VL. Transition-state analysis of S. pneumoniae 5'-methylthioadenosine nucleosidase. J Am Chem Soc 2007; 129:2783-95. [PMID: 17298059 PMCID: PMC2522316 DOI: 10.1021/ja065082r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kinetic isotope effects (KIEs) and computer modeling are used to approximate the transition state of S. pneumoniae 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN). Experimental KIEs were measured and corrected for a small forward commitment factor. Intrinsic KIEs were obtained for [1'-3H], [1'-14C], [2'-3H], [4'-3H], [5'-3H(2)], [9-15N] and [Me-3H(3)] MTAs. The intrinsic KIEs suggest an SN1 transition state with no covalent participation of the adenine or the water nucleophile. The transition state was modeled as a stable ribooxacarbenium ion intermediate and was constrained to fit the intrinsic KIEs. The isotope effects predicted a 3-endo conformation for the ribosyl oxacarbenium-ion corresponding to H1'-C1'-C2'-H2' dihedral angle of 70 degrees. Ab initio Hartree-Fock and DFT calculations were performed to study the effect of polarization of ribosyl hydroxyls, torsional angles, and the effect of base orientation on isotope effects. Calculations suggest that the 4'-3H KIE arises from hyperconjugation between the lonepair (n(p)) of O4' and the sigma* (C4'-H4') antibonding orbital owing to polarization of the 3'-hydroxyl by Glu174. A [methyl-3H(3)] KIE is due to hyperconjugation between np of sulfur and sigma* of methyl C-H bonds. The van der Waal contacts increase the 1'-3H KIE because of induced dipole-dipole interactions. The 1'-3H KIE is also influenced by the torsion angles of adjacent atoms and by polarization of the 2'-hydroxyl. Changing the virtual solvent (dielectric constant) does not influence the isotope effects. Unlike most N-ribosyltransferases, N7 of the leaving group adenine is not protonated at the transition state of S. pneumoniae MTAN. This feature differentiates the S. pneumoniae and E. coli transition states and explains the 10(3)-fold decrease in the catalytic efficiency of S. pneumoniae MTAN relative to that from E. coli.
Collapse
Affiliation(s)
- Vipender Singh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, 1300 Morris Park Avenue, Bronx, New York-10461
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, 1300 Morris Park Avenue, Bronx, New York-10461
| |
Collapse
|
31
|
Rzewuski G, Cornell KA, Rooney L, Bürstenbinder K, Wirtz M, Hell R, Sauter M. OsMTN encodes a 5'-methylthioadenosine nucleosidase that is up-regulated during submergence-induced ethylene synthesis in rice (Oryza sativa L.). JOURNAL OF EXPERIMENTAL BOTANY 2007; 58:1505-14. [PMID: 17339651 DOI: 10.1093/jxb/erm014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Methylthioadenosine (MTA) is released as a by-product of S-adenosylmethionine (AdoMet)-dependent reactions central to ethylene, polyamine, or phytosiderophore biosynthesis. MTA is hydrolysed by methylthioadenosine nucleosidase (MTN; EC 3.2.2.16) into adenine and methylthioribose which is processed through the methionine (Met) cycle to produce a new molecule of AdoMet. In deepwater rice, submergence enhances ethylene biosynthesis, and ethylene in turn influences the methionine cycle through positive feedback regulation of the acireductone dioxygenase gene OsARD1. In rice, MTN is encoded by a single gene designated OsMTN. Recombinant OsMTN enzyme had a KM for MTA of 2.1 mM and accepted a wide array of 5' substitutions of the substrate. OsMTN also metabolized S-adenosylhomocysteine (AdoHcy) with 15.9% the rate of MTA. OsMTN transcripts and OsMTN-specific activity increased slowly and in parallel upon submergence, indicating that regulation occurred mainly at the transcriptional level. Neither ethylene, MTA, nor Met regulated OsMTN expression. Analysis of steady-state metabolite levels showed that MTN activity was sufficiently high to prevent Met and AdoMet depletion during long-term ethylene biosynthesis.
Collapse
Affiliation(s)
- Guillaume Rzewuski
- Botanisches Institut, Universität Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | | | | | | | | | | | | |
Collapse
|
32
|
Singh V, Shi W, Almo SC, Evans GB, Furneaux RH, Tyler PC, Zheng R, Schramm VL. Structure and inhibition of a quorum sensing target from Streptococcus pneumoniae. Biochemistry 2006; 45:12929-41. [PMID: 17059210 PMCID: PMC2517848 DOI: 10.1021/bi061184i] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Streptococcus pneumoniae 5'-methylthioadenosine/S-adenosylhomocysteine hydrolase (MTAN) catalyzes the hydrolytic deadenylation of its substrates to form adenine and 5-methylthioribose or S-ribosylhomocysteine (SRH). MTAN is not found in mammals but is involved in bacterial quorum sensing. MTAN gene disruption affects the growth and pathogenicity of bacteria, making it a target for antibiotic design. Kinetic isotope effects and computational studies have established a dissociative S(N)1 transition state for Escherichia coli MTAN, and transition state analogues resembling the transition state are powerful inhibitors of the enzyme [Singh, V., Lee, J. L., Núñez, S., Howell, P. L., and Schramm, V. L. (2005) Biochemistry 44, 11647-11659]. The sequence of MTAN from S. pneumoniae is 40% identical to that of E. coli MTAN, but S. pneumoniae MTAN exhibits remarkably distinct kinetic and inhibitory properties. 5'-Methylthio-Immucillin-A (MT-ImmA) is a transition state analogue resembling an early S(N)1 transition state. It is a weak inhibitor of S. pneumoniae MTAN with a K(i) of 1.0 microM. The X-ray structure of S. pneumoniae MTAN with MT-ImmA indicates a dimer with the methylthio group in a flexible hydrophobic pocket. Replacing the methyl group with phenyl (PhT-ImmA), tolyl (p-TolT-ImmA), or ethyl (EtT-ImmA) groups increases the affinity to give K(i) values of 335, 60, and 40 nM, respectively. DADMe-Immucillins are geometric and electrostatic mimics of a fully dissociated transition state and bind more tightly than Immucillins. MT-DADMe-Immucillin-A inhibits with a K(i) value of 24 nM, and replacing the 5'-methyl group with p-Cl-phenyl (p-Cl-PhT-DADMe-ImmA) gave a K(i) value of 0.36 nM. The inhibitory potential of DADMe-Immucillins relative to the Immucillins supports a fully dissociated transition state structure for S. pneumoniae MTAN. Comparison of active site contacts in the X-ray crystal structures of E. coli and S. pneumoniae MTAN with MT-ImmA would predict equal binding, yet most analogues bind 10(3)-10(4)-fold more tightly to the E. coli enzyme. Catalytic site efficiency is primarily responsible for this difference since k(cat)/K(m) for S. pneumoniae MTAN is decreased 845-fold relative to that of E. coli MTAN.
Collapse
Affiliation(s)
- Vipender Singh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Wuxian Shi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Gary B. Evans
- Carbohydrate Chemistry Team, Industrial Research Limited, P. O. Box 31310, Lower Hutt, New Zealand
| | - Richard H. Furneaux
- Carbohydrate Chemistry Team, Industrial Research Limited, P. O. Box 31310, Lower Hutt, New Zealand
| | - Peter C. Tyler
- Carbohydrate Chemistry Team, Industrial Research Limited, P. O. Box 31310, Lower Hutt, New Zealand
| | - Renjian Zheng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
- *Corresponding author: telephone (718) 430-2813, Fax (718) 430-8565, Email
| |
Collapse
|
33
|
Li J, Wang L, Hashimoto Y, Tsao CY, Wood TK, Valdes JJ, Zafiriou E, Bentley WE. A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways. Mol Syst Biol 2006; 2:67. [PMID: 17170762 PMCID: PMC1762088 DOI: 10.1038/msb4100107] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 09/18/2006] [Indexed: 01/08/2023] Open
Abstract
Quorum sensing (QS) is an important determinant of bacterial phenotype. Many cell functions are regulated by intricate and multimodal QS signal transduction processes. The LuxS/AI-2 QS system is highly conserved among Eubacteria and AI-2 is reported as a 'universal' signal molecule. To understand the hierarchical organization of AI-2 circuitry, a comprehensive approach incorporating stochastic simulations was developed. We investigated the synthesis, uptake, and regulation of AI-2, developed testable hypotheses, and made several discoveries: (1) the mRNA transcript and protein levels of AI-2 synthases, Pfs and LuxS, do not contribute to the dramatically increased level of AI-2 found when cells are grown in the presence of glucose; (2) a concomitant increase in metabolic flux through this synthesis pathway in the presence of glucose only partially accounts for this difference. We predict that 'high-flux' alternative pathways or additional biological steps are involved in AI-2 synthesis; and (3) experimental results validate this hypothesis. This work demonstrates the utility of linking cell physiology with systems-based stochastic models that can be assembled de novo with partial knowledge of biochemical pathways.
Collapse
Affiliation(s)
- Jun Li
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, MD, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, MD, USA
| | - Liang Wang
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, MD, USA
| | - Yoshifumi Hashimoto
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, MD, USA
| | - Chen-Yu Tsao
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, MD, USA
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - James J Valdes
- Edgewood Chemical Biological Center, US Army, Aberdeen Proving Ground, MD, USA
| | - Evanghelos Zafiriou
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD, USA
| | - William E Bentley
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland, MD, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, MD, USA
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, MD, USA
| |
Collapse
|
34
|
Guillerm G, Allart B. Practical synthesis of 14C S-ribosyl-l-homocysteine uniformely labelled on the sugar moiety. An enzymatic route from (U-14C) adenosine. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580310911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
35
|
Synthesis of S-ribosyl-L-homocysteine specifically tritiated at the 5-C position. J Labelled Comp Radiopharm 2006. [DOI: 10.1002/jlcr.2580290907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
36
|
Parveen N, Cornell KA, Bono JL, Chamberland C, Rosa P, Leong JM. Bgp, a secreted glycosaminoglycan-binding protein of Borrelia burgdorferi strain N40, displays nucleosidase activity and is not essential for infection of immunodeficient mice. Infect Immun 2006; 74:3016-20. [PMID: 16622242 PMCID: PMC1459710 DOI: 10.1128/iai.74.5.3016-3020.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bgp, one of the surface-localized glycosaminoglycan-binding proteins of the Lyme disease spirochete, Borrelia burgdorferi, exhibited nucleosidase activity. Infection of SCID mice with B. burgdorferi strain N40 mutants harboring a targeted insertion in bgp and apparently retaining all endogenous plasmids revealed that Bgp is not essential for colonization of immunocompromised mice.
Collapse
Affiliation(s)
- Nikhat Parveen
- Department of Microbiology and Molecular Genetics, ICPH Building, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, NJ 07103-2714, USA.
| | | | | | | | | | | |
Collapse
|
37
|
Shimizu S, Abe T, Yamada H. Distribution of methylthioadenosine phosphorylase in eubacteria. FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1988.tb02993.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
38
|
Choi-Rhee E, Cronan JE. A nucleosidase required for in vivo function of the S-adenosyl-L-methionine radical enzyme, biotin synthase. ACTA ACUST UNITED AC 2005; 12:589-93. [PMID: 15911379 DOI: 10.1016/j.chembiol.2005.04.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 03/04/2005] [Accepted: 04/04/2005] [Indexed: 11/15/2022]
Abstract
Biotin synthase is an S-adenosyl-L-methionine (SAM) radical enzyme that inserts sulfur into dethiobiotin to produce biotin. The reaction proceeds through 5'-deoxyadenosyl radical intermediates that become reduced during the sulfur insertion step to give another product of the reaction, 5'-deoxyadenosine. We report that Escherichia coli strains lacking the 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase encoded by the pfs gene are deficient in biotin synthase activity due to accumulation of 5'-deoxyadenosine, a new substrate of the pfs-encoded nucleosidase. Physiological experiments indicate that lipoic acid synthase, another SAM radical enzyme, is also inhibited by 5'-deoxyadenosine accumulation.
Collapse
Affiliation(s)
- Eunjoo Choi-Rhee
- Department of Microbiology, University of Illinois, Urbana 61801, USA
| | | |
Collapse
|
39
|
Cacciapuoti G, Forte S, Moretti MA, Brio A, Zappia V, Porcelli M. A novel hyperthermostable 5′-deoxy-5′-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. FEBS J 2005; 272:1886-99. [PMID: 15819883 DOI: 10.1111/j.1742-4658.2005.04619.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report herein the first molecular characterization of 5'-deoxy-5'-methylthio-adenosine phosphorylase II from Sulfolobus solfataricus (SsMTAPII). The isolated gene of SsMTAPII was overexpressed in Escherichia coli BL21. Purified recombinant SsMTAPII is a homohexamer of 180 kDa with an extremely low Km (0.7 microm) for 5'-deoxy-5'-methylthioadenosine. The enzyme is highly thermophilic with an optimum temperature of 120 degrees C and extremely thermostable with an apparent Tm of 112 degrees C that increases in the presence of substrates. The enzyme is characterized by high kinetic stability and remarkable SDS resistance and is also resistant to guanidinium chloride-induced unfolding with a transition midpoint of 3.3 m after 22-h incubation. Limited proteolysis experiments indicated that the only one proteolytic cleavage site is localized in the C-terminal region and that the C-terminal peptide is necessary for the integrity of the active site. Moreover, the binding of 5'-deoxy-5'-methylthioadenosine induces a conformational transition that protected the enzyme against protease inactivation. By site-directed mutagenesis we demonstrated that Cys259, Cys261 and Cys262 play an important role in the enzyme stability since the mutants C259S/C261S and C262S show thermophilicity and thermostability features significantly lower than those of the wild-type enzyme. In order to get insight into the physiological role of SsMTAPII a comparative kinetic analysis with the homologous 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus (SsMTAP) was carried out. Finally, the alignment of the protein sequence of SsMTAPII with those of SsMTAP and human 5'-deoxy-5'-methylthioadenosine phosphorylase (hMTAP) shows several key residue changes that may account why SsMTAPII, unlike hMTAP, is able to recognize adenosine as substrate.
Collapse
Affiliation(s)
- Giovanna Cacciapuoti
- Dipartimento di Biochimica e Biofisica F. Cedrangolo, Seconda Università di Napoli, Italy.
| | | | | | | | | | | |
Collapse
|
40
|
Singh V, Evans GB, Lenz DH, Mason JM, Clinch K, Mee S, Painter GF, Tyler PC, Furneaux RH, Lee JE, Howell PL, Schramm VL. Femtomolar transition state analogue inhibitors of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Escherichia coli. J Biol Chem 2005; 280:18265-73. [PMID: 15749708 DOI: 10.1074/jbc.m414472200] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli 5'-methylthioadenosine/S-adenosyl-homocysteine nucleosidase (MTAN) hydrolyzes its substrates to form adenine and 5-methylthioribose (MTR) or S-ribosylhomocysteine (SRH). 5'-Methylthioadenosine (MTA) is a by-product of polyamine synthesis and SRH is a precursor to the biosynthesis of one or more quorum sensing autoinducer molecules. MTAN is therefore involved in quorum sensing, recycling MTA from the polyamine pathway via adenine phosphoribosyltransferase and recycling MTR to methionine. Hydrolysis of MTA by E. coli MTAN involves a highly dissociative transition state with ribooxacarbenium ion character. Iminoribitol mimics of MTA at the transition state of MTAN were synthesized and tested as inhibitors. 5'-Methylthio-Immucillin-A (MT-ImmA) is a slow-onset tight-binding inhibitor giving a dissociation constant (K(i)(*)) of 77 pm. Substitution of the methylthio group with a p-Cl-phenylthio group gives a more powerful inhibitor with a dissociation constant of 2 pm. DADMe-Immucillins are better inhibitors of E. coli MTAN, since they are more closely related to the highly dissociative nature of the transition state. MT-DADMe-Immucillin-A binds with a K(i)(*) value of 2 pm. Replacing the 5'-methyl group with other hydrophobic groups gave 17 transition state analogue inhibitors with dissociation constants from 10(-12) to 10(-14) m. The most powerful inhibitor was 5'-p-Cl-phenylthio-DADMe-Immucillin-A (pClPhT-DADMe-ImmA) with a K(i)(*) value of 47 fm (47 x 10(-15) m). These are among the most powerful non-covalent inhibitors reported for any enzyme, binding 9-91 million times tighter than the MTA and SAH substrates, respectively. The inhibitory potential of these transition state analogue inhibitors supports a transition state structure closely resembling a fully dissociated ribooxacarbenium ion. Powerful inhibitors of MTAN are candidates to disrupt key bacterial pathways including methylation, polyamine synthesis, methionine salvage, and quorum sensing. The accompanying article reports crystal structures of MTAN with these analogues.
Collapse
Affiliation(s)
- Vipender Singh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Tedder ME, Nie Z, Margosiak S, Chu S, Feher VA, Almassy R, Appelt K, Yager KM. Structure-based design, synthesis, and antimicrobial activity of purine derived SAH/MTA nucleosidase inhibitors. Bioorg Med Chem Lett 2005; 14:3165-8. [PMID: 15149667 DOI: 10.1016/j.bmcl.2004.04.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Revised: 04/02/2004] [Accepted: 04/03/2004] [Indexed: 11/19/2022]
Abstract
The structure-based design, synthesis, and biological activity of novel inhibitors of S-adenosyl homocysteine/methylthioadenosine (SAH/MTA) nucleosidase are described. Using 6-substituted purine and deaza purines as the core scaffolds, a systematic and structure guided series of modifications provided low nM inhibitors with broad-spectrum antimicrobial activity.
Collapse
Affiliation(s)
- Martina E Tedder
- Department of Medicinal Chemistry, Quorex Pharmaceuticals, Carlsbad, CA 92008, USA
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Lee JE, Settembre EC, Cornell KA, Riscoe MK, Sufrin JR, Ealick SE, Howell PL. Structural comparison of MTA phosphorylase and MTA/AdoHcy nucleosidase explains substrate preferences and identifies regions exploitable for inhibitor design. Biochemistry 2004; 43:5159-69. [PMID: 15122881 DOI: 10.1021/bi035492h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of new and effective antiprotozoal drugs has been a difficult challenge because of the close similarity of the metabolic pathways between microbial and mammalian systems. 5'-Methylthioadenosine/S-adenosylhomocysteine (MTA/AdoHcy) nucleosidase is thought to be an ideal target for therapeutic drug design as the enzyme is present in many microbes but not in mammals. MTA/AdoHcy nucleosidase (MTAN) irreversibly depurinates MTA or AdoHcy to form adenine and the corresponding thioribose. The inhibition of MTAN leads to a buildup of toxic byproducts that affect various microbial pathways such as quorum sensing, biological methylation, polyamine biosynthesis, and methionine recycling. The design of nucleosidase-specific inhibitors is complicated by its structural similarity to the human MTA phosphorylase (MTAP). The crystal structures of human MTAP complexed with formycin A and 5'-methylthiotubercidin have been solved to 2.0 and 2.1 A resolution, respectively. Comparisons of the MTAP and MTAN inhibitor complexes reveal size and electrostatic potential differences in the purine, ribose, and 5'-alkylthio binding sites, which account for the substrate specificity and reactions catalyzed. In addition, the differences between the two enzymes have allowed the identification of exploitable regions that can be targeted for the development of high-affinity nucleosidase-specific inhibitors. Sequence alignments of Escherichia coli MTAN, human MTAP, and plant MTA nucleosidases also reveal potential structural changes to the 5'-alkylthio binding site that account for the substrate preference of plant MTA nucleosidases.
Collapse
Affiliation(s)
- Jeffrey E Lee
- Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | | | | | | | | | | | | |
Collapse
|
43
|
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 2004; 32:3340-53. [PMID: 15215334 PMCID: PMC443535 DOI: 10.1093/nar/gkh659] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Regulation of the methionine biosynthesis and transport genes in bacteria is rather diverse and involves two RNA-level regulatory systems and at least three DNA-level systems. In particular, the methionine metabolism in Gram-positive bacteria was known to be controlled by the S-box and T-box mechanisms, both acting on the level of premature termination of transcription. Using comparative analysis of genes, operons and regulatory elements, we described the methionine metabolic pathway and the methionine regulons in available genomes of Gram-positive bacteria. A large number of methionine-specific RNA elements were identified. S-boxes were shown to be widely distributed in Bacillales and Clostridia, whereas methionine-specific T-boxes occurred mostly in Lactobacillales. A candidate binding signal (MET-box) for a hypothetical methionine regulator, possibly MtaR, was identified in Streptococcaceae, the only family in the Bacillus/Clostridium group of Gram-positive bacteria having neither S-boxes, nor methionine-specific T-boxes. Positional analysis of methionine-specific regulatory sites complemented by genome context analysis lead to identification of new members of the methionine regulon, both enzymes and transporters, and reconstruction of the methionine metabolism in various bacterial genomes. In particular, we found candidate transporters for methionine (MetT) and methylthioribose (MtnABC), as well as new enzymes forming the S-adenosylmethionine recycling pathway. Methionine biosynthetic enzymes in various bacterial species are quite variable. In particular, Oceanobacillus iheyensis possibly uses a homolog of the betaine-homocysteine methyltransferase bhmT gene from vertebrates to substitute missing bacterial-type methionine synthases.
Collapse
Affiliation(s)
- Dmitry A Rodionov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny pereulok 19, Moscow 127994, Russia.
| | | | | | | |
Collapse
|
44
|
Cacciapuoti G, Bertoldo C, Brio A, Zappia V, Porcelli M. Purification and characterization of 5'-methylthioadenosine phosphorylase from the hyperthermophilic archaeon Pyrococcus furiosus: substrate specificity and primary structure analysis. Extremophiles 2003; 7:159-68. [PMID: 12664268 DOI: 10.1007/s00792-002-0307-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2002] [Accepted: 11/08/2002] [Indexed: 10/28/2022]
Abstract
5'-Methylthioadenosine phosphorylase (MTAP) was purified to homogeneity from the hyperthermophilic archaeon Pyrococcus furiosus. The protein is a homoexamer of 180 kDa. The enzyme is highly thermoactive, with an optimum temperature of 125 degrees C, and extremely thermostable, retaining 98% residual activity after 5 h at 100 degrees C and showing a half-life of 43 min at 130 degrees C. In the presence of 100 mM phosphate, the apparent T(m) (137 degrees C) increases to 139 degrees C. The enzyme is extremely stable to proteolytic cleavage and after incubation with protein denaturants, detergents, organic solvents, and salts even at high temperature. Thiol groups are not involved in the catalytic process, whereas disulfide bond(s) are present, since incubation with 0.8 M dithiothreitol significantly reduces the thermostability of the enzyme. N-Terminal sequence analysis of the purified enzyme is 100% identical to the predicted amino acid sequence of the gene PF0016 from the partially sequenced P. furiosus genome. The deduced amino acid sequence of the gene revealed a high degree of identity (52%) with human MTAP. Nevertheless, unlike human MTAP, MTAP from P. furiosus is not specific for 5'-methylthioadenosine, since it phosphorolytically cleaves adenosine, inosine, and guanosine. The calculated k(cat)/ K(m) values for 5'-methylthioadenosine and adenosine, about 20-fold higher than for inosine and guanosine, indicate that 6-amino purine nucleosides are preferred substrates of MTAP from P. furiosus. The structural features and the substrate specificity of MTAP from P. furiosus document that it represents a 5'-methylthioadenosine-metabolizing enzyme different from those previously characterized among Archaea, Bacteria, and Eukarya. The functional and structural relationships among MTAP from P. furiosus, human MTAP, and two putative MTAPs from P. furiosus and Sulfolobus solfataricus are discussed here for the first time.
Collapse
Affiliation(s)
- Giovanna Cacciapuoti
- Dipartimento di Biochimica e Biofisica "F Cedrangolo", Seconda Università di Napoli, Via Costantinopoli 16, 80138, Naples, Italy.
| | | | | | | | | |
Collapse
|
45
|
Beeston AL, Surette MG. pfs-dependent regulation of autoinducer 2 production in Salmonella enterica serovar Typhimurium. J Bacteriol 2002; 184:3450-6. [PMID: 12057938 PMCID: PMC135139 DOI: 10.1128/jb.184.13.3450-3456.2002] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial intercellular communication provides a mechanism for signal-dependent regulation of gene expression to promote coordinated population behavior. Salmonella enterica serovar Typhimurium produces a non-homoserine lactone autoinducer in exponential phase as detected by a Vibrio harveyi reporter assay for autoinducer 2 (AI-2) (M. G. Surette and B. L. Bassler, Proc. Natl. Acad. Sci. USA 95:7046-7050, 1998). The luxS gene product mediates the production of AI-2 (M. G. Surette, M. B. Miller, and B. L. Bassler, Proc. Natl. Acad. Sci. USA 96:1639-1644, 1999). Environmental cues such as rapid growth, the presence of preferred carbon sources, low pH, and/or high osmolarity were found to influence the production of AI-2 (M. G. Surette and B. L. Bassler, Mol. Microbiol. 31:585-595, 1999). In addition to LuxS, the pfs gene product (Pfs) is required for AI-2 production, as well as S-adenosylhomocysteine (SAH) (S. Schauder, K. Shokat, M. G. Surette, and B. L. Bassler, Mol. Microbiol. 41:463-476, 2001). In bacterial cells, Pfs exhibits both 5'-methylthioadenosine (MTA) and SAH nucleosidase functions. Pfs is involved in methionine metabolism, regulating intracellular MTA and SAH levels (elevated levels of MTA and SAH are potent inhibitors of polyamine synthetases and S-adenosylmethionine dependent methyltransferase reactions, respectively). To further investigate regulation of AI-2 production in Salmonella, we constructed pfs and luxS promoter fusions to a luxCDABE reporter in a low-copy-number vector, allowing an examination of transcription of the genes in the pathway for signal synthesis. Here we report that luxS expression is constitutive but that the transcription of pfs is tightly correlated to AI-2 production in Salmonella serovar Typhimurium 14028. Neither luxS nor pfs expression appears to be regulated by AI-2. These results suggest that AI-2 production is regulated at the level of LuxS substrate availability and not at the level of luxS expression. Our results indicate that AI-2-dependent signaling is a reflection of metabolic state of the cell and not cell density.
Collapse
Affiliation(s)
- Anne L Beeston
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | | |
Collapse
|
46
|
Chen X, Schauder S, Potier N, Van Dorsselaer A, Pelczer I, Bassler BL, Hughson FM. Structural identification of a bacterial quorum-sensing signal containing boron. Nature 2002; 415:545-9. [PMID: 11823863 DOI: 10.1038/415545a] [Citation(s) in RCA: 1018] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cell-cell communication in bacteria is accomplished through the exchange of extracellular signalling molecules called autoinducers. This process, termed quorum sensing, allows bacterial populations to coordinate gene expression. Community cooperation probably enhances the effectiveness of processes such as bioluminescence, virulence factor expression, antibiotic production and biofilm development. Unlike other autoinducers, which are specific to a particular species of bacteria, a recently discovered autoinducer (AI-2) is produced by a large number of bacterial species. AI-2 has been proposed to serve as a 'universal' signal for inter-species communication. The chemical identity of AI-2 has, however, proved elusive. Here we present the crystal structure of an AI-2 sensor protein, LuxP, in a complex with autoinducer. The bound ligand is a furanosyl borate diester that bears no resemblance to previously characterized autoinducers. Our findings suggest that addition of naturally occurring borate to an AI-2 precursor generates active AI-2. Furthermore, they indicate a potential biological role for boron, an element required by a number of organisms but for unknown reasons.
Collapse
Affiliation(s)
- Xin Chen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1014, USA
| | | | | | | | | | | | | |
Collapse
|
47
|
Lee JE, Cornell KA, Riscoe MK, Howell PL. Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases. Structure 2001; 9:941-53. [PMID: 11591349 DOI: 10.1016/s0969-2126(01)00656-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND 5'-methylthioadenosine/S-adenosyl-homocysteine (MTA/AdoHcy) nucleosidase catalyzes the irreversible cleavage of 5'-methylthioadenosine and S-adenosylhomocysteine to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. While this enzyme is crucial for the metabolism of AdoHcy and MTA nucleosides in many prokaryotic and lower eukaryotic organisms, it is absent in mammalian cells. This metabolic difference represents an exploitable target for rational drug design. RESULTS The crystal structure of E. coli MTA/AdoHcy nucleosidase was determined at 1.90 A resolution with the multiwavelength anomalous diffraction (MAD) technique. Each monomer of the MTA/AdoHcy nucleosidase dimer consists of a mixed alpha/beta domain with a nine-stranded mixed beta sheet, flanked by six alpha helices and a small 3(10) helix. Intersubunit contacts between the two monomers present in the asymmetric unit are mediated primarily by helix-helix and helix-loop hydrophobic interactions. The unexpected presence of an adenine molecule in the active site of the enzyme has allowed the identification of both substrate binding and potential catalytic amino acid residues. CONCLUSIONS Although the sequence of E. coli MTA/AdoHcy nucleosidase has almost no identity with any known enzyme, its tertiary structure is similar to both the mammalian (trimeric) and prokaryotic (hexameric) purine nucleoside phosphorylases. The structure provides evidence that this protein is functional as a dimer and that the dual specificity for MTA and AdoHcy results from the truncation of a helix. The structure of MTA/AdoHcy nucleosidase is the first structure of a prokaryotic nucleoside N-ribohydrolase specific for 6-aminopurines.
Collapse
Affiliation(s)
- J E Lee
- Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
| | | | | | | |
Collapse
|
48
|
Schauder S, Shokat K, Surette MG, Bassler BL. The LuxS family of bacterial autoinducers: biosynthesis of a novel quorum-sensing signal molecule. Mol Microbiol 2001; 41:463-76. [PMID: 11489131 DOI: 10.1046/j.1365-2958.2001.02532.x] [Citation(s) in RCA: 698] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many bacteria control gene expression in response to cell population density, and this phenomenon is called quorum sensing. In Gram-negative bacteria, quorum sensing typically involves the production, release and detection of acylated homoserine lactone signalling molecules called autoinducers. Vibrio harveyi, a Gram-negative bioluminescent marine bacterium, regulates light production in response to two distinct autoinducers (AI-1 and AI-2). AI-1 is a homoserine lactone. The structure of AI-2 is not known. We have suggested previously that V. harveyi uses AI-1 for intraspecies communication and AI-2 for interspecies communication. Consistent with this idea, we have shown that many species of Gram-negative and Gram-positive bacteria produce AI-2 and, in every case, production of AI-2 is dependent on the function encoded by the luxS gene. We show here that LuxS is the AI-2 synthase and that AI-2 is produced from S-adenosylmethionine in three enzymatic steps. The substrate for LuxS is S-ribosylhomocysteine, which is cleaved to form two products, one of which is homocysteine, and the other is AI-2. In this report, we also provide evidence that the biosynthetic pathway and biochemical intermediates in AI-2 biosynthesis are identical in Escherichia coli, Salmonella typhimurium, V. harveyi, Vibrio cholerae and Enterococcus faecalis. This result suggests that, unlike quorum sensing via the family of related homoserine lactone autoinducers, AI-2 is a unique, 'universal' signal that could be used by a variety of bacteria for communication among and between species.
Collapse
Affiliation(s)
- S Schauder
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, USA
| | | | | | | |
Collapse
|
49
|
Affiliation(s)
- S Schauder
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1014, USA
| | | |
Collapse
|
50
|
Allart B, Guillerm D, Guillerm G. On the catalytic mechanism of adenosylhomocysteine/methylthioadenosine nucleosidase from E. coli. NUCLEOSIDES & NUCLEOTIDES 1999; 18:861-2. [PMID: 10432695 DOI: 10.1080/15257779908041582] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AdoHcy/MTA nucleosidase has been under scrutiny in a series of studies to explore its catalytic mechanism.
Collapse
Affiliation(s)
- B Allart
- UMR 6519 CNRS-UFR Sciences de Reims, France
| | | | | |
Collapse
|