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Mitsuhashi T, Barra L, Powers Z, Kojasoy V, Cheng A, Yang F, Taniguchi Y, Kikuchi T, Fujita M, Tantillo DJ, Porco JA, Abe I. Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids. Angew Chem Int Ed Engl 2020; 59:23772-23781. [PMID: 32931152 PMCID: PMC8957209 DOI: 10.1002/anie.202011171] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Indexed: 12/20/2022]
Abstract
Fungal meroterpenoids are a diverse group of hybrid natural products with impressive structural complexity and high potential as drug candidates. In this work, we evaluate the promiscuity of the early structure diversity-generating step in fungal meroterpenoid biosynthetic pathways: the multibond-forming polyene cyclizations catalyzed by the yet poorly understood family of fungal meroterpenoid cyclases. In total, 12 unnatural meroterpenoids were accessed chemoenzymatically using synthetic substrates. Their complex structures were determined by 2D NMR studies as well as crystalline-sponge-based X-ray diffraction analyses. The results obtained revealed a high degree of enzyme promiscuity and experimental results which together with quantum chemical calculations provided a deeper insight into the catalytic activity of this new family of non-canonical, terpene cyclases. The knowledge obtained paves the way to design and engineer artificial pathways towards second generation meroterpenoids with valuable bioactivities based on combinatorial biosynthetic strategies.
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Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
| | - Lena Barra
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
| | - Zachary Powers
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Volga Kojasoy
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - Andrea Cheng
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies, Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi, Kanagawa, 236-0004 (Japan)
| | - Takashi Kikuchi
- Rigaku Corporation, 3-9-12 Matsubara-cho, Akishima-shi, Tokyo 196-8666 (Japan)
| | - Makoto Fujita
- Division of Advanced Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787 (Japan)
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan)
| | - Dean J. Tantillo
- Department of Chemistry, University of California Davis 1 Shields Avenue, Davis, California 95616 (USA)
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts, 02215 (USA)
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan)
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657 (Japan)
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2
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Mitsuhashi T, Barra L, Powers Z, Kojasoy V, Cheng A, Yang F, Taniguchi Y, Kikuchi T, Fujita M, Tantillo DJ, Porco JA, Abe I. Exploiting the Potential of Meroterpenoid Cyclases to Expand the Chemical Space of Fungal Meroterpenoids. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011171] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Division of Advanced Molecular Science Institute for Molecular Science National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
| | - Lena Barra
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Zachary Powers
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Volga Kojasoy
- Department of Chemistry University of California Davis 1 Shields Avenue Davis California 95616 USA
| | - Andrea Cheng
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Feng Yang
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Yoshimasa Taniguchi
- Central Laboratories for Key Technologies Kirin Holdings Co. Ltd. 1-13-5, Fukuura Kana-zawa-ku, Yokohama-shi Kanagawa 236-0004 Japan
| | - Takashi Kikuchi
- Rigaku Corporation 3-9-12 Matsubara-cho, Akishima-shi Tokyo 196-8666 Japan
| | - Makoto Fujita
- Division of Advanced Molecular Science Institute for Molecular Science National Institutes of Natural Sciences 5-1 Higashiyama, Myodaiji Okazaki 444-8787 Japan
- Department of Applied Chemistry Graduate School of Engineering The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Dean J. Tantillo
- Department of Chemistry University of California Davis 1 Shields Avenue Davis California 95616 USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University Boston Massachusetts 02215 USA
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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Abe T, Ozaki S, Ueda D, Sato T. Insight into Isoprenoid Biosynthesis by Functional Analysis of Isoprenyl Diphosphate Synthases from Mycobacterium vanbaalenii and Mycobacterium tuberculosis. Chembiochem 2020; 21:2931-2938. [PMID: 32495977 DOI: 10.1002/cbic.202000235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/01/2020] [Indexed: 12/27/2022]
Abstract
Comprehensive functional analyses of E-isoprenyl diphosphate synthases (E-IDSs) from nonpathogenic Mycobacterium vanbaalenii have been performed. Mv0992 and Mv1577 represent a nonaprenyl diphosphate (E-C45 ) synthase and a geranylgeranyl diphosphate (E-C20 ) synthase, respectively. Although Mv3536 was identified as an E-C20 synthase using a single enzyme, co-incubation of Mv3536 and Z-IDSs (Mv4662 and Mv3822) strongly suggested it releases an intermediate geranyl diphosphate (E-C10 ) during a continuous condensation reaction. Mv0992 and Mv3536 functions differed from those of the previously reported pathogenic Mycobacterium tuberculosis homologues Rv0562 and Rv2173, respectively. Re-analysis of Rv0562 and Rv2173 demonstrated that their functions were similar to those of Mv0992 and Mv3536 (Rv0562: E-C45 synthase; Rv2173: E-C10-15 synthase). The newly proposed functions of Rv0562 and Rv2173 would be in the biosynthesis of menaquinone and glycosyl carrier lipids essential for growth. Furthermore, a reduced allylic diphosphate could be used as the Z-IDS of the Mv3822 substrate, thereby introducing a potentially novel pathway of cyclic sesquarterpene biosynthesis.
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Affiliation(s)
- Tohru Abe
- Department of Agriculture, Faculty of Agriculture and, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata, 950-2181, Japan
| | - Sadamu Ozaki
- Department of Agriculture, Faculty of Agriculture and, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata, 950-2181, Japan
| | - Daijiro Ueda
- Department of Agriculture, Faculty of Agriculture and, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata, 950-2181, Japan
| | - Tsutomu Sato
- Department of Agriculture, Faculty of Agriculture and, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata, 950-2181, Japan
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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5
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Vattekkatte A, Garms S, Brandt W, Boland W. Enhanced structural diversity in terpenoid biosynthesis: enzymes, substrates and cofactors. Org Biomol Chem 2019; 16:348-362. [PMID: 29296983 DOI: 10.1039/c7ob02040f] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The enormous diversity of terpenes found in nature is generated by enzymes known as terpene synthases, or cyclases. Some are also known for their ability to convert a single substrate into multiple products. This review comprises monoterpene and sesquiterpene synthases that are multiproduct in nature along with the regulation factors that can alter the product specificity of multiproduct terpene synthases without genetic mutations. Variations in specific assay conditions with focus on shifts in product specificity based on change in metal cofactors, assay pH and substrate geometry are described. Alterations in these simple cellular conditions provide the organism with enhanced chemodiversity without investing into new enzymatic architecture. This versatility to modulate product diversity grants organisms, especially immobile ones like plants with access to an enhanced defensive repertoire by simply altering cofactors, pH level and substrate geometry.
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Affiliation(s)
- Abith Vattekkatte
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany.
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Nagel R, Thomas JA, Adekunle FA, Mann FM, Peters RJ. Arginine in the FARM and SARM: A Role in Chain-Length Determination for Arginine in the Aspartate-Rich Motifs of Isoprenyl Diphosphate Synthases from Mycobacterium tuberculosis. Molecules 2018; 23:molecules23102546. [PMID: 30301210 PMCID: PMC6214179 DOI: 10.3390/molecules23102546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/02/2018] [Accepted: 10/05/2018] [Indexed: 01/20/2023] Open
Abstract
Isoprenyl chains are found in many important metabolites. These are derived from precursors of the appropriate length produced by isoprenyl diphosphate synthases (IDSs). The human pathogen Mycobacterium tuberculosis makes various isoprenoids/terpenoids, with important roles in their biosynthesis played by two closely related IDSs, encoded by grcC1 (Rv0562) and grcC2 (Rv0989c), with Rv0989c generating the 10-carbon precursor (E)-geranyl diphosphate (GPP), and Rv0562 the 20-carbon precursor (E,E,E)-geranylgeranyl diphosphate (GGPP). Intriguingly, while Rv0562 contains the prototypical trans-IDS first and second aspartate-rich (DDxxD) motifs (FARM and SARM, respectively), Rv0989c uniquely contains arginine in place of the second Asp in the FARM and first Asp in the SARM. Here site-directed mutagenesis of the corresponding residues in both Rv0562 and Rv0989c reveals that these play a role in determination of product chain length. Specifically, substitution of Asp for the Arg in the FARM and SARM of Rv0989c leads to increased production of the longer 15-carbon farnesyl diphosphate (FPP), while substitution of Arg for the corresponding Asp in Rv0562 leads to increased release of shorter products, both FPP and GPP. Accordingly, while the primary role of the FARM and SARM is known to be chelation of the divalent magnesium ion co-factors that assist substrate binding and catalysis, the Arg substitutions found in Rv0989c seem to provide a novel means by which product chain length is moderated, at least in these M. tuberculosis IDSs.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Jill A Thomas
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - Faith A Adekunle
- Department of Chemistry, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
| | - Francis M Mann
- Department of Chemistry, University of Wisconsin-Parkside, Kenosha, WI 53141, USA.
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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7
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Kataev VE, Khaybullin RN, Garifullin BF, Sharipova RR. New Targets for Growth Inhibition of Mycobacterium tuberculosis: Why Do Natural Terpenoids Exhibit Antitubercular Activity? RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Vattekkatte A, Garms S, Boland W. Alternate Cyclization Cascade Initiated by Substrate Isomer in Multiproduct Terpene Synthase from Medicago truncatula. J Org Chem 2017; 82:2855-2861. [DOI: 10.1021/acs.joc.6b02696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abith Vattekkatte
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Stefan Garms
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
| | - Wilhelm Boland
- Department of Bioorganic
Chemistry, Max Planck Institute for Chemical Ecology, Beutenberg Campus, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
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9
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Abstract
This article summarizes what is currently known of the structures, physiological roles, involvement in pathogenicity, and biogenesis of a variety of noncovalently bound cell envelope lipids and glycoconjugates of Mycobacterium tuberculosis and other Mycobacterium species. Topics addressed in this article include phospholipids; phosphatidylinositol mannosides; triglycerides; isoprenoids and related compounds (polyprenyl phosphate, menaquinones, carotenoids, noncarotenoid cyclic isoprenoids); acyltrehaloses (lipooligosaccharides, trehalose mono- and di-mycolates, sulfolipids, di- and poly-acyltrehaloses); mannosyl-beta-1-phosphomycoketides; glycopeptidolipids; phthiocerol dimycocerosates, para-hydroxybenzoic acids, and phenolic glycolipids; mycobactins; mycolactones; and capsular polysaccharides.
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10
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Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. Proc Natl Acad Sci U S A 2015; 112:13087-92. [PMID: 26438867 DOI: 10.1073/pnas.1514135112] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Peptidoglycan (PG), a complex polymer composed of saccharide chains cross-linked by short peptides, is a critical component of the bacterial cell wall. PG synthesis has been extensively studied in model organisms but remains poorly understood in mycobacteria, a genus that includes the important human pathogen Mycobacterium tuberculosis (Mtb). The principle PG synthetic enzymes have similar and, at times, overlapping functions. To determine how these are functionally organized, we carried out whole-genome transposon mutagenesis screens in Mtb strains deleted for ponA1, ponA2, and ldtB, major PG synthetic enzymes. We identified distinct factors required to sustain bacterial growth in the absence of each of these enzymes. We find that even the homologs PonA1 and PonA2 have unique sets of genetic interactions, suggesting there are distinct PG synthesis pathways in Mtb. Either PonA1 or PonA2 is required for growth of Mtb, but both genetically interact with LdtB, which has its own distinct genetic network. We further provide evidence that each interaction network is differentially susceptible to antibiotics. Thus, Mtb uses alternative pathways to produce PG, each with its own biochemical characteristics and vulnerabilities.
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11
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Kim MO, Feng X, Feixas F, Zhu W, Lindert S, Bogue S, Sinko W, de Oliveira C, Rao G, Oldfield E, McCammon JA. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility and Implications for Computer-aided Drug Discovery. Chem Biol Drug Des 2014; 85:756-69. [PMID: 25352216 DOI: 10.1111/cbdd.12463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/26/2014] [Accepted: 10/17/2014] [Indexed: 01/09/2023]
Abstract
With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS), are involved in bacterial cell wall biosynthesis, while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 μm inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC(50) ~0.5- to 20-μm inhibitor (depending on substrate) of cis-DPPS, a ~660-nm inhibitor of Rv3378c as well as a 4.8-μm inhibitor of cis-FPPS, opening up the possibility of multitarget inhibition involving both cell wall biosynthesis and virulence factor formation.
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Affiliation(s)
- Meekyum Olivia Kim
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xinxin Feng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ferran Feixas
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wei Zhu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Steffen Lindert
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Shannon Bogue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - William Sinko
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - César de Oliveira
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - James Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA, 92093, USA
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Engineered heterologous FPP synthases-mediated Z,E-FPP synthesis in E. coli. Metab Eng 2013; 18:53-9. [DOI: 10.1016/j.ymben.2013.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/21/2013] [Accepted: 04/01/2013] [Indexed: 02/03/2023]
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13
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Substrate specificity of undecaprenyl diphosphate synthase from the hyperthermophilic archaeon Aeropyrum pernix. Biochem Biophys Res Commun 2013; 436:230-4. [PMID: 23726912 DOI: 10.1016/j.bbrc.2013.05.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/21/2013] [Indexed: 11/20/2022]
Abstract
Cis-prenyltransferase from a hyperthermophilic archaeon Aeropyrum pernix was expressed in Escherichia coli and purified for characterization. Properties such as substrate specificity, product chain-length, thermal stability and cofactor requirement were investigated using the recombinant enzyme. In particular, the substrate specificity of the enzyme attracts interest because only dimethylallyl diphosphate and geranylfarnesyl diphosphate, both of which are unusual substrates for known cis-prenyltransferases, are likely available as an allylic primer substrate in A. pernix. From the enzymatic study, the archaeal enzyme was shown to be undecaprenyl diphosphate synthase that has anomalous substrate specificity, which results in a preference for geranylfarnesyl diphosphate. This means that the product of the enzyme, which is probably used as the precursor of the glycosyl carrier lipid, would have an undiscovered structure.
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15
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Farnesyl pyrophosphate synthase: a key enzyme in isoprenoid biosynthetic pathway and potential molecular target for drug development. N Biotechnol 2013; 30:114-23. [DOI: 10.1016/j.nbt.2012.07.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 11/19/2022]
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16
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Kera K, Takahashi S, Sutoh T, Koyama T, Nakayama T. Identification and characterization of a cis,trans-mixed heptaprenyl diphosphate synthase from Arabidopsis thaliana. FEBS J 2012; 279:3813-27. [PMID: 22883514 DOI: 10.1111/j.1742-4658.2012.08742.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Revised: 08/03/2012] [Accepted: 08/08/2012] [Indexed: 11/29/2022]
Abstract
In eukaryotes, dolichols (C(70-120)) play indispensable roles as glycosyl carrier lipids in the biosynthesis of glycoproteins on endoplasmic reticulum. In addition to dolichols, seed plants have other types of Z,E-mixed polyisoprenoids termed ficaprenol (tri-trans,poly-cis-polyprenol, C(45-75)) and betulaprenol (di-trans,poly-cis-polyprenol, C(30-45) and C(≥70)) in abundance. However, the physiological significance of these polyprenols has not been elucidated because of limited information regarding cis-prenyltransferases (cPTs) which catalyze the formation of the structural backbone of Z,E-mixed polyisoprenoids. In the comprehensive identification and characterization of cPT homologues from Arabidopsis thaliana, AtHEPS was identified as a novel cis,trans-mixed heptaprenyl diphosphate synthase. AtHEPS heterologously expressed in Escherichia coli catalyzed the formation of C(35) polyisoprenoid as a major product, independent of the chain lengths of all-trans allylic primer substrates. Kinetic analyses revealed that farnesyl diphosphate was the most favorable for AtHEPS among the allylic substrates tested suggesting that AtHEPS was responsible for the formation of C(35) betulaprenol. AtHEPS partially suppressed the phenotypes of a yeast cPT mutant deficient in the biosynthesis of dolichols. Moreover, in A. thaliana cells, subcellular localization of AtHEPS on the endoplasmic reticulum was shown by using green fluorescent protein fused proteins. However, a cold-stress-inducible expression of AtHEPS suggested that AtHEPS and its product might function in response to abiotic stresses rather than in cell maintenance as a glycosyl carrier lipid on the endoplasmic reticulum.
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Affiliation(s)
- Kota Kera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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17
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Substrate specificities of E- and Z-farnesyl diphosphate synthases with substrate analogs. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mann FM, Thomas JA, Peters RJ. Rv0989c encodes a novel (E)-geranyl diphosphate synthase facilitating decaprenyl diphosphate biosynthesis in Mycobacterium tuberculosis. FEBS Lett 2011; 585:549-54. [PMID: 21237161 DOI: 10.1016/j.febslet.2011.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/01/2011] [Accepted: 01/05/2011] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has a highly complex cell wall, which is required for both bacterial survival and infection. Cell wall biosynthesis is dependent on decaprenyl diphosphate as a glyco-carrier, which is hence an essential metabolite in this pathogen. Previous biochemical studies indicated (E)-geranyl diphosphate (GPP) is required for the synthesis of decaprenyl diphosphate. Here we demonstrate that Rv0989c encodes the "missing" GPP synthase, representing the first such enzyme to be characterized from bacteria, and which presumably is involved in decaprenyl diphosphate biosynthesis in Mtb. Our investigation also has revealed previously unrecognized substrate plasticity of the farnesyl diphosphate synthases from Mtb, resolving previous discrepancies between biochemical and genetic studies of cell wall biosynthesis.
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Affiliation(s)
- Francis M Mann
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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19
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Sato T, Takizawa K, Orito Y, Kudo H, Hoshino T. Insight into C35 terpene Biosyntheses by Nonpathogenic Mycobacterium Species: Functional Analyses of Three Z-Prenyltransferases and Identification of Dehydroheptaprenylcyclines. Chembiochem 2010; 11:1874-81. [DOI: 10.1002/cbic.201000328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Noel JP, Dellas N, Faraldos JA, Zhao M, Hess BA, Smentek L, Coates RM, O’Maille PE. Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates. ACS Chem Biol 2010; 5:377-92. [PMID: 20175559 PMCID: PMC2860371 DOI: 10.1021/cb900295g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 02/22/2010] [Indexed: 11/29/2022]
Abstract
Sesquiterpene skeletal complexity in nature originates from the enzyme-catalyzed ionization of (trans,trans)-farnesyl diphosphate (FPP) (1a) and subsequent cyclization along either 2,3-transoid or 2,3-cisoid farnesyl cation pathways. Tobacco 5-epi-aristolochene synthase (TEAS), a transoid synthase, produces cisoid products as a component of its minor product spectrum. To investigate the cryptic cisoid cyclization pathway in TEAS, we employed (cis,trans)-FPP (1b) as an alternative substrate. Strikingly, TEAS was catalytically robust in the enzymatic conversion of (cis,trans)-FPP (1b) to exclusively (>/=99.5%) cisoid products. Further, crystallographic characterization of wild-type TEAS and a catalytically promiscuous mutant (M4 TEAS) with 2-fluoro analogues of both all-trans FPP (1a) and (cis,trans)-FPP (1b) revealed binding modes consistent with preorganization of the farnesyl chain. These results provide a structural glimpse into both cisoid and transoid cyclization pathways efficiently templated by a single enzyme active site, consistent with the recently elucidated stereochemistry of the cisoid products. Further, computational studies using density functional theory calculations reveal concerted, highly asynchronous cyclization pathways leading to the major cisoid cyclization products. The implications of these discoveries for expanded sesquiterpene diversity in nature are discussed.
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Affiliation(s)
- Joseph P. Noel
- Howard Hughes Medical Institute
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
| | - Nikki Dellas
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
- Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093
| | - Juan A. Faraldos
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Marylin Zhao
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - B. Andes Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
| | - Lidia Smentek
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
- Institute of Physics, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Robert M. Coates
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Paul E. O’Maille
- Howard Hughes Medical Institute
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 Torrey Pines Road, La Jolla, California 92037
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21
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Faraldos JA, O'Maille PE, Dellas N, Noel JP, Coates RM. Bisabolyl-derived sesquiterpenes from tobacco 5-epi-aristolochene synthase-catalyzed cyclization of (2Z,6E)-farnesyl diphosphate. J Am Chem Soc 2010; 132:4281-9. [PMID: 20201526 DOI: 10.1021/ja909886q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the structures and stereochemistry of seven bisabolyl-derived sesquiterpenes arising from an unprecedented 1,6-cyclization (cisoid pathway) efficiently catalyzed by tobacco 5-epi-aristolochene synthase (TEAS). The use of (2Z,6E)-farnesyl diphosphate as an alternate substrate for recombinant TEAS resulted in a robust enzymatic cyclization to an array of products derived exclusively (>/=99.5%) from the cisoid pathway, whereas these same products account for ca. 2.5% of the total hydrocarbons obtained using (2E,6E)-farnesyl diphosphate. Chromatographic fractionations of extracts from preparative incubations with the 2Z,6E substrate afforded, in addition to the acyclic allylic alcohols (2Z,6E)-farnesol (6.7%) and nerolidol (3.6%), five cyclic sesquiterpene hydrocarbons and two cyclic sesquiterpene alcohols: (+)-2-epi-prezizaene (44%), (-)-alpha-cedrene (21.5%), (R)-(-)-beta-curcumene (15.5%), alpha-acoradiene (3.9%), 4-epi-alpha-acoradiene (1.3%), and equal amounts of alpha-bisabolol (1.8%) and epi-alpha-bisalolol (1.8%). The structures, stereochemistry, and enantiopurities were established by comprehensive spectroscopic analyses, optical rotations, chemical correlations with known sesquiterpenes, comparisons with literature data, and GC analyses. The major product, (+)-2-epi-prezizaene, is structurally related to the naturally occurring tricyclic alcohol, jinkohol (2-epi-prezizaan-7beta-ol). Cisoid cyclization pathways are proposed by which all five sesquiterpene hydrocarbons are derived from a common (7R)-beta-bisabolyl(+)/pyrophosphate(-) ion pair intermediate. The implications of the "cisoid" catalytic activity of TEAS are discussed.
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Affiliation(s)
- Juan A Faraldos
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Umesiri FE, Sanki AK, Boucau J, Ronning DR, Sucheck SJ. Recent advances toward the inhibition of mAG and LAM synthesis in Mycobacterium tuberculosis. Med Res Rev 2010; 30:290-326. [DOI: 10.1002/med.20190] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Johnston JB, Kells PM, Podust LM, Ortiz de Montellano PR. Biochemical and structural characterization of CYP124: a methyl-branched lipid omega-hydroxylase from Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2009; 106:20687-92. [PMID: 19933331 PMCID: PMC2791619 DOI: 10.1073/pnas.0907398106] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) produces a variety of methyl-branched lipids that serve important functions, including modulating the immune response during pathogenesis and contributing to a robust cell wall that is impermeable to many chemical agents. Here, we report characterization of Mtb CYP124 (Rv2266) that includes demonstration of preferential oxidation of methyl-branched lipids. Spectrophotometric titrations and analysis of reaction products indicate that CYP124 tightly binds and hydroxylates these substrates at the chemically disfavored omega-position. We also report X-ray crystal structures of the ligand-free and phytanic acid-bound protein at a resolution of 1.5 A and 2.1 A, respectively, which provide structural insights into a cytochrome P450 with predominant omega-hydroxylase activity. The structures of ligand-free and substrate-bound CYP124 reveal several differences induced by substrate binding, including reorganization of the I helix and closure of the active site by elements of the F, G, and D helices that bind the substrate and exclude solvent from the hydrophobic active site cavity. The observed regiospecific catalytic activity suggests roles of CYP124 in the physiological oxidation of relevant Mtb methyl-branched lipids. The enzymatic specificity and structures reported here provide a scaffold for the design and testing of specific inhibitors of CYP124.
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Affiliation(s)
- Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
| | - Petrea M. Kells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
| | - Larissa M. Podust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517
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24
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Vandermoten S, Haubruge E, Cusson M. New insights into short-chain prenyltransferases: structural features, evolutionary history and potential for selective inhibition. Cell Mol Life Sci 2009; 66:3685-95. [PMID: 19633972 PMCID: PMC11115643 DOI: 10.1007/s00018-009-0100-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 06/28/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022]
Abstract
Isoprenoids form an extensive group of natural products involved in a number of important biological processes. Their biosynthesis proceeds through sequential 1'-4 condensations of isopentenyl diphosphate (C5) with an allylic acceptor, the first of which is dimethylallyl diphosphate (C5). The reactions leading to the production of geranyl diphosphate (C10), farnesyl diphosphate (C15) and geranylgeranyl diphosphate (C20), which are the precursors of mono-, sesqui- and diterpenes, respectively, are catalyzed by a group of highly conserved enzymes known as short-chain isoprenyl diphosphate synthases, or prenyltransferases. In recent years, the sequences of many new prenyltransferases have become available, including those of several plant and animal geranyl diphosphate synthases, revealing novel mechanisms of product chain-length selectivity and an intricate evolutionary path from a putative common ancestor. Finally, there is considerable interest in designing inhibitors specific to short-chain prenyltransferases, for the purpose of developing new drugs or pesticides that target the isoprenoid biosynthetic pathway.
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Affiliation(s)
- Sophie Vandermoten
- Department of Functional and Evolutionary Entomology, Gembloux Agricultural University, Passage des Déportés 2, 5030 Gembloux, Belgium.
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25
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Nakano C, Hoshino T. Characterization of the Rv3377c gene product, a type-B diterpene cyclase, from the Mycobacterium tuberculosis H37 genome. Chembiochem 2009; 10:2060-71. [PMID: 19618417 DOI: 10.1002/cbic.200900248] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Rv3377c gene from the Mycobacterium tuberculosis H37 genome is specifically limited to those Mycobacterium species that cause tuberculosis. We have demonstrated that the gene product of Rv3377c is a diterpene cyclase that catalyzes the formation of tuberculosinol from geranylgeranyl diphosphate (GGPP). However, the characteristics of this enzyme had not previously been studied in detail with homogeneously purified enzyme. The purified enzyme catalyzed the synthesis of tuberculosinyl diphosphate from GGPP, but it did not bring about the synthesis of tuberculosinol. Optimal conditions for the highest activity were found to be as follows: pH 7.5, 30 degrees C, Mg(II) (0.1 mM), and Triton X-100 (0.1 %). Under these conditions, the kinetic values of K(M) and k(cat) were determined to be 11.7+/-1.9 microM for GGPP and 12.7+/-0.7 min(-1), respectively, whereas the specific activity was 186 nmol min(-1) mg(-1). The enzyme activity was inhibited at substrate concentrations higher than 50 microM. The catalytic activity was strongly inhibited by 15-aza-dihydrogeranylgeraniol and 5-isopropyl-N,N,N,2-tetramethyl-4-(piperidine-1-carbonyloxy)benzenaminium chloride (Amo-1618). The DXDTT(293-297) motif, corresponding to the DXDDTA motif conserved among terpene cyclases, was mutated in order to investigate its function. The middle D295 was found to be the most crucial entity for the catalysis. D293 and two threonine residues function synergistically to enhance the acidity of D295, possibly through hydrogen-bonding networks. The Rv3377c enzyme could also react with (14R/S)-14,15-oxidoGGPP to generate 3alpha- and 3beta-hydroxytuberculosinyl diphosphate. Conformational analyses were carried out with deuterium-labeled GGPP and oxidoGGPP. We found that GGPP and (14R)-oxidoGGPP adopted a chair/chair conformation, but (14S)-oxidoGGPP adopted a boat/chair conformation. Interestingly, the conformations of oxidoGGPP for the A-ring formation are the opposite of those of oxidosqualene when it is used as a substrate by squalene cyclases for the biosynthesis of hopene and tetrahymanol. (3R)-Oxidosqualene is folded in a boat conformation, whereas (3S)-2,3-oxidosqualene folds into a chair conformation, for the formation of the A-rings of the hopene and tetrahymanol skeletons, respectively.
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Affiliation(s)
- Chiaki Nakano
- Department of Applied Biological Chemistry, Faculty of Agriculture and Graduate School of Science and Technology, Niigata University, Nishi-ku, Niigata 950-2181 (Japan)
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26
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Yamada Y, Fukuda W, Hirooka K, Hiromoto T, Nakayama JI, Imanaka T, Fukusaki EI, Fujiwara S. Efficient in vitro synthesis of cis-polyisoprenes using a thermostable cis-prenyltransferase from a hyperthermophilic archaeon Thermococcus kodakaraensis. J Biotechnol 2009; 143:151-6. [PMID: 19583987 DOI: 10.1016/j.jbiotec.2009.06.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 05/26/2009] [Accepted: 06/21/2009] [Indexed: 10/20/2022]
Abstract
The Tk-idsB encoding cis-prenyltransferase which catalyzes consecutive cis-condensation of isopentenyl diphosphate to allylic diphosphate was isolated from a hyperthermophilic archaeon Thermococcus kodakaraensis, and enzymatic characteristics of the recombinant Tk-IdsB were examined. Tk-IdsB was not fully denatured even at 90 degrees C and preferably utilizes both C(10) and C(15) allylic diphosphates to yield mainly the C(60)-C(65) products. Based on structural models, single alanine-substitution mutants at Glu68, Lys109, or Leu113 were constructed, showing that all the three produced longer chains (C(65)-C(70)) than the wild-type and the substitution at 109 (K109A) was the most effective. Tk-IdsB was applied to an organic-aqueous dual-phase system and more than 90% of the products were recovered from the organic phase when 1-butanol or 1-pentanol was overlaid. When 1-octanol was overlaid, 70% of the products were obtained from the upper organic phase. The product distributions were changed depending on the hydrophobicity of organic solvents used. Tk-IdsB was then immobilized onto silica beads to make Tk-IdsB more tolerant, showing that half-life of enzyme at 80 degrees C was prolonged by immobilization. When the immobilized Tk-IdsB was applied in the organic-aqueous dual-phase system, immobilized Tk-IdsB catalyzed consecutive condensation more efficiently than the unimmobilized one.
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Affiliation(s)
- Yosuke Yamada
- Department of Bioscience, Nanobiotechnology Research Center, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Hyogo, Japan
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27
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Ambo T, Noike M, Kurokawa H, Koyama T. Cloning and functional analysis of cis-prenyltransferase from Thermobifida fusca. J Biosci Bioeng 2009; 107:620-2. [PMID: 19447338 DOI: 10.1016/j.jbiosc.2009.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 01/31/2009] [Accepted: 02/02/2009] [Indexed: 11/18/2022]
Abstract
cis-Prenyltransferase catalyzes the synthesis of Z,E-mixed prenyl diphosphates by a condensation of isopentenyl diphosphate to an allylic diphosphate. A novel gene encoding a cis-prenyltransferase is cloned from Thermobifida fusca. It showed a unique substrate specificity accepting dimethylallyl diphosphate as a shortest allylic substrate, and synthesizes polyprenyl products up to C(70).
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Affiliation(s)
- Takanori Ambo
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
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28
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Grimes KD, Lu YJ, Zhang YM, Luna VA, Hurdle JG, Carson EI, Qi J, Kudrimoti S, Rock CO, Lee RE. Novel acyl phosphate mimics that target PlsY, an essential acyltransferase in gram-positive bacteria. ChemMedChem 2009. [PMID: 19016283 DOI: 10.1002/cmdc.200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
PlsY is a recently discovered acyltransferase that executes an essential step in membrane phospholipid biosynthesis in Gram- positive bacteria. By using a bioisosteric replacement approach to generate substrate-based inhibitors of PlsY as potential novel antibacterial agents, a series of stabilized acyl phosphate mimetics, including acyl phosphonates, acyl alpha,alpha-difluoromethyl phosphonates, acyl phosphoramides, reverse amide phosphonates, acyl sulfamates, and acyl sulfamides were designed and synthesized. Several acyl phosphonates, phosphoramides, and sulfamates were identified as inhibitors of PlsY from Streptococcus pneumoniae and Bacillus anthracis. As anticipated, these inhibitors were competitive inhibitors with respect to the acyl phosphate substrate. Antimicrobial testing showed the inhibitors to have generally weak activity against Gram-positive bacteria with the exception of some acyl phosphonates, reverse amide phosphonates, and acyl sulfamates, which had potent activity against multiple strains of B. anthracis.
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Affiliation(s)
- Kimberly D Grimes
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, USA
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29
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Ranzer LK, Brück TB, Brück WM, Lopez JV, Kerr RG. A new prokaryotic farnesyldiphosphate synthase from the octocoral Eunicea fusca: differential display, inverse PCR, cloning, and characterization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2009; 11:62-73. [PMID: 18626710 DOI: 10.1007/s10126-008-9120-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 06/03/2008] [Indexed: 05/26/2023]
Abstract
We recently reported that the biosynthesis of fuscol, a diterpene from the octocoral Eunicea fusca, is inducible by the application of plant signaling factors such as salicylic acid to the coral's algal symbiont. In this study, an mRNA differential display approach has been employed with the dinoflagellate symbiont of this octocoral which has led to the isolation of a farnesyldiphosphate synthase (FPPS) that was transcriptionally activated under conditions that led to an induction of fuscol biosynthesis. Using a degenerate primer based on the aspartate-rich motifs found in prenylsynthases and a cassette ligation strategy, we report the cloning of the complete FPPS associated with the E. fusca dinoflagellate symbiont Symbiodinium sp. The protein exhibited the enzymatic properties associated with FPPS, namely, the synthesis of farnesyl diphosphate from geranyldiphosphate and isopentenyl diphosphate. The amino acid sequence of this FPPS has a high sequence similarity (82%) to known archaeal isoprenyl diphosphate synthases. This is the first description of a prokaryotic FPPS derived from a marine source.
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Affiliation(s)
- Llanie K Ranzer
- Center of Excellence in Biomedical and Marine Biotechnology, Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Rd., Boca Raton, FL 33431, USA
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Sartain MJ, Belisle JT. N-Terminal clustering of the O-glycosylation sites in the Mycobacterium tuberculosis lipoprotein SodC. Glycobiology 2009; 19:38-51. [PMID: 18842962 PMCID: PMC2733778 DOI: 10.1093/glycob/cwn102] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 09/26/2008] [Accepted: 09/28/2008] [Indexed: 12/16/2022] Open
Abstract
SodC is one of two superoxide dismutases produced by Mycobacterium tuberculosis. This protein was previously shown to contribute to virulence and to act as a B-cell antigen. SodC is also a putative lipoprotein, and like other Sec-translocated mycobacterial proteins it was suggested to be modified with glycosyl units. To definitively define the glycosylation of SodC, we applied an approach that combined site-directed mutagenesis, lectin binding, and mass spectrometry. This resulted in identification of six O-glycosylated residues within a 13-amino-acid region near the N-terminus. Each residue was modified with one to three hexose units, and the most dominant SodC glycoform was modified with nine hexose units. In addition to O-glycosylation of threonine residues, this study provides the first evidence of serine O-glycosylation in mycobacteria. When combined with bioinformatic analyses, the clustering of O-glycosylation appeared to occur in a region of SodC with a disordered structure and not in regions important to the enzymatic activity of SodC. The use of recombinant amino acid substitutions to alter glycosylation sites provided further evidence that glycosylation influences proteolytic processing and ultimately positioning of cell wall proteins.
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Affiliation(s)
- Mark J Sartain
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523, USA
| | - John T Belisle
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO 80523, USA
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31
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Grimes KD, Lu YJ, Zhang YM, Luna VA, Hurdle JG, Carson EI, Qi J, Kudrimoti S, Rock CO, Lee RE. Novel acyl phosphate mimics that target PlsY, an essential acyltransferase in gram-positive bacteria. ChemMedChem 2008; 3:1936-45. [PMID: 19016283 PMCID: PMC2722063 DOI: 10.1002/cmdc.200800218] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Indexed: 11/09/2022]
Abstract
PlsY is a recently discovered acyltransferase that executes an essential step in membrane phospholipid biosynthesis in Gram- positive bacteria. By using a bioisosteric replacement approach to generate substrate-based inhibitors of PlsY as potential novel antibacterial agents, a series of stabilized acyl phosphate mimetics, including acyl phosphonates, acyl alpha,alpha-difluoromethyl phosphonates, acyl phosphoramides, reverse amide phosphonates, acyl sulfamates, and acyl sulfamides were designed and synthesized. Several acyl phosphonates, phosphoramides, and sulfamates were identified as inhibitors of PlsY from Streptococcus pneumoniae and Bacillus anthracis. As anticipated, these inhibitors were competitive inhibitors with respect to the acyl phosphate substrate. Antimicrobial testing showed the inhibitors to have generally weak activity against Gram-positive bacteria with the exception of some acyl phosphonates, reverse amide phosphonates, and acyl sulfamates, which had potent activity against multiple strains of B. anthracis.
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Affiliation(s)
- Kimberly D. Grimes
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
| | - Ying-Jie Lu
- Dr. Y. Lu, Dr. Y. Zhang, Dr. C. O. Rock, Department of Infectious Diseases, St. Jude Children’s Research Hospital, 332 N. Lauderdale, Memphis, TN 38105
| | - Yong-Mei Zhang
- Dr. Y. Lu, Dr. Y. Zhang, Dr. C. O. Rock, Department of Infectious Diseases, St. Jude Children’s Research Hospital, 332 N. Lauderdale, Memphis, TN 38105
| | - Vicki A. Luna
- Dr. V. A. Luna, Center for Biological Defense, University of South Florida, 3602 Spectrum Blvd, Tampa FL 33612
| | - Julian G. Hurdle
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
| | - Elizabeth I. Carson
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
| | - Jianjun Qi
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
| | - Sucheta Kudrimoti
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
| | - Charles O. Rock
- Dr. Y. Lu, Dr. Y. Zhang, Dr. C. O. Rock, Department of Infectious Diseases, St. Jude Children’s Research Hospital, 332 N. Lauderdale, Memphis, TN 38105
| | - Richard E. Lee
- Dr. K. D. Grimes, Dr .J. Qi, Dr. J. G. Hurdle, Dr. E. Carson, Dr. S.Kudrimoti, Dr. R. E. Lee, Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 847 Monroe Ave, Memphis, TN 38163, Fax: (901)448-6828, E-mail:
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Cloning and functional analysis of novel short-chain cis-prenyltransferases. Biochem Biophys Res Commun 2008; 375:536-40. [DOI: 10.1016/j.bbrc.2008.08.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2008] [Accepted: 08/11/2008] [Indexed: 11/30/2022]
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Wolucka BA. Biosynthesis of D-arabinose in mycobacteria - a novel bacterial pathway with implications for antimycobacterial therapy. FEBS J 2008; 275:2691-711. [PMID: 18422659 DOI: 10.1111/j.1742-4658.2008.06395.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Decaprenyl-phospho-arabinose (beta-D-arabinofuranosyl-1-O-monophosphodecaprenol), the only known donor of d-arabinose in bacteria, and its precursor, decaprenyl-phospho-ribose (beta-D-ribofuranosyl-1-O-monophosphodecaprenol), were first described in 1992. En route to D-arabinofuranose, the decaprenyl-phospho-ribose 2'-epimerase converts decaprenyl-phospho-ribose to decaprenyl-phospho-arabinose, which is a substrate for arabinosyltransferases in the synthesis of the cell-wall arabinogalactan and lipoarabinomannan polysaccharides of mycobacteria. The first step of the proposed decaprenyl-phospho-arabinose biosynthesis pathway in Mycobacterium tuberculosis and related actinobacteria is the formation of D-ribose 5-phosphate from sedoheptulose 7-phosphate, catalysed by the Rv1449 transketolase, and/or the isomerization of d-ribulose 5-phosphate, catalysed by the Rv2465 d-ribose 5-phosphate isomerase. d-Ribose 5-phosphate is a substrate for the Rv1017 phosphoribosyl pyrophosphate synthetase which forms 5-phosphoribosyl 1-pyrophosphate (PRPP). The activated 5-phosphoribofuranosyl residue of PRPP is transferred by the Rv3806 5-phosphoribosyltransferase to decaprenyl phosphate, thus forming 5'-phosphoribosyl-monophospho-decaprenol. The dephosphorylation of 5'-phosphoribosyl-monophospho-decaprenol to decaprenyl-phospho-ribose by the putative Rv3807 phospholipid phosphatase is the committed step of the pathway. A subsequent 2'-epimerization of decaprenyl-phospho-ribose by the heteromeric Rv3790/Rv3791 2'-epimerase leads to the formation of the decaprenyl-phospho-arabinose precursor for the synthesis of the cell-wall arabinans in Actinomycetales. The mycobacterial 2'-epimerase Rv3790 subunit is similar to the fungal D-arabinono-1,4-lactone oxidase, the last enzyme in the biosynthesis of D-erythroascorbic acid, thus pointing to an evolutionary link between the D-arabinofuranose- and L-ascorbic acid-related pathways. Decaprenyl-phospho-arabinose has been a lead compound for the chemical synthesis of substrates for mycobacterial arabinosyltransferases and of new inhibitors and potential antituberculosis drugs. The peculiar (omega,mono-E,octa-Z) configuration of decaprenol has yielded insights into lipid biosynthesis, and has led to the identification of the novel Z-polyprenyl diphosphate synthases of mycobacteria. Mass spectrometric methods were developed for the analysis of anomeric linkages and of dolichol phosphate-related lipids. In the field of immunology, the renaissance in mycobacterial polyisoprenoid research has led to the identification of mimetic mannosyl-beta-1-phosphomycoketides of pathogenic mycobacteria as potent lipid antigens presented by CD1c proteins to human T cells.
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Affiliation(s)
- Beata A Wolucka
- Laboratory of Mycobacterial Biochemistry, Institute of Public Health, Brussels, Belgium.
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Ostash B, Saghatelian A, Walker S. A streamlined metabolic pathway for the biosynthesis of moenomycin A. ACTA ACUST UNITED AC 2007; 14:257-67. [PMID: 17379141 PMCID: PMC1936435 DOI: 10.1016/j.chembiol.2007.01.008] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/10/2007] [Accepted: 01/26/2007] [Indexed: 11/27/2022]
Abstract
Moenomycin A (MmA) is a member of the phosphoglycolipid family of antibiotics, which are the only natural products known to directly target the extracellular peptidoglycan glycosyltransferases involved in bacterial cell wall biosynthesis. The structural and biological uniqueness of MmA make it an attractive starting point for the development of new antibacterial drugs. In order both to elucidate the biosynthesis of this unusual compound and to develop tools to manipulate its structure, we have identified the MmA biosynthetic genes in Streptomyces ghanaensis (ATCC14672). We show via heterologous expression of a subset of moe genes that the economy of the MmA pathway is enabled through the use of sugar-nucleotide and isoprenoid building blocks derived from primary metabolism. The work reported lays the foundation for genetic engineering of MmA biosynthesis to produce novel derivatives.
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Affiliation(s)
- Bohdan Ostash
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Suzanne Walker
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA
- * Corresponding author: Suzanne Walker, Department of Microbiology and Molecular Genetics, Harvard Medical School, Armenise Room 630, 200 Longwood Avenue, Boston, MA 02115, Phone: 617-432-5488, Fax: 617-738-7664,
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Barry CE, Crick DC, McNeil MR. Targeting the formation of the cell wall core of M. tuberculosis. Infect Disord Drug Targets 2007; 7:182-202. [PMID: 17970228 PMCID: PMC4747060 DOI: 10.2174/187152607781001808] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mycobacteria have a unique cell wall, which is rich in drug targets. The cell wall core consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide connecting them. The detailed structure of the cell wall core is largely, although not completely, understood and will be presented. The biosynthetic pathways of all three components reveal significant drug targets that are the basis of present drugs and/or have potential for new drugs. These pathways will be reviewed and include enzymes involved in polyisoprene biosynthesis, soluble arabinogalactan precursor production, arabinogalactan polymerization, fatty acid synthesis, mycolate maturation, and soluble peptidoglycan precursor formation. Information relevant to targeting all these enzymes will be presented in tabular form. Selected enzymes will then be discussed in more detail. It is thus hoped this chapter will aid in the selection of targets for new drugs to combat tuberculosis.
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Affiliation(s)
- Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Host Defense, NIAID, NIH, Twinbrook 2, Room 239, 12441 Parklawn Drive, Rockville, MD 20852
| | - Dean C. Crick
- Mycobacterial Research Laboratories, Dept. of Microbiology, Immunology, and Pathology, 1682 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1682
| | - Michael R. McNeil
- Mycobacterial Research Laboratories, Dept. of Microbiology, Immunology, and Pathology, 1682 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1682
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Kinhikar AG, Vargas D, Li H, Mahaffey SB, Hinds L, Belisle JT, Laal S. Mycobacterium tuberculosis malate synthase is a laminin-binding adhesin. Mol Microbiol 2006; 60:999-1013. [PMID: 16677310 DOI: 10.1111/j.1365-2958.2006.05151.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (M. tb) uses the glyoxalate bypass for intracellular survival in vivo. These studies provide evidence that the M. tb malate synthase (MS) has adapted to function as an adhesin which binds to laminin and fibronectin. This binding is achieved via the unique C-terminal region of the M. tb MS. The ability to function as an adhesin necessitates extracellular localization. We provide evidence that despite the absence of a Sec-translocation signal sequence the M. tb MS is secreted/excreted, and is anchored on the cell wall by an undefined mechanism. The MS of Mycobacterium smegmatis is cytoplasmic but the M. tb MS expressed in M. smegmatis localizes to the cell wall and enhances the adherence of the bacteria to lung epithelial A549 cells. Antibodies to the C-terminal laminin/fibronectin-binding domain interfere with the binding of the M. tb MS to laminin and fibronectin and reduce the adherence of M. tb to A549 cells. Coupled to the earlier evidence of in vivo expression of M. tb MS during active but not latent infection in humans, these studies show that a housekeeping enzyme of M. tb contributes to its armamentarium of virulence promoting factors.
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Affiliation(s)
- Arvind G Kinhikar
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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37
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Kharel Y, Takahashi S, Yamashita S, Koyama T. Manipulation of prenyl chain length determination mechanism of cis-prenyltransferases. FEBS J 2006; 273:647-57. [PMID: 16420487 DOI: 10.1111/j.1742-4658.2005.05097.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The carbon backbones of Z,E-mixed isoprenoids are synthesized by sequential cis-condensation of isopentenyl diphosphate (IPP) and an allylic diphosphate through actions of a series of enzymes called cis-prenyltransferases. Recent molecular analyses of Micrococcus luteus B-P 26 undecaprenyl diphosphate (UPP, C55) synthase [Fujihashi M, Zhang Y-W, Higuchi Y, Li X-Y, Koyama T & Miki K (2001) Proc Natl Acad Sci USA98, 4337-4342.] showed that not only the primary structure but also the crystal structure of cis-prenyltransferases were totally different from those of trans-prenyltransferases. Although many studies on structure-function relationships of cis-prenyltransferases have been reported, regulation mechanisms for the ultimate prenyl chain length have not yet been elucidated. We report here that the ultimate chain length of prenyl products can be controlled through structural manipulation of UPP synthase of M. luteus B-P 26, based on comparisons between structures of various cis-prenyltransferases. Replacements of Ala72, Phe73, and Trp78, which are located in the proximity of the substrate binding site, with Leu--as in Z,E-farnesyl diphosphate (C15) synthase--resulted in shorter ultimate products with C(20-35). Additional mutation of F223H resulted in even shorter products. On the other hand, insertion of charged residues originating from long-chain cis-prenyltransferases into helix-3, which participates in constitution of the large hydrophobic cleft, resulted in lengthening of the ultimate product chain length, leading to C(60-75). These results helped us understand reaction mechanisms of cis-prenyltransferase including regulation of the ultimate prenyl chain-length.
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Affiliation(s)
- Yugesh Kharel
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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Mahapatra S, Yagi T, Belisle JT, Espinosa BJ, Hill PJ, McNeil MR, Brennan PJ, Crick DC. Mycobacterial lipid II is composed of a complex mixture of modified muramyl and peptide moieties linked to decaprenyl phosphate. J Bacteriol 2005; 187:2747-57. [PMID: 15805521 PMCID: PMC1070386 DOI: 10.1128/jb.187.8.2747-2757.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Structural analysis of compounds identified as lipid I and II from Mycobacterium smegmatis demonstrated that the lipid moiety is decaprenyl phosphate; thus, M. smegmatis is the first bacterium reported to utilize a prenyl phosphate other than undecaprenyl phosphate as the lipid carrier involved in peptidoglycan synthesis. In addition, mass spectrometry showed that the muropeptides from lipid I are predominantly N-acetylmuramyl-L-alanine-D-glutamate-meso-diaminopimelic acid-D-alanyl-D-alanine, whereas those isolated from lipid II form an unexpectedly complex mixture in which the muramyl residue and the pentapeptide are modified singly and in combination. The muramyl residue is present as N-acetylmuramic acid, N-glycolylmuramic acid, and muramic acid. The carboxylic functions of the peptide side-chains of lipid II showed three types of modification, with the dominant one being amidation. The preferred site for amidation is the free carboxyl group of the meso-diaminopimelic acid residue. Diamidated species were also observed. The carboxylic function of the terminal D-alanine of some molecules is methylated, as are all three carboxylic acid functions of other molecules. This study represents the first structural analysis of mycobacterial lipid I and II and the first report of extensive modifications of these molecules. The observation that lipid I was unmodified strongly suggests that the lipid II intermediates of M. smegmatis are substrates for a variety of enzymes that introduce modifications to the sugar and amino acid residues prior to the synthesis of peptidoglycan.
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Affiliation(s)
- Sebabrata Mahapatra
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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Kaur D, Brennan PJ, Crick DC. Decaprenyl diphosphate synthesis in Mycobacterium tuberculosis. J Bacteriol 2004; 186:7564-70. [PMID: 15516568 PMCID: PMC524883 DOI: 10.1128/jb.186.22.7564-7570.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Accepted: 08/12/2004] [Indexed: 11/20/2022] Open
Abstract
Z-prenyl diphosphate synthases catalyze the sequential condensation of isopentenyl diphosphate with allylic diphosphates to synthesize polyprenyl diphosphates. In mycobacteria, these are precursors of decaprenyl phosphate, a molecule which plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan. Recently, it was demonstrated that open reading frame Rv2361c of the Mycobacterium tuberculosis H37Rv genome encodes a unique prenyl diphosphate synthase (M. C. Schulbach, P. J. Brennan, and D. C. Crick, J. Biol. Chem. 275:22876-22881, 2000). We have now purified the enzyme to near homogeneity by using an Escherichia coli expression system and have shown that the product of this enzyme is decaprenyl diphosphate. Rv2361c has an absolute requirement for divalent cations and an optimal pH range of 7.5 to 8.5, and the activity is stimulated by both detergent and dithiothreitol. The enzyme catalyzes the addition of isopentenyl diphosphate to geranyl diphosphate, neryl diphosphate, omega,E,E-farnesyl diphosphate, omega,E,Z-farnesyl diphosphate, or omega,E,E,E-geranylgeranyl diphosphate, with Km values for the allylic substrates of 490, 29, 84, 290, and 40 microM, respectively. The Km value for isopentenyl diphosphate is 89 microM. The catalytic efficiency is greatest when omega,E,Z-farnesyl diphosphate is used as the allylic acceptor, suggesting that this is the natural substrate in vivo, a conclusion that is supported by previous structural studies of decaprenyl phosphoryl mannose isolated from M. tuberculosis. This is the first report of a bacterial Z-prenyl diphosphate synthase that preferentially utilizes an allylic diphosphate primer having the alpha-isoprene unit in the Z configuration, indicating that Rv1086 (omega,E,Z-farnesyl diphosphate synthase) and Rv2361c act sequentially in the biosynthetic pathway that leads to the formation of decaprenyl phosphate in M. tuberculosis.
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Affiliation(s)
- Devinder Kaur
- Mycobacterial Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523-1682, USA
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40
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Dover LG, Cerdeño-Tárraga AM, Pallen MJ, Parkhill J, Besra GS. Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae. FEMS Microbiol Rev 2004; 28:225-50. [PMID: 15109786 DOI: 10.1016/j.femsre.2003.10.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 09/23/2003] [Accepted: 10/04/2003] [Indexed: 11/17/2022] Open
Abstract
The recent determination of the complete genome sequence of Corynebacterium diphtheriae, the aetiological agent of diphtheria, has allowed a detailed comparison of its physiology with that of its closest sequenced pathogenic relative Mycobacterium tuberculosis. Of major importance to the pathogenicity and resilience of the latter is its particularly complex cell envelope. The corynebacteria share many of the features of this extraordinary structure although to a lesser level of complexity. The cell envelope of M. tuberculosis has provided the molecular targets for several of the major anti-tubercular drugs. Given a backdrop of emerging multi-drug resistant strains of the organism (MDR-TB) and its continuing global threat to human health, the search for novel anti-tubercular agents is of paramount importance. The unique structure of this cell wall and the importance of its integrity to the viability of the organism suggest that the search for novel drug targets within the array of enzymes responsible for its construction may prove fruitful. Although the application of modern bioinformatics techniques to the 'mining' of the M. tuberculosis genome has already increased our knowledge of the biosynthesis and assembly of the mycobacterial cell wall, several issues remain uncertain. Further analysis by comparison with its relatives may bring clarity and aid the early identification of novel cellular targets for new anti-tuberculosis drugs. In order to facilitate this aim, this review intends to illustrate the broad similarities and highlight the structural differences between the two bacterial envelopes and discuss the genetics of their biosynthesis.
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Affiliation(s)
- Lynn G Dover
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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41
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Dhiman RK, Schulbach MC, Mahapatra S, Baulard AR, Vissa V, Brennan PJ, Crick DC. Identification of a novel class of omega,E,E-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J Lipid Res 2004; 45:1140-7. [PMID: 15060088 DOI: 10.1194/jlr.m400047-jlr200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified an omega,E,E-farnesyl diphosphate (omega,E,E-FPP) synthase, encoded by the open reading frame Rv3398c, from Mycobacterium tuberculosis that is unique among reported FPP synthases in that it does not contain the type I (eukaryotic) or the type II (eubacterial) omega,E,E-FPP synthase signature motif. Instead, it has a structural motif similar to that of the type I geranylgeranyl diphosphate synthase found in Archaea. Thus, the enzyme represents a novel class of omega,E,E-FPP synthase. Rv3398c was cloned from the M. tuberculosis H37Rv genome and expressed in Mycobacterium smegmatis using a new mycobacterial expression vector (pVV2) that encodes an in-frame N-terminal affinity tag fusion with the protein of interest. The fusion protein was well expressed and could be purified to near homogeneity, allowing facile kinetic analysis of recombinant Rv3398c. Of the potential allylic substrates tested, including dimethylallyl diphosphate, only geranyl diphosphate served as an acceptor for isopentenyl diphosphate. The enzyme has an absolute requirement for divalent cation and has a K(m) of 43 microM for isopentenyl diphosphate and 9.8 microM for geranyl diphosphate and is reported to be essential for the viability of M. tuberculosis.
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Affiliation(s)
- Rakesh K Dhiman
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523-1677, USA
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42
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Minutolo F, Bertini S, Betti L, Di Bussolo V, Giannaccini G, Placanica G, Rapposelli S, Spielmann HP, Macchia M. Synthesis of aniline-type analogues of farnesyl diphosphate and their biological assays for prenyl protein transferase inhibitory activity. ACTA ACUST UNITED AC 2003; 58:1277-81. [PMID: 14630239 DOI: 10.1016/j.farmac.2003.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Stable analogues of farnesyl diphosphate, possessing an aniline-type portion in the prenyl-mimic moiety and phosphonoacetamido(oxy) groups in the place of the metabolically unstable diphosphate unit, were synthesised and submitted to biological assays. The enzyme inhibition tests performed on FTase and GGTase I show that the newly synthesised compounds based on a combination of the aniline-containing portions with (phosphonoacetamido)oxy groups do not afford potent inhibitors.
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Affiliation(s)
- Filippo Minutolo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
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43
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GrabiÅska K, Palamarczyk G. Dolichol biosynthesis in the yeastSaccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase. FEMS Yeast Res 2002. [DOI: 10.1111/j.1567-1364.2002.tb00093.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
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Crick DC, Mahapatra S, Brennan PJ. Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis. Glycobiology 2001; 11:107R-118R. [PMID: 11555614 DOI: 10.1093/glycob/11.9.107r] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The compositional complexity of the mycobacterial cell envelope differentiates Mycobacterium species from most other prokaryotes. Historically, research in this area has focused on the elucidation of the structure of the mycobacterial cell envelope with the result that the structures of the mycolic acid-arabinogalactan-peptidoglycan complex from M. tuberculosis are fairly well understood. However, the current impetus for studying M. tuberculosis and other pathogenic mycobacteria is the need to identify targets for the development of new drugs. Therefore, emphasis has been shifting to the study of cell envelope biosynthesis and the identification of enzymes that are essential to the viability of M. tuberculosis. The publication of the complete M. tuberculosis genome in 1998 has greatly aided these studies. To date, thirteen enzymes involved in the synthesis of the arabinogalactan-peptidoglycan complex of M. tuberculosis have been identified and at least partially characterized. Eleven of these enzymes were reported subsequent to the publication of the M. tuberculosis genome, a clear indication of the rapid evolution of knowledge stimulated by the sequencing of the genome. In this article we review the current understanding of M. tuberculosis arabinogalactan-peptidoglycan structure and biosynthesis.
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Affiliation(s)
- D C Crick
- Department of Microbiology, Colorado State University, 200 W. Lake St., Fort Collins, CO 80523-1677, USA
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45
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Metzler DE, Metzler CM, Sauke DJ. Polyprenyl (Isoprenoid) Compounds. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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