1
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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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2
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Abstract
Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.
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Affiliation(s)
- Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7011, USA.
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
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3
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Tarasova EV, Luchnikova NA, Grishko VV, Ivshina IB. Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents. Pharmaceuticals (Basel) 2023; 16:872. [PMID: 37375819 PMCID: PMC10301674 DOI: 10.3390/ph16060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.
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Affiliation(s)
- Ekaterina V. Tarasova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia; (N.A.L.); (V.V.G.); (I.B.I.)
| | - Natalia A. Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia; (N.A.L.); (V.V.G.); (I.B.I.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Victoria V. Grishko
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia; (N.A.L.); (V.V.G.); (I.B.I.)
| | - Irina B. Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia; (N.A.L.); (V.V.G.); (I.B.I.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
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Lemke C, Roach K, Ortega T, Tantillo DJ, Siegel JB, Peters RJ. Investigation of Acid–Base Catalysis in Halimadienyl Diphosphate Synthase Involved in Mycobacterium tuberculosis Virulence. ACS BIO & MED CHEM AU 2022; 2:490-498. [PMID: 36281298 PMCID: PMC9585517 DOI: 10.1021/acsbiomedchemau.2c00023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The devastating human
pathogenMycobacterium tuberculosis (Mtb)
is able to parasitize phagosomal compartments within alveolar
macrophage cells due, in part, to the activity of its cell-surface
lipids. Prominent among these is 1-tuberculosinyl-adenosine (1-TbAd),
a derivative of the diterpenoid tuberculosinyl (halima-5,13-dienyl)
diphosphate produced by the class II diterpene cyclase encoded by
Rv3377c, termed here MtHPS. Given the demonstrated ability of 1-TbAd
to act as a virulence factor for Mtb and the necessity for Rv3377c
for its production, there is significant interest in MtHPS activity.
Class II diterpene cyclases catalyze a general acid–base-mediated
carbocation cascade reaction initiated by protonation of the terminal
alkene in the general diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate and terminated by deprotonation of the
final cyclized (and sometimes also rearranged) intermediate. Here,
structure-guided mutagenesis was applied to characterize the various
residues contributing to activation of the enzymatic acid, as well
as identify the enzymatic base in MtHPS. Particularly given the ability
of conservative substitution for the enzymatic base (Y479F) to generate
an alternative product (labda-7,13-dienyl diphosphate) via deprotonation
of an earlier unrearranged intermediate, further mutational analysis
was carried out to introduce potential alternative catalytic bases.
The results were combined with mechanistic molecular modeling to elucidate
how these mutations affect the catalytic activity of this important
enzyme. This not only provided detailed structure–function
insight into MtHPS but also further emphasized the inert nature of
the active site of MtHPS and class II diterpene cyclases more generally.
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Affiliation(s)
- Cody Lemke
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Kristin Roach
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Teresa Ortega
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States
- Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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Mi J, Gong W, Wu X. Advances in Key Drug Target Identification and New Drug Development for Tuberculosis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5099312. [PMID: 35252448 PMCID: PMC8896939 DOI: 10.1155/2022/5099312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
Tuberculosis (TB) is a severe infectious disease worldwide. The increasing emergence of drug-resistant Mycobacterium tuberculosis (Mtb) has markedly hampered TB control. Therefore, there is an urgent need to develop new anti-TB drugs to treat drug-resistant TB and shorten the standard therapy. The discovery of targets of drug action will lay a theoretical foundation for new drug development. With the development of molecular biology and the success of Mtb genome sequencing, great progress has been made in the discovery of new targets and their relevant inhibitors. In this review, we summarized 45 important drug targets and 15 new drugs that are currently being tested in clinical stages and several prospective molecules that are still at the level of preclinical studies. A comprehensive understanding of the drug targets of Mtb can provide extensive insights into the development of safer and more efficient drugs and may contribute new ideas for TB control and treatment.
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Affiliation(s)
- Jie Mi
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
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6
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Nontuberculous Mycobacteria, Macrophages, and Host Innate Immune Response. Infect Immun 2021; 89:e0081220. [PMID: 34097459 DOI: 10.1128/iai.00812-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Although nontuberculous mycobacteria (NTM) are considered opportunistic infections, incidence and prevalence of NTM infection are increasing worldwide becoming a major public health threat. Innate immunity plays an essential role in mediating the initial host response against these intracellular bacteria. Specifically, macrophages phagocytose and eliminate NTM and act as antigen-presenting cells, which trigger downstream activation of cellular and humoral adaptive immune responses. Identification of macrophage receptors, mycobacterial ligands, phagosome maturation, autophagy/necrosis, and escape mechanisms are important components of this immunity network. The role of the macrophage in mycobacterial disease has mainly been studied in tuberculosis (TB), but limited information exists on its role in NTM. In this review, we focus on NTM immunity, the role of macrophages, and host interaction in NTM infection.
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7
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Holzheimer M, Buter J, Minnaard AJ. Chemical Synthesis of Cell Wall Constituents of Mycobacterium tuberculosis. Chem Rev 2021; 121:9554-9643. [PMID: 34190544 PMCID: PMC8361437 DOI: 10.1021/acs.chemrev.1c00043] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
The pathogen Mycobacterium tuberculosis (Mtb), causing
tuberculosis disease, features an extraordinary
thick cell envelope, rich in Mtb-specific lipids,
glycolipids, and glycans. These cell wall components are often directly
involved in host–pathogen interaction and recognition, intracellular
survival, and virulence. For decades, these mycobacterial natural
products have been of great interest for immunology and synthetic
chemistry alike, due to their complex molecular structure and the
biological functions arising from it. The synthesis of many of these
constituents has been achieved and aided the elucidation of their
function by utilizing the synthetic material to study Mtb immunology. This review summarizes the synthetic efforts of a quarter
century of total synthesis and highlights how the synthesis layed
the foundation for immunological studies as well as drove the field
of organic synthesis and catalysis to efficiently access these complex
natural products.
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Affiliation(s)
- Mira Holzheimer
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jeffrey Buter
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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8
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Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
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9
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Xu B, Li Z, Alsup TA, Ehrenberger MA, Rudolf JD. Bacterial diterpene synthases prenylate small molecules. ACS Catal 2021; 11:5906-5915. [PMID: 34796043 PMCID: PMC8594881 DOI: 10.1021/acscatal.1c01113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biosynthesis of terpenoid natural products begins with a carbocation-based cyclization or prenylation reaction. While these reactions are mechanistically similar, there are several families of enzymes, namely terpene synthases and prenyltransferases, that have evolved to specifically catalyze terpene cyclization or prenylation reactions. Here, we report that bacterial diterpene synthases, enzymes that are traditionally considered to be specific for cyclization, are capable of efficiently catalyzing both diterpene cyclization and the prenylation of small molecules. We investigated this unique dual reactivity of terpene synthases through a series of kinetic, biocatalytic, structural, and bioinformatics studies. Overall, this study unveils the ability of terpene synthases to catalyze C-, N-, O-, and S-prenylation on small molecules, proposes a substrate decoy mechanism for prenylation by terpene synthases, supports the physiological relevance of terpene synthase-catalyzed prenylation in vivo, and addresses questions regarding the evolution of prenylation function and its potential role in natural products biosynthesis.
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Affiliation(s)
- Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Tyler A. Alsup
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | - Jeffrey D. Rudolf
- Department of Chemistry, University of Florida, Gainesville, FL, USA
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10
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Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c. Biochemistry 2020; 59:4507-4515. [PMID: 33182997 DOI: 10.1021/acs.biochem.0c00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
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Affiliation(s)
- Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Lisa M Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Terrence E O'Brien
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob E Corn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tom Alber
- Department of Molecular & Cell Biology and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Justin B Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States.,Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
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11
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Heterologous Production of 1-Tuberculosinyladenosine in Mycobacterium kansasii Models Pathoevolution towards the Transcellular Lifestyle of Mycobacterium tuberculosis. mBio 2020; 11:mBio.02645-20. [PMID: 33082253 PMCID: PMC7587436 DOI: 10.1128/mbio.02645-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium kansasii is an environmental nontuberculous mycobacterium that causes opportunistic tuberculosis-like disease. It is one of the most closely related species to the Mycobacterium tuberculosis complex. Using M. kansasii as a proxy for the M. kansasii-M. tuberculosis common ancestor, we asked whether introducing the M. tuberculosis-specific gene pair Rv3377c-Rv3378c into M. kansasii affects the course of experimental infection. Expression of these genes resulted in the production of an adenosine-linked lipid species, known as 1-tuberculosinyladenosine (1-TbAd), but did not alter growth in vitro under standard conditions. Production of 1-TbAd enhanced growth of M. kansasii under acidic conditions through a bacterial cell-intrinsic mechanism independent of controlling pH in the bulk extracellular and intracellular spaces. Production of 1-TbAd led to greater burden of M. kansasii in the lungs of C57BL/6 mice during the first 24 h after infection, and ex vivo infections of alveolar macrophages recapitulated this phenotype within the same time frame. However, in long-term infections, production of 1-TbAd resulted in impaired bacterial survival in both C57BL/6 mice and Ccr2-/- mice. We have demonstrated that M. kansasii is a valid surrogate of M. tuberculosis to study virulence factors acquired by the latter organism, yet shown the challenge inherent to studying the complex evolution of mycobacterial pathogenicity with isolated gene complementation.IMPORTANCE This work sheds light on the role of the lipid 1-tuberculosinyladenosine in the evolution of an environmental ancestor to M. tuberculosis On a larger scale, it reinforces the importance of horizontal gene transfer in bacterial evolution and examines novel models and methods to provide a better understanding of the subtle effects of individual M. tuberculosis-specific virulence factors in infection settings that are relevant to the pathogen.
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12
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Antibacterial Natural Halimanes: Potential Source of Novel Antibiofilm Agents. Molecules 2020; 25:molecules25071707. [PMID: 32276434 PMCID: PMC7180734 DOI: 10.3390/molecules25071707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
The development of new agents against bacteria is an urgent necessity for human beings. The structured colony of bacterial cells, called the biofilm, is used to defend themselves from biocide attacks. For this reason, it is necessary to know their structures, develop new agents to eliminate them and to develop new procedures that allow an early diagnosis, by using biomarkers. Among natural products, some derivatives of diterpenes with halimane skeleton show antibacterial activity. Some halimanes have been isolated from marine organisms, structurally related with halimanes isolated from Mycobacterium tuberculosis. These halimanes are being evaluated as virulence factors and as tuberculosis biomarkers, this disease being one of the major causes of mortality and morbidity. In this work, the antibacterial halimanes will be reviewed, with their structural characteristics, activities, sources and the synthesis known until now.
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13
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Mycobacterium tuberculosis releases an antacid that remodels phagosomes. Nat Chem Biol 2019; 15:889-899. [PMID: 31427817 DOI: 10.1038/s41589-019-0336-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 06/28/2019] [Indexed: 12/25/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the world's most deadly pathogen. Unlike less virulent mycobacteria, Mtb produces 1-tuberculosinyladenosine (1-TbAd), an unusual terpene nucleoside of unknown function. In the present study 1-TbAd has been shown to be a naturally evolved phagolysosome disruptor. 1-TbAd is highly prevalent among patient-derived Mtb strains, where it is among the most abundant lipids produced. Synthesis of TbAd analogs and their testing in cells demonstrate that their biological action is dependent on lipid linkage to the 1-position of adenosine, which creates a strong conjugate base. Furthermore, C20 lipid moieties confer passage through membranes. 1-TbAd selectively accumulates in acidic compartments, where it neutralizes the pH and swells lysosomes, obliterating their multilamellar structure. During macrophage infection, a 1-TbAd biosynthesis gene (Rv3378c) confers marked phagosomal swelling and intraphagosomal inclusions, demonstrating an essential role in regulating the Mtb cellular microenvironment. Although macrophages kill intracellular bacteria through phagosome acidification, Mtb coats itself abundantly with antacid.
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14
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Jia M, Mishra SK, Tufts S, Jernigan RL, Peters RJ. Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases. Metab Eng 2019; 55:44-58. [PMID: 31220664 DOI: 10.1016/j.ymben.2019.06.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 02/04/2023]
Abstract
Terpene synthases are capable of mediating complex reactions, but fundamentally simply catalyze lysis of allylic diphosphate esters with subsequent deprotonation. Even with the initially generated tertiary carbocation this offers a variety of product outcomes, and deprotonation further can be preceded by the addition of water. This is particularly evident with labdane-related diterpenes (LRDs) where such lysis follows bicyclization catalyzed by class II diterpene cyclases (DTCs) that generates preceding structural variation. Previous investigation revealed that two diterpene synthases (DTSs), one bacterial and the other plant-derived, exhibit extreme substrate promiscuity, but yet still typically produce exo-ene or tertiary alcohol LRD derivatives, respectively (i.e., demonstrating high catalytic specificity), enabling rational combinatorial biosynthesis. Here two DTSs that produce either cis or trans endo-ene LRD derivatives, also plant and bacterial (respectively), were examined for their potential analogous utility. Only the bacterial trans-endo-ene forming DTS was found to exhibit significant substrate promiscuity (with moderate catalytic specificity). This further led to investigation of the basis for substrate promiscuity, which was found to be more closely correlated with phylogenetic origin than reaction complexity. Specifically, bacterial DTSs exhibited significantly more substrate promiscuity than those from plants, presumably reflecting their distinct evolutionary context. In particular, plants typically have heavily elaborated LRD metabolism, in contrast to the rarity of such natural products in bacteria, and the lack of potential substrates presumably alleviates selective pressure against such promiscuity. Regardless of such speculation, this work provides novel biosynthetic access to almost 19 LRDs, demonstrating the power of the combinatorial approach taken here.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sambit K Mishra
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Samuel Tufts
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Robert L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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15
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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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16
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Roncero AM, Tobal IE, Moro RF, Díez D, Marcos IS. Halimane diterpenoids: sources, structures, nomenclature and biological activities. Nat Prod Rep 2018; 35:955-991. [DOI: 10.1039/c8np00016f] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Diterpenes with a halimane skeleton constitute a small group of natural products that can be biogenetically considered as being between labdane and clerodane diterpenoids.
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Affiliation(s)
- Alejandro M. Roncero
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Ignacio E. Tobal
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Rosalina F. Moro
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - David Díez
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
| | - Isidro S. Marcos
- Departamento de Química Orgánica
- Facultad de Ciencias Químicas
- Universidad de Salamanca
- 37008 Salamanca
- Spain
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17
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Mafu S, Fischer E, Addison JB, Riberio Barbosana I, Zerbe P. Substitution of Two Active-Site Residues Alters C9-Hydroxylation in a Class II Diterpene Synthase. Chembiochem 2016; 17:2304-2307. [PMID: 27735121 DOI: 10.1002/cbic.201600419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Indexed: 11/06/2022]
Abstract
Diterpenes form a vast and diverse class of natural products of both ecological and economic importance. Class II diterpene synthase (diTPS) enzymes control the committed biosynthetic reactions underlying diterpene chemical diversity. Homology modelling with site-directed mutagenesis identified two active-site residues in the horehound (Marrubium vulgare) class II diTPS peregrinol diphosphate synthase (MvCPS1); residue substitutions abolished the unique MvCPS1-catalysed water-capture reaction at C9 and redirected enzyme activity toward formation of an alternative product, halima-5(10),13-dienyl diphosphate. These findings contributed new insight into the steric interactions that govern diTPS-catalysed regiospecific oxygenation reactions and highlight the feasibility of diTPS engineering to provide a broader spectrum of bioactive diterpene natural products.
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Affiliation(s)
- Sibongile Mafu
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Emil Fischer
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.,Present address: The Scripps Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - J Bennett Addison
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Isabel Riberio Barbosana
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA.,Present address: Federal University of Ceara, Mister Hull Avenue, 60455-760, Fortaleza, Brazil
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
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18
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Buter J, Heijnen D, Wan IC, Bickelhaupt FM, Young DC, Otten E, Moody DB, Minnaard AJ. Stereoselective Synthesis of 1-Tuberculosinyl Adenosine; a Virulence Factor of Mycobacterium tuberculosis. J Org Chem 2016; 81:6686-96. [PMID: 27398789 PMCID: PMC6202681 DOI: 10.1021/acs.joc.6b01332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite its status as one of the world's most prevalent and deadly bacterial pathogens, Mycobacterium tuberculosis (Mtb) infection is not routinely diagnosed by rapid and highly reliable tests. A program to discover Mtb-specific biomarkers recently identified two natural compounds, 1-tuberculosinyl adenosine (1-TbAd) and N(6)-tuberculosinyl adenosine (N(6)-TbAd). Based on their association with virulence, the lack of similar compounds in nature, the presence of multiple stereocenters, and the need for abundant products to develop diagnostic tests, synthesis of these compounds was considered to be of high value but challenging. Here, a multigram-scale stereoselective synthesis of 1-TbAd and N(6)-TbAd is described. As a key-step, a chiral auxiliary-mediated Diels-Alder cycloaddition was developed, introducing the three stereocenters with a high exo endo ratio (10:1) and excellent enantioselectivity (>98% ee). This constitutes the first entry into the stereoselective synthesis of diterpenes with the halimane skeleton. Computational studies explain the observed stereochemical outcome.
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Affiliation(s)
- Jeffrey Buter
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dorus Heijnen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Ieng Chim Wan
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - David C. Young
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School Smith Building, Room 538,1 Jimmy Fund Way, Boston, Massachusetts 02115, United States
| | - Edwin Otten
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Branch Moody
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School Smith Building, Room 538,1 Jimmy Fund Way, Boston, Massachusetts 02115, United States
| | - Adriaan J. Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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19
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Shin B, Kim BY, Cho E, Oh KB, Shin J, Goodfellow M, Oh DC. Actinomadurol, an Antibacterial Norditerpenoid from a Rare Actinomycete, Actinomadura sp. KC 191. JOURNAL OF NATURAL PRODUCTS 2016; 79:1886-1890. [PMID: 27367579 DOI: 10.1021/acs.jnatprod.6b00268] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new secondary metabolite, actinomadurol (1), was isolated along with the known compound JBIR-65 (2) from a rare actinomycete, Actinomadura strain KC 191. The structure of 1 was established as a rare member of the bacterial C-19 norditerpenoid class by NMR data and ECD calculations. The absolute configuration of 2, which was previously reported without stereochemical analysis, was determined by using the modified Mosher's method and ECD calculations. Actinomadurol (1) exhibited potent antibacterial activity against pathogenic strains, such as Staphylococcus aureus, Kocuria rhizophila, and Proteus hauseri (MIC = 0.39-0.78 μg/mL), whereas JBIR-65 (2) showed no antibacterial activity.
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Affiliation(s)
| | - Byung-Yong Kim
- School of Biology, Newcastle University , Newcastle upon Tyne, NE1 7RU, United Kingdom
| | | | | | | | - Michael Goodfellow
- School of Biology, Newcastle University , Newcastle upon Tyne, NE1 7RU, United Kingdom
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20
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Liu J, Bedell TA, West JG, Sorensen EJ. Design and Synthesis of Molecular Scaffolds with Anti-infective Activity. Tetrahedron 2016; 72:3579-3592. [PMID: 27284210 PMCID: PMC4894353 DOI: 10.1016/j.tet.2016.01.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - T. Aaron Bedell
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
| | - Julian G. West
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
| | - Erik J. Sorensen
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, New Jersey 08544, USA
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21
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Abstract
Breath testing has enormous potential in the medical diagnostic field. The underlying complexity and perceived availability of adequate specimens, combined with a lack of knowledge of the metabolic pathways that give rise to compounds that are sources of analytes detectable in breath, has greatly slowed development. These real obstacles have recently been largely overcome in the use of breath testing to identify patients with cystic fibrosis associated Pseudomonas aeruginosa infection and tuberculosis. This review summarizes progress made in the characterization of microbial volatiles produced by major lower respiratory tract bacterial pathogens, and their potential use as diagnostic markers in patient breath testing.
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Affiliation(s)
- James E Graham
- Department of Microbiology and Immunology, and Department of Biology, University of Louisville, Louisville, KY, USA; E-mail:
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22
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Jia M, Potter KC, Peters RJ. Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis. Metab Eng 2016; 37:24-34. [PMID: 27060773 DOI: 10.1016/j.ymben.2016.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/25/2016] [Accepted: 04/06/2016] [Indexed: 11/30/2022]
Abstract
Diterpenes are widely distributed across many biological kingdoms, where they serve a diverse range of physiological functions, and some have significant industrial utility. Their biosynthesis involves class I diterpene synthases (DTSs), whose activity can be preceded by that of class II diterpene cyclases (DTCs). Here, a modular metabolic engineering system was used to examine the promiscuity of DTSs. Strikingly, both a bacterial and plant DTS were found to exhibit extreme promiscuity, reacting with all available precursors with orthogonal activity, producing an olefin or hydroxyl group, respectively. Such DTS promiscuity enables combinatorial biosynthesis, with remarkably high yields for these unoptimized non-native enzymatic combinations (up to 15mg/L). Indeed, it was possible to readily characterize the 13 unknown products. Notably, 16 of the observed diterpenes were previously inaccessible, and these results provide biosynthetic routes that are further expected to enable assembly of more extended pathways to produce additionally elaborated 'non-natural' diterpenoids.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Kevin C Potter
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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23
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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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24
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Farah SI, Abdelrahman AA, North EJ, Chauhan H. Opportunities and Challenges for Natural Products as Novel Antituberculosis Agents. Assay Drug Dev Technol 2016; 14:29-38. [DOI: 10.1089/adt.2015.673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Shrouq I. Farah
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
| | | | - E. Jeffrey North
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
| | - Harsh Chauhan
- Department of Pharmacy Sciences, School of Pharmacy and Health Professions, Creighton University, Omaha, Nebraska
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25
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Abstract
This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.
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Affiliation(s)
- Jeroen S. Dickschat
- University of Bonn
- Kekulé-Institute of Organic Chemistry and Biochemistry
- 53121 Bonn
- Germany
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26
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Nakano C, Oshima M, Kurashima N, Hoshino T. Identification of a New Diterpene Biosynthetic Gene Cluster that ProducesO-Methylkolavelool inHerpetosiphon aurantiacus. Chembiochem 2015; 16:772-81. [DOI: 10.1002/cbic.201402652] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Indexed: 11/12/2022]
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27
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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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28
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Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Wang J, Behr MA. Building a better bacillus: the emergence of Mycobacterium tuberculosis. Front Microbiol 2014; 5:139. [PMID: 24765091 PMCID: PMC3982062 DOI: 10.3389/fmicb.2014.00139] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/18/2014] [Indexed: 11/29/2022] Open
Abstract
The genus Mycobacterium is comprised of more than 150 species that reside in a wide variety of habitats. Most mycobacteria are environmental organisms that are either not associated with disease or are opportunistic pathogens that cause non-transmissible disease in immunocompromised individuals. In contrast, a small number of species, such as the tubercle bacillus, Mycobacterium tuberculosis, are host-adapted pathogens for which there is no known environmental reservoir. In recent years, gene disruption studies using the host-adapted pathogen have uncovered a number of “virulence factors,” yet genomic data indicate that many of these elements are present in non-pathogenic mycobacteria. This suggests that much of the genetic make-up that enables virulence in the host-adapted pathogen is already present in environmental members of the genus. In addition to these generic factors, we hypothesize that molecules elaborated exclusively by professional pathogens may be particularly implicated in the ability of M. tuberculosis to infect, persist, and cause transmissible pathology in its host species, Homo sapiens. One approach to identify these molecules is to employ comparative analysis of mycobacterial genomes, to define evolutionary events such as horizontal gene transfer (HGT) that contributed M. tuberculosis-specific genetic elements. Independent studies have now revealed the presence of HGT genes in the M. tuberculosis genome and their role in the pathogenesis of disease is the subject of ongoing investigations. Here we review these studies, focusing on the hypothesized role played by HGT loci in the emergence of M. tuberculosis from a related environmental species into a highly specialized human-adapted pathogen.
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Affiliation(s)
- Joyce Wang
- Department of Microbiology and Immunology, McGill University Montreal, QC, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University Montreal, QC, Canada ; Department of Medicine, McGill University Montreal, QC, Canada ; McGill International TB Centre Montreal, QC, Canada
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30
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Gong HY, Zeng Y, Chen XY. Diterpene synthases and their responsible cyclic natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2014; 4:59-72. [PMID: 24858310 PMCID: PMC4004862 DOI: 10.1007/s13659-014-0012-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/23/2014] [Indexed: 05/11/2023]
Abstract
This review provides an overview of diterpene synthases which were initially identified via genetic and/or biochemical means, traversing all organisms researched to date.
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Affiliation(s)
- Hai-Yan Gong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ying Zeng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201 China
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, 200032 China
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31
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Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. Proc Natl Acad Sci U S A 2014; 111:2978-83. [PMID: 24516143 DOI: 10.1073/pnas.1315883111] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify lipids with roles in tuberculosis disease, we systematically compared the lipid content of virulent Mycobacterium tuberculosis with the attenuated vaccine strain Mycobacterium bovis bacillus Calmette-Guérin. Comparative lipidomics analysis identified more than 1,000 molecular differences, including a previously unknown, Mycobacterium tuberculosis-specific lipid that is composed of a diterpene unit linked to adenosine. We established the complete structure of the natural product as 1-tuberculosinyladenosine (1-TbAd) using mass spectrometry and NMR spectroscopy. A screen for 1-TbAd mutants, complementation studies, and gene transfer identified Rv3378c as necessary for 1-TbAd biosynthesis. Whereas Rv3378c was previously thought to function as a phosphatase, these studies establish its role as a tuberculosinyl transferase and suggest a revised biosynthetic pathway for the sequential action of Rv3377c-Rv3378c. In agreement with this model, recombinant Rv3378c protein produced 1-TbAd, and its crystal structure revealed a cis-prenyl transferase fold with hydrophobic residues for isoprenoid binding and a second binding pocket suitable for the nucleoside substrate. The dual-substrate pocket distinguishes Rv3378c from classical cis-prenyl transferases, providing a unique model for the prenylation of diverse metabolites. Terpene nucleosides are rare in nature, and 1-TbAd is known only in Mycobacterium tuberculosis. Thus, this intersection of nucleoside and terpene pathways likely arose late in the evolution of the Mycobacterium tuberculosis complex; 1-TbAd serves as an abundant chemical marker of Mycobacterium tuberculosis, and the extracellular export of this amphipathic molecule likely accounts for the known virulence-promoting effects of the Rv3378c enzyme.
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32
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Chan HC, Feng X, Ko TP, Huang CH, Hu Y, Zheng Y, Bogue S, Nakano C, Hoshino T, Zhang L, Lv P, Liu W, Crick DC, Liang PH, Wang AHJ, Oldfield E, Guo RT. Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. J Am Chem Soc 2014; 136:2892-6. [PMID: 24475925 PMCID: PMC3986019 DOI: 10.1021/ja413127v] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
We
have obtained the structure of the bacterial diterpene synthase,
tuberculosinol/iso-tuberculosinol synthase (Rv3378c)
from Mycobacterium tuberculosis, a
target for anti-infective therapies that block virulence factor formation.
This phosphatase adopts the same fold as found in the Z- or cis-prenyltransferases. We also obtained structures
containing the tuberculosinyl diphosphate substrate together with
one bisphosphonate inhibitor-bound structure. These structures together
with the results of site-directed mutagenesis suggest an unusual mechanism
of action involving two Tyr residues. Given the similarity in local
and global structure between Rv3378c and the M. tuberculosis cis-decaprenyl diphosphate synthase (DPPS; Rv2361c),
the possibility exists for the development of inhibitors that target
not only virulence but also cell wall biosynthesis, based in part
on the structures reported here.
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Affiliation(s)
- Hsiu-Chien Chan
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology , Tianjin 300308, China
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Soldati T, Neyrolles O. Mycobacteria and the intraphagosomal environment: take it with a pinch of salt(s)! Traffic 2012; 13:1042-52. [PMID: 22462580 DOI: 10.1111/j.1600-0854.2012.01358.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/27/2012] [Accepted: 03/30/2012] [Indexed: 01/13/2023]
Abstract
Ancient protozoan phagocytes and modern professional phagocytes of metazoans, such as macrophages, employ evolutionarily conserved mechanisms to kill microbes. These mechanisms rely on microbial ingestion, followed by maturation of the phagocytic vacuole, or so-called phagosome. Phagosome maturation includes a series of fusion and fission events with the host cell endosomes and lysosomes, leading to a rapid increase of the degradative properties of the vacuole and to the destruction of the ingested microbe within a very hostile intracellular compartment, the phagolysosome. Historically, the mechanisms and weapons used by phagocytes to kill microbes have been separated into different classes. Phagosomal acidification, together with the production of reactive oxygen and nitrogen species, the selective manipulation of various ions in the phagosomal lumen, and finally the engagement of a battery of acidic hydrolases, are well-recognized players in this process. However, it is relatively recently that interconnections among these mechanisms have become apparent. In this review, we will focus on some emerging concepts about these interconnected aspects of the warfare at the host-pathogen interface, using mostly Mycobacterium tuberculosis as an example of intracellular pathogen. In particular, recent discoveries on the role of phagosomal ions and other chemicals in the control of pathogens, as well as mechanisms evolved by intracellular pathogens to circumvent or even exploit the weapons of the host cell will be discussed.
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Affiliation(s)
- Thierry Soldati
- Départment de Biochimie, Faculté des Sciences, Université de Genève, Sciences II, 30 quai Ernest Ansermet, CH-1211, Genève-4, Switzerland.
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Smanski MJ, Peterson RM, Huang SX, Shen B. Bacterial diterpene synthases: new opportunities for mechanistic enzymology and engineered biosynthesis. Curr Opin Chem Biol 2012; 16:132-41. [PMID: 22445175 DOI: 10.1016/j.cbpa.2012.03.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Revised: 02/22/2012] [Accepted: 03/02/2012] [Indexed: 11/15/2022]
Abstract
Diterpenoid biosynthesis has been extensively studied in plants and fungi, yet cloning and engineering diterpenoid pathways in these organisms remain challenging. Bacteria are emerging as prolific producers of diterpenoid natural products, and bacterial diterpene synthases are poised to make significant contributions to our understanding of terpenoid biosynthesis. Here we will first survey diterpenoid natural products of bacterial origin and briefly review their biosynthesis with emphasis on diterpene synthases (DTSs) that channel geranylgeranyl diphosphate to various diterpenoid scaffolds. We will then highlight differences of DTSs of bacterial and higher organism origins and discuss the challenges in discovering novel bacterial DTSs. We will conclude by discussing new opportunities for DTS mechanistic enzymology and applications of bacterial DTS in biocatalysis and metabolic pathway engineering.
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Affiliation(s)
- Michael J Smanski
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
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Mann FM, Peters RJ. Isotuberculosinol: the unusual case of an immunomodulatory diterpenoid from Mycobacterium tuberculosis.. MEDCHEMCOMM 2012; 3:899-904. [PMID: 23926455 DOI: 10.1039/c2md20030a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Francis M Mann
- Department of Chemistry, Winona Sate University, Winona, MN 55987
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Abstract
Mycobacterium tuberculosis is an extremely successful pathogen that demonstrates the capacity to modulate its host both at the cellular and tissue levels. At the cellular level, the bacterium enters its host macrophage and arrests phagosome maturation, thus avoiding many of the microbicidal responses associated with this phagocyte. Nonetheless, the intracellular environment places certain demands on the pathogen, which, in response, senses the environmental shifts and upregulates specific metabolic programs to allow access to nutrients, minimize the consequences of stress, and sustain infection. Despite its intracellular niche, Mycobacterium tuberculosis demonstrates a marked capacity to modulate the tissues surrounding infected cells through the release of potent, bioactive cell wall constituents. These cell wall lipids are released from the host cell by an exocytic process and induce physiological changes in neighboring phagocytes, which drives formation of a granuloma. This tissue response leads to the generation and accumulation of caseous debris and the progression of the human tuberculosis granuloma. Completion of the life cycle of tuberculosis requires damaging the host to release infectious bacteria into the airways to spread the infection. This damage reflects the pathogen's ability to subvert the host's innate and acquired immune responses to its own nefarious ends.
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Affiliation(s)
- David G Russell
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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Mann FM, VanderVen BC, Peters RJ. Magnesium depletion triggers production of an immune modulating diterpenoid in Mycobacterium tuberculosis. Mol Microbiol 2011; 79:1594-601. [PMID: 21244530 DOI: 10.1111/j.1365-2958.2011.07545.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of the human disease Tuberculosis, and remains a worldwide health threat responsible for ∼1.7 million deaths annually. During infection, Mtb prevents acidification of the engulfing phagosome, thus blocking endocytic progression and eventually leading to stable residence. The diterpenoid metabolite isotuberculosinol (isoTb) exhibits biological activity indicative of a role in this early arrest of phagosome maturation. Presumably, isoTb production should be induced by phagosomal entry. However, the relevant enzymatic genes are not transcriptionally upregulated during engulfment. Previous examination of the initial biosynthetic enzyme (Rv3377c/MtHPS) involved in isoTb biosynthesis revealed striking inhibition by its Mg(2+) cofactor, leading to the hypothesis that the depletion of Mg(2+) observed upon phagosomal engulfment may act to trigger isoTb biosynthesis. While Mtb is typically grown in relatively high levels of Mg(2+) (0.43 mM), shifting Mtb to media with phagosomal levels (0.1 mM) led to a significant (∼10-fold) increase in accumulation of the MtHPS product, halimadienyl diphosphate, as well as easily detectable amounts of the derived bioactive isoTb. These results demonstrate isoTb production by Mtb specifically under conditions that mimic phagosomal cation concentrations, and further support a role for isoTb in the Mtb infection process.
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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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Characterization of the Rv3378c gene product, a new diterpene synthase for producing tuberculosinol and (13R, S)-isotuberculosinol (nosyberkol), from the Mycobacterium tuberculosis H37Rv genome. Biosci Biotechnol Biochem 2011; 75:75-81. [PMID: 21228491 DOI: 10.1271/bbb.100570] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Rv3377c and Rv3378c genes from Mycobacterium tuberculosis are specifically found in the virulent Mycobacterium species, but not in the avirulent species. The Rv3378c-encoded enzyme produced tuberculosinol 2 (5(6), 13(14)-halimadiene-15-ol), 13R-5a and 13S-isotuberculosinol 5b (5(6), 14(15)-halimadiene-13-ol) as its enzymatic products from tuberculosinyl diphosphate 3, indicating that the Rv3378c enzyme catalyzed the nucleophilic addition of a water molecule after the release of a diphosphate moiety. The three enzymatic products 2, 5a, and 5b were produced irrespective of the N- and C-terminal His-tagged Rv3378c enzymes, and of the maltose-binding protein fusion enzyme; the product distribution ratio was identical between the enzymes as 1:1 for 2:5, and 1:3 for 5a:5b. The successful separation of 5a and 5b by a chiral HPLC column provided the first complete assignments of ¹H- and ¹³C-NMR data for 5a and 5b. The enzymatic mechanism for producing 2, 5a, and 5b is proposed here, and the optimal catalytic conditions and kinetic parameters, in addition to the divalent metal effects, are described. Site-directed mutagenesis of Asp into Asn, targeted at the DDXXD motif, resulted in significantly decreased enzymatic activity.
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Hoshino T, Nakano C, Ootsuka T, Shinohara Y, Hara T. Substrate specificity of Rv3378c, an enzyme from Mycobacterium tuberculosis, and the inhibitory activity of the bicyclic diterpenoids against macrophagephagocytosis. Org Biomol Chem 2011; 9:2156-65. [DOI: 10.1039/c0ob00884b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Cao R, Zhang Y, Mann FM, Huang C, Mukkamala D, Hudock MP, Mead ME, Prisic S, Wang K, Lin FY, Chang TK, Peters RJ, Oldfield E. Diterpene cyclases and the nature of the isoprene fold. Proteins 2010; 78:2417-32. [PMID: 20602361 DOI: 10.1002/prot.22751] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The structures and mechanism of action of many terpene cyclases are known, but no structures of diterpene cyclases have yet been reported. Here, we propose structural models based on bioinformatics, site-directed mutagenesis, domain swapping, enzyme inhibition, and spectroscopy that help explain the nature of diterpene cyclase structure, function, and evolution. Bacterial diterpene cyclases contain approximately 20 alpha-helices and the same conserved "QW" and DxDD motifs as in triterpene cyclases, indicating the presence of a betagamma barrel structure. Plant diterpene cyclases have a similar catalytic motif and betagamma-domain structure together with a third, alpha-domain, forming an alphabetagamma structure, and in H(+)-initiated cyclases, there is an EDxxD-like Mg(2+)/diphosphate binding motif located in the gamma-domain. The results support a new view of terpene cyclase structure and function and suggest evolution from ancient (betagamma) bacterial triterpene cyclases to (betagamma) bacterial and thence to (alphabetagamma) plant diterpene cyclases.
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Affiliation(s)
- Rong Cao
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Maugel N, Mann FM, Hillwig ML, Peters RJ, Snider BB. Synthesis of (+/-)-nosyberkol (isotuberculosinol, revised structure of edaxadiene) and (+/-)-tuberculosinol. Org Lett 2010; 12:2626-9. [PMID: 20462237 DOI: 10.1021/ol100832h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Me(2)AlCl-catalyzed Diels-Alder reaction of N-tigloyloxazolidinone with 6,6-dimethyl-1-vinylcyclohexene selectively provided the exo adduct, which was converted to nosyberkol (isotuberculosinol) and tuberculosinol. The spectral data for nosyberkol are identical with those reported for edaxadiene, whose structure is revised accordingly.
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Affiliation(s)
- Nathan Maugel
- Department of Chemistry MS 015, Brandeis University, Waltham, Massachusetts 02454-9110, USA
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Abstract
Diterpenes are a structurally diverse class of molecules common in plants, although they are very rarely found in bacteria. We report the identification in Mycobacterium tuberculosis (Mtb) of three diterpenes proposed to promote phagolysosome maturation arrest. MS analysis reveals that these diterpenes are novel compounds not previously identified in other organisms. The diterpene with highest abundance in Mtb has a mass fragmentation pattern identical to edaxadiene, which is produced in vitro from geranylgeranyl diphosphate by the enzymes Rv3377c and Rv3378c. A second diterpene found in Mtb has a similar mass spectrum, and is always observed in the same proportion relative to edaxadiene, indicating that it is a side product of the Rv3378c reaction in vivo. We name this second diterpene olefin edaxadiene B. The least abundant of the three diterpenes in Mtb extracts is tuberculosinol, a dephosphorylated side-product of the edaxadiene pathway intermediate produced by Rv3377c. A frameshift in Rv3377c in Mtb completely eliminates diterpene production, whereas expression of Rv3377c and Rv3378c in the nonpathogenic M. smegmatis is sufficient to produce edaxadiene and edaxadiene B. These studies define the pathway of edaxadiene and edaxadiene B biosynthesis in vivo. Rv3377c and Rv3378c are unique to Mtb and M. bovis, making them candidates for selective therapeutics and diagnostics.
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Affiliation(s)
- Lisa Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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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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Spangler JE, Carson CA, Sorensen EJ. Synthesis enables a structural revision of the Mycobacterium tuberculosis-produced diterpene, edaxadiene. Chem Sci 2010; 1:202-205. [PMID: 22114734 DOI: 10.1039/c0sc00284d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A stereodivergent synthesis of the [3.3.1] bicyclic core of edaxadiene was completed utilizing a key intramolecular oxidative ketone allylation. Significant discrepancies between the spectroscopic data obtained for the synthetic construct and the natural isolate raised questions about the structural assignment of edaxadiene. A subsequent structural reassignment was validated by completion of a total synthesis of the correct structure of the natural product.
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Affiliation(s)
- Jillian E Spangler
- Department of Chemistry, Princeton University, Frick Chemical Laboratory, Princeton, NJ, 08544, USA
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Mann FM, Prisic S, Hu H, Xu M, Coates RM, Peters RJ. Characterization and inhibition of a class II diterpene cyclase from Mycobacterium tuberculosis: implications for tuberculosis. J Biol Chem 2009; 284:23574-9. [PMID: 19574210 PMCID: PMC2749132 DOI: 10.1074/jbc.m109.023788] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Mycobacterium tuberculosis remains a widespread and devastating human pathogen, whose ability to infiltrate macrophage host cells from the human immune system is an active area of investigation. We have recently reported the discovery of a novel diterpene from M. tuberculosis, edaxadiene, whose ability to arrest phagosomal maturation in isolation presumably contributes to this critical process in M. tuberculosis infections. (Mann, F. M., Xu, M., Chen, X., Fulton, D. B., Russell, D. G., and Peters, R. J. (2009) J. Am. Chem. Soc., in press). Here, we present characterization of the class II diterpene cyclase that catalyzes the committed step in edaxadiene biosynthesis, i.e. the previously identified halimadienyl-diphosphate synthase (HPS; EC 5.5.1.16). Intriguingly, our kinetic analysis suggests a potential biochemical regulatory mechanism that triggers edaxadiene production upon phagosomal engulfment. Furthermore, we report characterization of potential HPS inhibitors: specifically, two related transition state analogs (15-aza-14,15-dihydrogeranylgeranyl diphosphate (7a) and 15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (7b)) that exhibit very tight binding. Although arguably not suitable for clinical use, these nevertheless provide a basis for pharmaceutical design against this intriguing biosynthetic pathway. Finally, we provide evidence indicating that this pathway exists only in M. tuberculosis and is not functional in the closely related Mycobacterium bovis because of an inactivating frameshift in the HPS-encoding gene. Thus, we hypothesize that the inability to produce edaxadiene may be a contributing factor in the decreased infectivity and/or virulence of M. bovis relative to M. tuberculosis in humans.
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Affiliation(s)
- Francis M Mann
- Department of Biochemistry, Iowa State University, Ames, Iowa 50011, USA
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