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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 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
| | - Natalia A Luchnikova
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- 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
| | - Irina B Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 13A Lenina Str., 614990 Perm, Russia
- 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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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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Bhaskar P, Sareen D. Bioinformatics approach to understand nature's unified mechanism of stereo-divergent synthesis of isoprenoid skeletons. World J Microbiol Biotechnol 2020; 36:142. [PMID: 32851438 DOI: 10.1007/s11274-020-02918-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/13/2020] [Indexed: 11/27/2022]
Abstract
In isoprenoid metabolism, cyclisation is the important gateway to chemical diversity. Terpene synthase is responsible for the cyclisation of a few universal substrates forming hundreds of often stereo-chemically complex mono- and poly-cyclic terpene hydrocarbons with a broad spectrum of functions in pharmaceuticals, flavours and fragrance industry. Although they are discovered and characterised mainly from plants and fungi, yet only a small share of bacterial terpenes has been investigated so far owing to their low level of expression in wild-type microorganisms. Extensive bacterial genome mining has revealed a treasure trove of terpene synthase genes and their regulated heterologous overexpression has pitched-in to describe the biochemical function of putative genes and sequester new terpene metabolites. This review deals with the modern genome mining techniques and molecular methods, providing more experimental tools for studying the structure and functions of terpenoid metabolites and strongly supports the idea that genome mining is a utile approach in deciphering the terpenoid diversity in bacteria.
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Affiliation(s)
- Pranav Bhaskar
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Dipti Sareen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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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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Chen CC, Zhang L, Yu X, Ma L, Ko TP, Guo RT. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lilan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
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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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Antitubercular and anti-inflammatory properties screening of natural products from Plectranthus species. Future Med Chem 2018; 10:1677-1691. [PMID: 29957070 DOI: 10.4155/fmc-2018-0043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM Confirm the use of Plectanthus spp. plants in traditional medicine, particularly as anti-inflammatory and anti-infective agents. MATERIALS & METHODS Compounds previously isolated from Plectranthus spp. were studied for their anti-inflammatory activity using the SNAP assay and RAW 264.7 cells, by the quantification of nitric oxide. An halimane diterpene and its derivatives were tested in infected macrophages with M. tuberculosis H37Rv, using CFU counts assay, at their minimum inhibitory concentration values. Results: The isolated compounds tested at noncytotoxic concentrations, did not reveal nitric oxide scavenging in the S-nitroso-N-acetylpenicillamine and the cellular assays. On the other hand, promising results were obtained regarding one semisynthetic halimane derivative (11R*,13E)-halima-5,13-diene-11,15-diol), previously prepared (2.1 × 105 CFU/mL), with an effect similar to the antitubercular drugs ethambutol (2.0 × 105 CFU/mL) and isoniazid (1.2 × 105 CFU/mL). CONCLUSION The present report demonstrates the relevance of Plectranthus spp. in medicinal chemistry drug development for TB and other infective respiratory complaints. Also, this work suggests that further studies involving other inflammatory mediators are needed to validate the anti-inflammatory use of these medicinal plants.
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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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10
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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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11
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Young DC, Layre E, Pan SJ, Tapley A, Adamson J, Seshadri C, Wu Z, Buter J, Minnaard AJ, Coscolla M, Gagneux S, Copin R, Ernst JD, Bishai WR, Snider BB, Moody DB. In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. ACTA ACUST UNITED AC 2016; 22:516-526. [PMID: 25910243 DOI: 10.1016/j.chembiol.2015.03.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/05/2015] [Accepted: 03/13/2015] [Indexed: 12/31/2022]
Abstract
Although small molecules shed from pathogens are widely used to diagnose infection, such tests have not been widely implemented for tuberculosis. Here we show that the recently identified compound, 1-tuberculosinyladenosine (1-TbAd), accumulates to comprise >1% of all Mycobacterium tuberculosis lipid. In vitro and in vivo, two isomers of TbAd were detected that might serve as infection markers. Using mass spectrometry and nuclear magnetic resonance, we established the structure of the previously unknown molecule, N(6)-tuberculosinyladenosine (N(6)-TbAd). Its biosynthesis involves enzymatic production of 1-TbAd by Rv3378c followed by conversion to N(6)-TbAd via the Dimroth rearrangement. Intact biosynthetic genes are observed only within M. tuberculosis complex bacteria, and TbAd was not detected among other medically important pathogens, environmental bacteria, and vaccine strains. With no substantially similar known molecules in nature, the discovery and in vivo detection of two abundant terpene nucleosides support their development as specific diagnostic markers of tuberculosis.
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Affiliation(s)
- 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, MA 02115, USA
| | - Emilie Layre
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Smith Building Room 538, 1 Jimmy Fund Way, Boston, MA 02115, USA
| | - Shih-Jung Pan
- K-RITH, KwuZulu-Natal Research Institute for Tuberculosis & HIV, Nelson R. Mandela School of Medicine-University of Kwazulu-Natal, K-RITH Tower Building, 719 Umbilo Road, Durban, 4001 Private Bag X7, Congela-Durban 4001, South Africa
| | - Asa Tapley
- K-RITH, KwuZulu-Natal Research Institute for Tuberculosis & HIV, Nelson R. Mandela School of Medicine-University of Kwazulu-Natal, K-RITH Tower Building, 719 Umbilo Road, Durban, 4001 Private Bag X7, Congela-Durban 4001, South Africa; UCSF School of Medicine, San Francisco, CA 94143, USA
| | - John Adamson
- K-RITH, KwuZulu-Natal Research Institute for Tuberculosis & HIV, Nelson R. Mandela School of Medicine-University of Kwazulu-Natal, K-RITH Tower Building, 719 Umbilo Road, Durban, 4001 Private Bag X7, Congela-Durban 4001, South Africa; Center for Tuberculosis Research, Division of Infections Diseases, Johns Hopkins University School of Medicine, 1550 Orleans Street Room 108, Baltimore, MD 21231, USA
| | - Chetan Seshadri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Smith Building Room 538, 1 Jimmy Fund Way, Boston, MA 02115, USA
| | - Zhongtao Wu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jeffrey Buter
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Richard Copin
- Division of Infectious Diseases & Immunology, New York University School of Medicine, 522 First Avenue, SRB 901, New York, NY 10016, USA
| | - Joel D Ernst
- Division of Infectious Diseases & Immunology, New York University School of Medicine, 522 First Avenue, SRB 901, New York, NY 10016, USA
| | - William R Bishai
- K-RITH, KwuZulu-Natal Research Institute for Tuberculosis & HIV, Nelson R. Mandela School of Medicine-University of Kwazulu-Natal, K-RITH Tower Building, 719 Umbilo Road, Durban, 4001 Private Bag X7, Congela-Durban 4001, South Africa; Center for Tuberculosis Research, Division of Infections Diseases, Johns Hopkins University School of Medicine, 1550 Orleans Street Room 108, Baltimore, MD 21231, USA
| | - Barry B Snider
- Department of Chemistry MS015, Brandeis University, Waltham, MA 02453-2728, USA
| | - 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, MA 02115, USA.
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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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13
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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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14
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Structural and functional analysis of Bacillus subtilis YisP reveals a role of its product in biofilm production. ACTA ACUST UNITED AC 2014; 21:1557-63. [PMID: 25308276 DOI: 10.1016/j.chembiol.2014.08.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/14/2014] [Accepted: 08/17/2014] [Indexed: 11/20/2022]
Abstract
YisP is involved in biofilm formation in Bacillus subtilis and has been predicted to produce C30 isoprenoids. We determined the structure of YisP and observed that it adopts the same fold as squalene and dehydrosqualene synthases. However, the first aspartate-rich motif found in essentially all isoprenoid synthases is aspartate poor in YisP and cannot catalyze head-to-head condensation reactions. We find that YisP acts as a phosphatase, catalyzing formation of farnesol from farnesyl diphosphate, and that it is the first phosphatase to adopt the fold seen in the head-to-head prenyl synthases. Farnesol restores biofilm formation in a Δyisp mutant and modifies lipid membrane structure similarly to the virulence factor staphyloxanthin. This work clarifies the role of YisP in biofilm formation and suggests an intriguing possibility that many of the YisP-like homologs found in other bacteria may also have interesting products and functions.
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15
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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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16
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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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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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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
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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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Meguro A, Tomita T, Nishiyama M, Kuzuyama T. Identification and characterization of bacterial diterpene cyclases that synthesize the cembrane skeleton. Chembiochem 2013; 14:316-21. [PMID: 23386483 PMCID: PMC3790952 DOI: 10.1002/cbic.201200651] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Indexed: 11/20/2022]
Affiliation(s)
- Ayuko Meguro
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan
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Ito R, Masukawa Y, Hoshino T. Purification, kinetics, inhibitors and CD for recombinant β-amyrin synthase fromEuphorbia tirucalli L and functional analysis of the DCTA motif, which is highly conserved among oxidosqualene cyclases. FEBS J 2013; 280:1267-80. [DOI: 10.1111/febs.12119] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/23/2012] [Accepted: 01/01/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Ryousuke Ito
- Graduate School of Science and Technology; Niigata University; Japan
| | - Yukari Masukawa
- Graduate School of Science and Technology; Niigata University; Japan
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21
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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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22
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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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23
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Oldfield E, Lin FY. Terpene biosynthesis: modularity rules. Angew Chem Int Ed Engl 2011; 51:1124-37. [PMID: 22105807 DOI: 10.1002/anie.201103110] [Citation(s) in RCA: 240] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Indexed: 01/10/2023]
Abstract
Terpenes are the largest class of small-molecule natural products on earth, and the most abundant by mass. Here, we summarize recent developments in elucidating the structure and function of the proteins involved in their biosynthesis. There are six main building blocks or modules (α, β, γ, δ, ε, and ζ) that make up the structures of these enzymes: the αα and αδ head-to-tail trans-prenyl transferases that produce trans-isoprenoid diphosphates from C(5) precursors; the ε head-to-head prenyl transferases that convert these diphosphates into the tri- and tetraterpene precursors of sterols, hopanoids, and carotenoids; the βγ di- and triterpene synthases; the ζ head-to-tail cis-prenyl transferases that produce the cis-isoprenoid diphosphates involved in bacterial cell wall biosynthesis; and finally the α, αβ, and αβγ terpene synthases that produce plant terpenes, with many of these modular enzymes having originated from ancestral α and β domain proteins. We also review progress in determining the structure and function of the two 4Fe-4S reductases involved in formation of the C(5) diphosphates in many bacteria, where again, highly modular structures are found.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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25
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Mafu S, Hillwig ML, Peters RJ. A novel labda-7,13e-dien-15-ol-producing bifunctional diterpene synthase from Selaginella moellendorffii. Chembiochem 2011; 12:1984-7. [PMID: 21751328 DOI: 10.1002/cbic.201100336] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Sibongile Mafu
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 4216 Molecular Biology Building, Ames, IA 50011, USA
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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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