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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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2
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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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Alvarez-Eraso KLF, Muñoz-Martínez LM, Alzate JF, Barrera LF, Baena A. Modulatory Impact of the sRNA Mcr11 in Two Clinical Isolates of Mycobacterium tuberculosis. Curr Microbiol 2022; 79:39. [PMID: 34982251 DOI: 10.1007/s00284-021-02733-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen causing tuberculosis (TB) disease in humans. It has been shown, that some circulating strains of Mtb in TB endemic populations, are more virulent and more transmissible than others, which may be related to their evolved adaptations to modulate the host immune responses. Underlying these adaptations to the stressful conditions, different genetic regulatory networks involved sRNAs that are mostly unknown for Mtb. We have previously shown that Mcr11 is one of the main sRNAs that determine transcriptomic differences among the Colombian clinical isolates UT127 and UT205 compared to the laboratory strain H37Rv. We found that the knock-down of mcr11 using CRISPRi has a major impact on phenotypic traits, especially in the clinical isolate UT205. Through the analysis of RNA-seq during the knock-down of mcr11 in UT205, we found a downregulation of genes mainly involved in lipid synthesis, lipid metabolism, ribosomal proteins, transport systems, respiratory and energy systems, membrane and cell wall components, intermediary metabolism, lipoproteins and virulence genes. One of the most interesting genes showing transcriptomic changes is OprA (encoded by the gene rv0516c), which has been involved in the K+ regulation. Overall, our data may suggest that one of the prominent roles of the sRNA Mcr11 is to regulate genes that control Mtb growth and osmoregulation.
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Affiliation(s)
| | | | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia
- Centro Nacional de Secuenciación Genómica-CNSG, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
- Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia.
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia.
- Sede de Investigación Universitaria-SIU, Medellín, Colombia.
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4
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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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5
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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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6
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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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7
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Metabolite Profiling: A Tool for the Biochemical Characterisation of Mycobacterium sp. Microorganisms 2019; 7:microorganisms7050148. [PMID: 31130621 PMCID: PMC6560386 DOI: 10.3390/microorganisms7050148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/25/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last decades, the prevalence of drug-resistance in Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has increased. These findings have rekindled interest in elucidating the unique adaptive molecular and biochemistry physiology of Mycobacterium. The use of metabolite profiling independently or in combination with other levels of "-omic" analyses has proven an effective approach to elucidate key physiological/biochemical mechanisms associated with Mtb throughout infection. The following review discusses the use of metabolite profiling in the study of tuberculosis, future approaches, and the technical and logistical limitations of the methodology.
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8
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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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9
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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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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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11
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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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12
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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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Structure, function and inhibition of ent-kaurene synthase from Bradyrhizobium japonicum. Sci Rep 2014; 4:6214. [PMID: 25269599 PMCID: PMC4180811 DOI: 10.1038/srep06214] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/07/2014] [Indexed: 11/12/2022] Open
Abstract
We report the first X-ray crystal structure of ent-kaur-16-ene synthase from Bradyrhizobium japonicum, together with the results of a site-directed mutagenesis investigation into catalytic activity. The structure is very similar to that of the α domains of modern plant terpene cyclases, a result that is of interest since it has been proposed that many plant terpene cyclases may have arisen from bacterial diterpene cyclases. The ent-copalyl diphosphate substrate binds to a hydrophobic pocket near a cluster of Asp and Arg residues that are essential for catalysis, with the carbocations formed on ionization being protected by Leu, Tyr and Phe residues. A bisphosphonate inhibitor binds to the same site. In the kaurene synthase from the moss Physcomitrella patens, 16-α-hydroxy-ent-kaurane as well as kaurene are produced since Leu and Tyr in the P. patens kaurene synthase active site are replaced by smaller residues enabling carbocation quenching by water. Overall, the results represent the first structure determination of a bacterial diterpene cyclase, providing insights into catalytic activity, as well as structural comparisons with diverse terpene synthases and cyclases which clearly separate the terpene cyclases from other terpene synthases having highly α-helical structures.
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14
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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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15
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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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16
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Kurtböke DI, French JRJ, Hayes RA, Quinn RJ. Eco-taxonomic insights into actinomycete symbionts of termites for discovery of novel bioactive compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 147:111-35. [PMID: 24817085 DOI: 10.1007/10_2014_270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics" sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics" science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia.
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Affiliation(s)
- D Ipek Kurtböke
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia,
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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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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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