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Esquirol L, Newman J, Nebl T, Scott C, Vickers C, Sainsbury F, Peat TS. Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii. Acta Crystallogr D Struct Biol 2024; 80:203-215. [PMID: 38411551 PMCID: PMC10910542 DOI: 10.1107/s2059798324001360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.
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Affiliation(s)
- Lygie Esquirol
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Janet Newman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Tom Nebl
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin Scott
- Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Claudia Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
- Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
- Synbio Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Thomas S. Peat
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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2
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Esquirol L, McNeale D, Douglas T, Vickers CE, Sainsbury F. Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors. ACS Synth Biol 2022; 11:2709-2718. [PMID: 35880829 DOI: 10.1021/acssynbio.2c00117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein cages are attractive as molecular scaffolds for the fundamental study of enzymes and metabolons and for the creation of biocatalytic nanoreactors for in vitro and in vivo use. Virus-like particles (VLPs) such as those derived from the P22 bacteriophage capsid protein make versatile self-assembling protein cages and can be used to encapsulate a broad range of protein cargos. In vivo encapsulation of enzymes within VLPs requires fusion to the coat protein or a scaffold protein. However, the expression level, stability, and activity of cargo proteins can vary upon fusion. Moreover, it has been shown that molecular crowding of enzymes inside VLPs can affect their catalytic properties. Consequently, testing of numerous parameters is required for production of the most efficient nanoreactor for a given cargo enzyme. Here, we present a set of acceptor vectors that provide a quick and efficient way to build, test, and optimize cargo loading inside P22 VLPs. We prototyped the system using a yellow fluorescent protein and then applied it to mevalonate kinases (MKs), a key enzyme class in the industrially important terpene (isoprenoid) synthesis pathway. Different MKs required considerably different approaches to deliver maximal encapsulation as well as optimal kinetic parameters, demonstrating the value of being able to rapidly access a variety of encapsulation strategies. The vector system described here provides an approach to optimize cargo enzyme behavior in bespoke P22 nanoreactors. This will facilitate industrial applications as well as basic research on nanoreactor-cargo behavior.
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Affiliation(s)
- Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Claudia E Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane 4000 Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia
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Downregulation of Squalene Synthase Broadly Impacts Isoprenoid Biosynthesis in Guayule. Metabolites 2022; 12:metabo12040303. [PMID: 35448489 PMCID: PMC9030042 DOI: 10.3390/metabo12040303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023] Open
Abstract
Production of natural rubber by Parthenium argentaum (guayule) requires increased yield for economic sustainability. An RNAi gene silencing strategy was used to engineer isoprenoid biosynthesis by downregulation of squalene synthase (SQS), such that the pool of farnesyl diphosphate (FPP) substrate might instead be available to initiate natural rubber synthesis. Downregulation of SQS resulted in significantly reduced squalene and slightly increased rubber, but not in the same tissues nor to the same extent, partially due to an apparent negative feedback regulatory mechanism that downregulated mevalonate pathway isoprenoid production, presumably associated with excess geranyl pyrophosphate levels. A detailed metabolomics analysis of isoprenoid production in guayule revealed significant differences in metabolism in different tissues, including in active mevalonate and methylerythritol phosphate pathways in stem tissue, where rubber and squalene accumulate. New insights and strategies for engineering isoprenoid production in guayule were identified.
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Cho SH, Tóth K, Kim D, Vo PH, Lin CH, Handakumbura PP, Ubach AR, Evans S, Paša-Tolić L, Stacey G. Activation of the plant mevalonate pathway by extracellular ATP. Nat Commun 2022; 13:450. [PMID: 35064110 PMCID: PMC8783019 DOI: 10.1038/s41467-022-28150-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/10/2022] [Indexed: 12/28/2022] Open
Abstract
The mevalonate pathway plays a critical role in multiple cellular processes in both animals and plants. In plants, the products of this pathway impact growth and development, as well as the response to environmental stress. A forward genetic screen of Arabidopsis thaliana using Ca2+-imaging identified mevalonate kinase (MVK) as a critical component of plant purinergic signaling. MVK interacts directly with the plant extracellular ATP (eATP) receptor P2K1 and is phosphorylated by P2K1 in response to eATP. Mutation of P2K1-mediated phosphorylation sites in MVK eliminates the ATP-induced cytoplasmic calcium response, MVK enzymatic activity, and suppresses pathogen defense. The data demonstrate that the plasma membrane associated P2K1 directly impacts plant cellular metabolism by phosphorylation of MVK, a key enzyme in the mevalonate pathway. The results underline the importance of purinergic signaling in plants and the ability of eATP to influence the activity of a key metabolite pathway with global effects on plant metabolism. Products of the mevalonate pathway support plant development. Here the authors show that the extracellular ATP receptor P2K1 phosphorylates mevalonate kinase and this affects the mevalonate pathway.
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Arian R, Hariri A, Mehridehnavi A, Fassihi A, Ghasemi F. Protein kinase inhibitors' classification using K-Nearest neighbor algorithm. Comput Biol Chem 2020; 86:107269. [PMID: 32413830 DOI: 10.1016/j.compbiolchem.2020.107269] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 03/15/2020] [Accepted: 04/20/2020] [Indexed: 10/24/2022]
Abstract
Protein kinases are enzymes acting as a source of phosphate through ATP to regulate protein biological activities by phosphorylating groups of specific amino acids. For that reason, inhibiting protein kinases with an active small molecule plays a significant role in cancer treatment. To achieve this aim, computational drug design, especially QSAR model, is one of the best economical approaches to reduce time and save in costs. In this respect, active inhibitors are attempted to be distinguished from inactive ones using hybrid QSAR model. Therefore, genetic algorithm and K-Nearest Neighbor method were suggested as a dimensional reduction and classification model, respectively. Finally, to evaluate the proposed model's performance, support vector machine and Naïve Bayesian algorithm were examined. The outputs of the proposed model demonstrated significant superiority to other QSAR models.
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Affiliation(s)
- Roya Arian
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amirali Hariri
- School of Pharmacology and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alireza Mehridehnavi
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Afshin Fassihi
- School of Pharmacology and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fahimeh Ghasemi
- Department of Bioinformatics and Systems Biology, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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Islam MT, Mubarak MS. Diterpenes and their derivatives as promising agents against dengue virus and dengue vectors: A literature‐based review. Phytother Res 2019; 34:674-684. [DOI: 10.1002/ptr.6562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/13/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Muhammad Torequl Islam
- Department for Management of Science and Technology DevelopmentTon Duc Thang University Ho Chi Minh City Vietnam
- Faculty of PharmacyTon Duc Thang University Ho Chi Minh City Vietnam
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Nouzova M, Rivera-Pérez C, Noriega FG. Omics approaches to study juvenile hormone synthesis. CURRENT OPINION IN INSECT SCIENCE 2018; 29:49-55. [PMID: 30551825 PMCID: PMC6470398 DOI: 10.1016/j.cois.2018.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/23/2018] [Indexed: 05/04/2023]
Abstract
The juvenile hormones (JHs) are a family of insect acyclic sesquiterpenoids produced by the corpora allata (CA), a pair of endocrine glands connected to the brain. They are involved in the regulation of development, reproduction, behavior, caste determination, diapause, stress response, and numerous polyphenisms. In the post-genomics era, comprehensive analyses using functional 'omics' technologies such as transcriptomics, proteomics and metabolomics have increased our understanding of the activity of the minute CA. This review attempts to summarize some of the 'omics' studies that have contributed to further understand JH synthesis in insects, with an emphasis on our own research on the mosquito Aedes aegypti.
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Affiliation(s)
- Marcela Nouzova
- Department of Biological Sciences and Biomolecular Science Institute, Florida International University, Miami, FL, USA
| | | | - Fernando G Noriega
- Department of Biological Sciences and Biomolecular Science Institute, Florida International University, Miami, FL, USA.
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Zhang W, Ma L, Xiao H, Liu C, Chen L, Wu S, Liang G. Identification and characterization of genes involving the early step of Juvenile Hormone pathway in Helicoverpa armigera. Sci Rep 2017; 7:16542. [PMID: 29185447 PMCID: PMC5707400 DOI: 10.1038/s41598-017-16319-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/09/2017] [Indexed: 12/17/2022] Open
Abstract
Juvenile hormones (JHs) are crucial regulators for multiple physiological processes in insects. In the current study, 10 genes in mevalonate pathway involved in JH biosynthesis were identified from Helicoverpa armigera. Tissue-specific expression analysis showed that six genes were highly expressed in the head which contained the JH biosynthetic gland (corpora allata). Temporal expression pattern showed that 10 of 12 genes were highly transcribed in the late 2nd-instar when the in vivo JH titer reached the peak, indicating a tight correlation between JH titer and the transcription of JH synthetic pathway genes. Moreover, ingestion of methoprene, a JH analogue, significantly suppressed the transcription of nine JH biosynthetic genes and caused a feedback upregulation of the JH degradation enzyme. Particularly, the Acetoacetyl CoA thiolase (HaAce) and Farnesyl diphosphate synthase gene 4 (HaFpps4) showed high transcript abundance, and their temporal expressions keep pace with JH fluctuations. Further study by RNAi showed that knockdown of HaFpps4 caused the decrease of JH titer, led to a negative effect on the transcript levels of other genes in JH pathway, and resulted in molting disturbance in larvae. Altogether, these results contribute to our understanding of JH biosynthesis in H. armigera and provide target genes for pest control based on JH-dependent regulation.
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Affiliation(s)
- Wanna Zhang
- Institute of Entomology, Jiangxi Agricultural University, Nanchang, 330045, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Long Ma
- Jiangxi Key Laboratory of Bioprocess Engineering, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Haijun Xiao
- Institute of Entomology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaolong Wu
- China Tobacco Midsouth Agricultural Experimental Station, Changsha, 410128, China
| | - Gemei Liang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Hayakawa H, Sobue F, Motoyama K, Yoshimura T, Hemmi H. Identification of enzymes involved in the mevalonate pathway of Flavobacterium johnsoniae. Biochem Biophys Res Commun 2017; 487:702-708. [DOI: 10.1016/j.bbrc.2017.04.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
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Martínez-Rincón RO, Rivera-Pérez C, Diambra L, Noriega FG. Modeling the flux of metabolites in the juvenile hormone biosynthesis pathway using generalized additive models and ordinary differential equations. PLoS One 2017; 12:e0171516. [PMID: 28158248 PMCID: PMC5291429 DOI: 10.1371/journal.pone.0171516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/03/2017] [Indexed: 11/19/2022] Open
Abstract
Juvenile hormone (JH) regulates development and reproductive maturation in insects. The corpora allata (CA) from female adult mosquitoes synthesize fluctuating levels of JH, which have been linked to the ovarian development and are influenced by nutritional signals. The rate of JH biosynthesis is controlled by the rate of flux of isoprenoids in the pathway, which is the outcome of a complex interplay of changes in precursor pools and enzyme levels. A comprehensive study of the changes in enzymatic activities and precursor pool sizes have been previously reported for the mosquito Aedes aegypti JH biosynthesis pathway. In the present studies, we used two different quantitative approaches to describe and predict how changes in the individual metabolic reactions in the pathway affect JH synthesis. First, we constructed generalized additive models (GAMs) that described the association between changes in specific metabolite concentrations with changes in enzymatic activities and substrate concentrations. Changes in substrate concentrations explained 50% or more of the model deviances in 7 of the 13 metabolic steps analyzed. Addition of information on enzymatic activities almost always improved the fitness of GAMs built solely based on substrate concentrations. GAMs were validated using experimental data that were not included when the model was built. In addition, a system of ordinary differential equations (ODE) was developed to describe the instantaneous changes in metabolites as a function of the levels of enzymatic catalytic activities. The results demonstrated the ability of the models to predict changes in the flux of metabolites in the JH pathway, and can be used in the future to design and validate experimental manipulations of JH synthesis.
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Affiliation(s)
- Raúl O. Martínez-Rincón
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), CONACYT, La Paz, Baja California Sur, México
| | - Crisalejandra Rivera-Pérez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), CONACYT, La Paz, Baja California Sur, México
| | - Luis Diambra
- Centro Regional de Estudios Genómicos (CREG), UNLP, La Plata, Buenos Aires, Argentina
| | - Fernando G. Noriega
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
- Biomolecular Science Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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Identification of ten mevalonate enzyme-encoding genes and their expression in response to juvenile hormone levels in Leptinotarsa decemlineata (Say). Gene 2016; 584:136-47. [DOI: 10.1016/j.gene.2016.02.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 11/17/2022]
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