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Yadav I, Rautela A, Gangwar A, Wagadre L, Rawat S, Kumar S. Enhancement of isoprene production in engineered Synechococcus elongatus UTEX 2973 by metabolic pathway inhibition and machine learning-based optimization strategy. BIORESOURCE TECHNOLOGY 2023; 387:129677. [PMID: 37579861 DOI: 10.1016/j.biortech.2023.129677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
An engineered Synechococcus elongatus UTEX 2973-IspS.IDI is used to enhance isoprene production through geranyl diphosphate synthase (CrtE) inhibition and process parameters (light intensity, NaHCO3 and growth temperature) optimization approach. A cumulative isoprene production of 1.21 mg/gDCW was achieved with productivity of 12.6 μg/gDCW/h in culture supplemented with 20 μg/mL alendronate. This inhibition strategy improvises the cumulative isoprene production 5.76-fold in presence of alendronate. The maximum cumulative production of isoprene is observed to be 5.22 and 6.20 mg/gDCW (54.4 and 64.6 μg/gDCW/h) at statistical and artificial neural network genetic algorithm (ANN-GA) optimized conditions, respectively. The overall increase of isoprene production is found to be 29.52-fold using an integrated approach of inhibition and ANN-GA optimization in comparison to unoptimized cultures without alendronate. This study reveals that alendronate use as a potential inhibitor and machine learning based optimization is a better approach in comparison to statistical optimization to enhance the isoprene production.
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Affiliation(s)
- Indrajeet Yadav
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Akhil Rautela
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Agendra Gangwar
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Lokesh Wagadre
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Shweta Rawat
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India
| | - Sanjay Kumar
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh 221005, India.
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Dive A, Singhal R, Srivastava S, Shukre K, James D, Shetty S. Isolation and functional characterization of novel isoprene synthase from Artocarpus heterophyllus (jackfruit). 3 Biotech 2023; 13:24. [PMID: 36573156 PMCID: PMC9789294 DOI: 10.1007/s13205-022-03441-7] [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: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Isoprene, a Natural Volatile Organic Compound (NVOC) is one of the chief by-products of plant metabolism with important applications in the synthesis of rubber and pharmaceuticals as a platform molecule. Isoprene was obtained earlier from petroleum sources; however, to synthesise it new fermentation-based strategies are being adopted. Bioinformatics tools were utilised to isolate the Isoprene Synthase (IspS) gene which converts the precursors Isopentenyl Diphosphate (IPP) and Dimethylallyl Diphosphate (DMAPP) into isoprene. Metabolic engineering strategies were to synthesise an isoprene-producing recombinant clone derived from Artocarpus heterophyllus (jackfruit). The functional characterization was done using the overexpression of the isoprene synthase gene in an Escherichia coli BL21 host. The recombinant clone, ISPS_GBL_001 (submitted to GenBank, National Centre for Biotechnology Information or NCBI) was used for fermentation in the batch and fed-batch mode to produce isoprene. Isoprene productivity of 0.08 g/g dextrose was obtained via the fed-batch mode maintaining the process parameters at optimum. The quantification and confirmation of isoprene was done using gas chromatography (GC) and GC-mass spectrometry (GC-MS) of the extracted sample, respectively. This study makes significant contribution to the ongoing research on bio-isoprene synthesis by highlighting a novel plant source of the IspS gene followed by, its successful expression in a recombinant host, validated by fermentation. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03441-7.
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Affiliation(s)
- Amol Dive
- Institute of Chemical Technology, Matunga, Mumbai, India
- Godavari Biorefineries Ltd., Mahape, Navi Mumbai, India
| | - Rekha Singhal
- Institute of Chemical Technology, Matunga, Mumbai, India
| | | | - Kedar Shukre
- Godavari Biorefineries Ltd., Mahape, Navi Mumbai, India
| | - Deepak James
- Godavari Biorefineries Ltd., Mahape, Navi Mumbai, India
| | - Sneha Shetty
- Godavari Biorefineries Ltd., Mahape, Navi Mumbai, India
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Isar J, Jain D, Joshi H, Dhoot S, Rangaswamy V. MICROBIAL isoprene production: an overview. World J Microbiol Biotechnol 2022; 38:122. [PMID: 35637362 DOI: 10.1007/s11274-022-03306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Isoprene, a volatile C5 hydrocarbon, is a precursor of synthetic rubber and an important building block for a variety of natural products, solely being produced by petrochemical routes. To mitigate the ever-increasing contribution of petrochemical industry to global warming through significant carbon (CO2) evolution, bio-based process for isoprene production using microbial cell factories have been explored. Highly efficient fermentation-based processes have been studied for little over a decade now with extensive research on the rational strain development for creating robust strains for commercial isoprene production. Most of these studies involved sugars as feedstocks and using naturally occurring isoprene pathways viz., mevalonate and methyl erythritol pathway in E. coli. Recent advances, driven by efforts in reducing environmental pollution, have focused on utilization of inorganic CO2 by cyanobacteria or syngas from waste gases by acetogens for isoprene production. This review endeavors to capture the latest relevant progress made in rational strain development, metabolic engineering and synthetic biology strategies used, challenges in fermentation process development at lab and commercial scale production of isoprene along with a future perspective pertaining to this area of research.
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Affiliation(s)
- Jasmine Isar
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Dharmendra Jain
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Harshvardhan Joshi
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Shrikant Dhoot
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Vidhya Rangaswamy
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India.
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Non-enzymatic formation of isoprene and 2-methyl-3-buten-2-ol (2-MBO) by manganese. Sci Rep 2022; 12:2465. [PMID: 35165356 PMCID: PMC8844067 DOI: 10.1038/s41598-022-06520-0] [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: 09/09/2021] [Accepted: 02/02/2022] [Indexed: 12/23/2022] Open
Abstract
It has been suggested that isoprene synthesis by isoprene synthase (IspS) proceeds via a substrate-assisted mechanism. The authors observed a non-enzymatic isoprene formation by Mn2+, which represents the basis of IspS enzyme reaction. Because IspS and many other terpene synthases require Mn2+ metal ions as cofactor, this study characterized the formation reaction for the first time. Metal ions including Mn2+ non-enzymatically produced both isoprene and 2-methyl-3-buten-2-ol (2-MBO) from dimethylallyl pyrophosphate (DMADP). Isoprene formation was most enhanced by Fe2+ and, to a lesser extent, by Mn2+ or Cu2+. Ni2+, Co2+, Mg2+, and Ba2+ exhibited a low activity to generate both isoprene and 2-MBO. The proportion of isoprene and 2-MBO varied with the Mn2+ concentration: isoprene predominated over 2-MBO at a higher Mn2+ concentration. Similarly, isoprene formation by Mn2+ increased exponentially as temperature increased with predominance of isoprene over 2-MBO at higher temperature. Both isoprene and 2-MBO formation was enhanced by acidic and neutral pH compared to alkaline conditions. Molecular dynamic simulation of DMADP suggested that the formation reaction is initiated by deprotonation of hydrogen on allyl terminal carbon by phosphate oxygen and generates carbocation and allyl anion intermediates. This is followed by quenching to produce isoprene or by hydroxyl addition to form 2-MBO. Thus, this study provided an insight into reaction mechanism of isoprene and 2-MBO biosynthesis and highlighted some parts of isoprene emission from terrestrial plants, which could be formed by non-enzymatic mechanism.
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Ashaari NS, Ab Rahim MH, Sabri S, Lai KS, Song AAL, Abdul Rahim R, Ong Abdullah J. Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus. Sci Rep 2021; 11:17094. [PMID: 34429465 PMCID: PMC8385045 DOI: 10.1038/s41598-021-96524-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Linalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis-Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10-3 µM-1 s-1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.
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Affiliation(s)
- Nur Suhanawati Ashaari
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Hairul Ab Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Industrial Biotechnology, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Kok Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012, Abu Dhabi, United Arab Emirates
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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Li M, Xu J, Lyu F, Khomenko I, Biasioli F, Villani M, Baldan B, Varotto C. Evolution of isoprene emission in Arecaceae (palms). Evol Appl 2021; 14:902-914. [PMID: 33897811 PMCID: PMC8061277 DOI: 10.1111/eva.13169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 01/05/2023] Open
Abstract
Isoprene synthase (IspS) is the sole enzyme in plants responsible for the yearly emission in the atmosphere of thousands of tonnes of the natural hydrocarbon isoprene worldwide. Species of the monocotyledonous family Arecaceae (palms) are among the highest plant emitters, but to date no IspS gene from this family has been identified. Here, we screened with PTR-ToF-MS 18 genera of the Arecaceae for isoprene emission and found that the majority of the sampled species emits isoprene. Putative IspS genes from six different genera were sequenced and three of them were functionally characterized by heterologous overexpression in Arabidopsis thaliana, demonstrating that they encode functional IspS genes. Site-directed mutagenesis and expression in Arabidopsis demonstrated the functional relevance of a novel IspS diagnostic tetrad from Arecaceae, whose most variable amino acids could not preserve catalytic function when substituted by a putatively dicotyledonous-specific tetrad. In particular, mutation of threonine 479 likely impairs the open-closed transition of the enzyme by altering the network of hydrogen bonds between helices H1α, H, and I. These results shed new light on the evolution of IspS in monocots, suggesting that isoprene emission is an ancestral trait within the Arecaceae family. The identification of IspS from Arecaceae provides promising novel enzymes for the production of isoprene in heterologous systems and allows the screening and selection of commercially relevant palm varieties with lower environmental impact.
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Affiliation(s)
- Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Jia Xu
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Fuling Lyu
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
- Experimental Center of Forestry in North ChinaChinese Academy of ForestryBeijingChina
| | - Iuliia Khomenko
- Department of Food Quality and Nutrition, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | - Franco Biasioli
- Department of Food Quality and Nutrition, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
| | | | - Barbara Baldan
- Botanical Garden of PadovaUniversity of PadovaPadovaItaly
- Department of BiologyUniversity of PadovaPadovaItaly
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeItaly
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Nagegowda DA, Gupta P. Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110457. [PMID: 32234216 DOI: 10.1016/j.plantsci.2020.110457] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/18/2020] [Accepted: 02/22/2020] [Indexed: 05/28/2023]
Abstract
Plant specialized terpenoids are natural products that have no obvious role in growth and development, but play many important functional roles to improve the plant's overall fitness. Besides, plant specialized terpenoids have immense value to humans due to their applications in fragrance, flavor, cosmetic, and biofuel industries. Understanding the fundamental aspects involved in the biosynthesis and regulation of these high-value molecules in plants not only paves the path to enhance plant traits, but also facilitates homologous or heterologous engineering for overproduction of target molecules of importance. Recent developments in functional genomics and high-throughput analytical techniques have led to unraveling of several novel aspects involved in the biosynthesis and regulation of plant specialized terpenoids. The knowledge thus derived has been successfully utilized to produce target specialized terpenoids of plant origin in homologous or heterologous host systems by metabolic engineering and synthetic biology approaches. Here, we provide an overview and highlights on advances related to the biosynthetic steps, regulation, and metabolic engineering of plant specialized terpenoids.
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Affiliation(s)
- Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
| | - Priyanka Gupta
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, 560065, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India
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