PhD student, Indian Institute of Technology Madras (IIT Madras)
Increasing Vitamin-E content in plants by metabolic engineering and process optimization strategies
Plants are natural producers of several medicinally important high-value compounds (eg: Antimalarial drug Artemesinin). They can be grown in lab as uniform cells/tissues mimicking attributes of whole plants at a large scale in limited space under controlled conditions. This is called as plant tissue culture. We can make them produce high quantity of desired/known/novel compounds by tinkering their metabolic pathways that produce the compound and/or by optimizing process conditions (nutrient composition for their growth, environment parameters such as temperature etc.).
Develop strategies to enhance Vitamin E content of plant cells using sunflower as a model system.
Why Vitamin E?
It is an essential(not produced in human body) dietary component of humans, the deficiency of which leads to diseases, It is sold as Vitamin E supplements. It is also used widely in cosmetics as it helps to prevent tissue damage from oxidative stress and in animal feed additives.
Why plant cells?
Chemical synthesis yields a less active than natural form of Vitamin E produced by plants. Green plants especially oilseeds are rich source of vitamin E. In particular, sunflower produces more of the active component of Vitamin E, namely alpha-tocopherol. Sunflower cells are also amenable to process optimization, vitamin E pathway engineering studies and scale-up to larger volumes
What tools do i employ?
Firstly, i use the sunflower genome (represents the genetic material) information to employ computational tools to identify gene targets - a rational genome scale modeling based approach instead of random hit and trial method for enhancing vitamin-E content. This is followed by it's experimental verification in lab which results in high vitamin E producing "metabolically engineered" sunflower cells. I use statistical bioprocess optimization studies in small volumes to further enhance the yield of Vitamin E in these cells. I finally use the optimized process for scaling up to larger volumes in bioreactors.
This technique can be applied to further enhance other high value byproducts/compounds that make sunflower a better candidate for biofuel production/biofortification of sunflower crops
Abstract: Vitamin E is a potent lipid-soluble antioxidant and essential nutrient for human health. Tocotrienols are the major form of vitamin E in seeds of most monocots. It has been known that homogentisate geranylgeranyl transferase (HGGT) catalyzes the committed step of tocotrienol biosynthesis. In the present study, we generated transgenic barley overexpressing HvHGGT under endogenous D-Hordein promoter (proHor). Overexpression of HvHGGT increased seed size and seed weight in transgenic barley. Notably, total tocotrienol content increased by 10-15% in seeds of transgenic lines, due to the increased levels of δ-, β- and γ-tocotrienol, but not α-tocotrienol. Total tocopherol content decreased by 14-18% in transgenic lines, compared to wild type. The antioxidant activity of seeds was determined by using 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS), and lipid peroxidation assays. Compared to wild type, radical scavenging activity of seed extracts was enhanced by 17-18% in transgenic lines. Meanwhile, the lipid peroxidation level was decreased by about 20% in transgenic barley seeds. Taken together, overexpression of HvHGGT enhanced the tocotrienol levels and antioxidant capacity in barley seeds.
Pub.: 06 Jun '17, Pinned: 30 Sep '17
Abstract: Vitamin E refers to four tocopherols and four tocotrienols that are exclusively synthesized by photosynthetic organisms. While α-tocopherol is the most potent vitamin E compound, it is not the main form consumed since the composition of most major crops is dominated by γ-tocopherol. Nutritional studies show that populations of developed countries do not consume enough vitamin E and that a large proportion of individuals exhibit plasma α-tocopherol deficiency. Following the identification of vitamin E biosynthetic genes, several strategies including metabolic engineering, classic breeding and mutation breeding, have been undertaken to improve the vitamin E content of crops. In addition to providing crops in which vitamin E content is enhanced, these studies are revealing the bottlenecks limiting its biosynthesis.
Pub.: 23 Mar '17, Pinned: 30 Sep '17
Abstract: Nargenicin A1, an antibacterial produced by Nocardia sp. CS682 (KCTC 11297BP), demonstrates effective activity against various Gram-positive bacteria. Hence, we attempted to enhance nargenicin A1 production by utilizing the cumulative effect of synthetic biology, metabolic engineering and statistical media optimization strategies. To facilitate the modular assembly of multiple genes for genetic engineering in Nocardia sp. CS682, we constructed a set of multi-monocistronic vectors, pNV18L1 and pNV18L2 containing hybrid promoter (derived from ermE* and promoter region of neo (r) ), ribosome binding sites (RBS), and restriction sites for cloning, so that each cloned gene was under its own promoter and RBS. The multi-monocistronic vector, pNV18L2 containing transcriptional terminator showed better efficiency in reporter gene assay. Thus, multiple genes involved in the biogenesis of pyrrole moiety (ngnN2, ngnN3, ngnN4, and ngnN5 from Nocardia sp. CS682), glucose utilization (glf and glk from Zymomonas mobilis), and malonyl-CoA synthesis (accA2 and accBE from Streptomyces coelicolor A3 (2)), were cloned in pNV18L2. Further statistical optimization of specific precursors (proline and glucose) and their feeding time led to ~84.9 mg/L nargenicin from Nocardia sp. GAP, which is ~24-fold higher than Nocardia sp. CS682 (without feeding). Furthermore, pikC from Streptomyces venezuelae was expressed to generate Nocardia sp. PikC. Nargenicin A1 acid was characterized as novel derivative of nargenicin A1 produced from Nocardia sp. PikC by mass spectrometry (MS) and nuclear magnetic resonance (NMR) analyses. We also performed comparative analysis of the anticancer and antibacterial activities of nargenicin A1 and nargenicin A1 acid, which showed a reduction in antibacterial potential for nargenicin A1 acid. Thus, the development of an efficient synthetic biological platform provided new avenues for enhancing or structurally diversifying nargenicin A1 by means of pathway designing and engineering.
Pub.: 15 Jul '16, Pinned: 01 Sep '17
Abstract: Plant cell suspension cultures are widely used for the production of recombinant proteins and secondary metabolites. One of the most important steps during process development is the optimization of yields by testing different cultivation parameters, including the components of the growth medium. However, we have shown that the biomass yield of a cell suspension culture derived from the pear cultivar Pyrus communis cv. Champagner Bratbirne can be significantly improved solely by varying the temperature, inoculum density, illumination, and incubation time. In contrast to medium optimization, these simple physical factors are easily controlled and varied, thereby reducing the effort required. Using an experimental design approach, we improved the biomass yield from 146 g fresh weight (FW)/L to 407 g FW/L in only 5 weeks, simultaneously reducing the costs of goods sold per kg biomass from €125 to €45. Our simple approach therefore offers a rapid, efficient and economical process for the optimization of plant cell suspension cultures.
Pub.: 19 Mar '16, Pinned: 31 Aug '17
Abstract: Genome-scale metabolic networks have been reconstructed for several organisms. These metabolic networks provide detailed information about the metabolism inside the cells, coupled with the genomic, proteomic and thermodynamic information. These networks are widely simulated using 'constraint-based' modelling techniques and find applications ranging from strain improvement for metabolic engineering to prediction of drug targets in pathogenic organisms. Components of these metabolic networks are represented in multiple file formats and also using different markup languages, with varying levels of annotations; this leads to inconsistencies and increases the complexities in comparing and analysing reconstructions on multiple platforms. In this work, we critically examine nearly 100 published genome-scale metabolic networks and their corresponding constraint-based models and discuss various issues with respect to model quality. One of the major concerns is the lack of annotations using standard identifiers that can uniquely describe several components such as metabolites, genes, proteins and reactions. We also find that many models do not have complete information regarding constraints on reactions fluxes and objective functions for carrying out simulations. Overall, our analysis highlights the need for a widely acceptable standard for representing constraint-based models. A rigorous standard can help in streamlining the process of reconstruction and improve the quality of reconstructed metabolic models.
Pub.: 01 Mar '15, Pinned: 01 Sep '17
Abstract: Great strides have been made in plant metabolic engineering over the last two decades, with notable success stories including Golden rice. Here, we discuss the field's progress in addressing four long-standing challenges: creating plants that satisfy their own nitrogen requirement, so reducing or eliminating the need for nitrogen fertilizer; enhancing the nutrient content of crop plants; engineering biofuel feed stocks that harbor easy-to-access fermentable saccharides by incorporating self-destructing lignin; and increasing photosynthetic efficiency. We also look to the future at emerging areas of research in this field.
Pub.: 11 Jun '14, Pinned: 30 Sep '17
Abstract: The present study involved strategies for enhancement in in vitro azadirachtin (commercially used biopesticide) production by hairy root cultivation of Azadirachta indica. Improvement in the azadirachtin production via triggering its biosynthetic pathway in plant cells was carried out by the exogenous addition of precursors and elicitors in the growth medium. Among the different abiotic stress inducers (Ag(+), Hg(+2), Co(+2), Cu(+2)) and signal molecules (methyl jasmonate and salicylic acid) tested, salicylic acid at 15 mg l(-1) of concentration was found to enhance the azadirachtin yield in the hairy roots to the maximum (up to 4.95 mg g(-1)). Similarly, among the different biotic elicitors tested (filter-sterilized fungal culture filtrates of Phoma herbarium, Alternaria alternata, Myrothecium sp., Fusarium solani, Curvularia lunata, and Sclerotium rolfsii; yeast extract; and yeast extract carbohydrate fraction), addition of filter-sterilized fungal culture filtrate of C. lunata (1 % v/v) resulted in maximum azadirachtin yield enhancement in hairy root biomass (up to 7.1 mg g(-1)) with respect to the control (3.3 mg g(-1)). Among all the biosynthetic precursors studied (sodium acetate, cholesterol, squalene, isopentynyl pyrophosphate, mavalonic acid lactone, and geranyl pyrophosphate), the overall azadirachtin production (70.42 mg l(-1) in 25 days) was found to be the highest with cholesterol (50 mg l(-1)) addition as an indirect precursor in the medium.
Pub.: 21 Dec '13, Pinned: 01 Sep '17
Abstract: While steady-state (13)C metabolic flux analysis is a powerful method for deducing multiple fluxes in the central metabolic network of heterotrophic and mixotrophic plant tissues, it is also time-consuming and technically challenging. Key steps in the design and interpretation of steady-state (13)C labeling experiments are illustrated with a generic protocol based on applications to plant cell suspension cultures.
Pub.: 14 Nov '13, Pinned: 01 Sep '17
Abstract: Plant metabolic engineering is commonly used in the production of functional foods and quality trait improvement. However, to date, computational model-based approaches have only been scarcely used in this important endeavor, in marked contrast to their prominent success in microbial metabolic engineering. In this study we present a computational pipeline for the reconstruction of fully compartmentalized tissue-specific models of Arabidopsis thaliana on a genome scale. This reconstruction involves automatic extraction of known biochemical reactions in Arabidopsis for both primary and secondary metabolism, automatic gap-filling, and the implementation of methods for determining subcellular localization and tissue assignment of enzymes. The reconstructed tissue models are amenable for constraint-based modeling analysis, and significantly extend upon previous model reconstructions. A set of computational validations (i.e., cross-validation tests, simulations of known metabolic functionalities) and experimental validations (comparison with experimental metabolomics datasets under various compartments and tissues) strongly testify to the predictive ability of the models. The utility of the derived models was demonstrated in the prediction of measured fluxes in metabolically engineered seed strains and the design of genetic manipulations that are expected to increase vitamin E content, a significant nutrient for human health. Overall, the reconstructed tissue models are expected to lay down the foundations for computational-based rational design of plant metabolic engineering. The reconstructed compartmentalized Arabidopsis tissue models are MIRIAM-compliant and are available upon request.
Pub.: 21 Dec '11, Pinned: 31 Aug '17
Abstract: Azadirachtin, a well-known biopesticide, is a secondary metabolite extracted from the seeds of Azadirachta indica. In the present study, azadirachtin was produced in hairy roots of A. indica, generated by Agrobacterium rhizogenes-mediated transformation of leaf explants. Liquid cultures of A. indica hairy roots were developed with a liquid-to-flask volume ratio of 0.15. The kinetics of growth and azadirachtin production were established in a basal plant growth medium containing MS medium major and minor salts, Gamborg’s medium vitamins, and 30 g l−1 sucrose. The highest azadirachtin accumulation in the hairy roots (up to 3.3 mg g−1) and azadirachtin production (∼44 mg l−1) was obtained on Day 25 of the growth cycle, with a biomass production of 13.3 g l−1 dry weight. To enhance the production of azadirachtin, a Plackett–Burman experimental design protocol was used to identify key medium nutrients and concentrations to support high root biomass production and azadirachtin accumulation in hairy roots. The optimal nutrients and concentrations were as follows: 40 g l−1 sucrose, 0.19 g l−1 potassium dihydrogen phosphate, 3.1 g l−1 potassium nitrate, and 0.41 g l−1 magnesium sulfate. Concentrations were determined by a central composite design protocol and verified in shake-flask cultivation. The optimized medium composition yielded a root biomass production of 14.2 g l−1 and azadirachtin accumulation of 5.2 mg g−1, which was equivalent to an overall azadirachtin production of 73.84 mg l−1, 68% more than that obtained under non-optimized conditions.
Pub.: 10 Sep '11, Pinned: 01 Sep '17
Abstract: The identification of genes to be deleted or amplified is an essential step in metabolic engineering for strain improvement toward the enhanced production of desired bioproducts. In the past, several methods based on flux analysis of genome-scale metabolic models have been developed for identifying gene targets for deletion. Genome-wide identification of gene targets for amplification, on the other hand, has been rather difficult. Here, we report a strategy called flux scanning based on enforced objective flux (FSEOF) to identify gene amplification targets. FSEOF scans all the metabolic fluxes in the metabolic model and selects fluxes that increase when the flux toward product formation is enforced as an additional constraint during flux analysis. This strategy was successfully employed for the identification of gene amplification targets for the enhanced production of the red-colored antioxidant lycopene. Additional metabolic engineering based on gene knockout simulation resulted in further synergistic enhancement of lycopene production. Thus, FSEOF can be used as a general strategy for selecting genome-wide gene amplification targets in silico.
Pub.: 30 Mar '10, Pinned: 01 Sep '17
Abstract: Tocopherols, collectively known as vitamin E, are lipophilic antioxidants, essential dietary components for mammals and exclusively synthesized by photosynthetic organisms. Of the four forms (alpha, beta, gamma and delta), alpha-tocopherol is the major vitamin E form present in green plant tissues, and has the highest vitamin E activity. Synthetic alpha-tocopherol, being a racemic mixture of eight different stereoisomers, always results less effective than the natural form (R,R,R) alpha-tocopherol. This raises interest in obtaining this molecule from natural sources, such as plant cell cultures. Plant cell and tissue cultures are able to produce and accumulate valuable metabolites that can be used as food additives, nutraceuticals and pharmaceuticals. Sunflower cell cultures, growing under heterotrophic conditions, were exploited to establish a suitable in vitro production system of natural alpha-tocopherol. Optimization of culture conditions, precursor feeding and elicitor application were used to improve the tocopherol yields of these cultures. Furthermore, these cell cultures were useful to investigate the relationship between alpha-tocopherol biosynthesis and photomixotrophic culture conditions, revealing the possibility to enhance tocopherol production by favouring sunflower cell photosynthetic properties. The modulation of alpha-tocopherol levels in plant cell cultures can provide useful hints for a regulatory impact on tocopherol metabolism.
Pub.: 19 Feb '10, Pinned: 31 Aug '17
Abstract: The presence of cytosolic and plastidic pathways of carbohydrate oxidation is a characteristic feature of plant cell metabolism. Ideally, steady-state metabolic flux analysis, an emerging tool for creating flux maps of heterotrophic plant metabolism, would capture this feature of the metabolic phenotype, but the extent to which this can be achieved is uncertain. To address this question, fluxes through the pathways of central metabolism in a heterotrophic Arabidopsis (Arabidopsis thaliana) cell suspension culture were deduced from the redistribution of label in steady-state (13)C-labeling experiments using [1-(13)C]-, [2-(13)C]-, and [U-(13)C(6)]glucose. Focusing on the pentose phosphate pathway (PPP), multiple data sets were fitted simultaneously to models in which the subcellular compartmentation of the PPP was altered. The observed redistribution of the label could be explained by any one of three models of the subcellular compartmentation of the oxidative PPP, but other biochemical evidence favored the model in which the oxidative steps of the PPP were duplicated in the cytosol and plastids, with flux through these reactions occurring largely in the cytosol. The analysis emphasizes the inherent difficulty of analyzing the PPP without predefining the extent of its compartmentation and the importance of obtaining high-quality data that report directly on specific subcellular processes. The Arabidopsis flux map also shows that the potential ATP yield of respiration in heterotrophic plant cells can greatly exceed the direct metabolic requirements for biosynthesis, highlighting the need for caution when predicting flux through metabolic networks using assumptions based on the energetics of resource utilization.
Pub.: 27 Nov '09, Pinned: 01 Sep '17
Abstract: Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.
Pub.: 17 Mar '09, Pinned: 01 Sep '17
Abstract: Tocochromanols are a group of four tocopherols and four tocotrienols that collectively constitute vitamin E, an essential nutrient in the human diet. Tocochromanols are only synthesized in oxygenic photosynthetic organisms. Although they have similar antioxidant activities in vitro, the individual tocochromanols vary widely in their in vivo vitamin E activities. During the past several years, mutant and transgenic approaches in model organisms, particularly in Arabidopsis thaliana and Synechocystis sp. PCC6803, have allowed the full complement of core pathway genes to be isolated and studied. Pathway engineering with these genes has provided significant insights into the molecular genetic and biochemical control of tocochromanol biosynthesis in plants. The resulting knowledge base is driving efforts to manipulate the levels of this essential nutrient in staple crops for populations in the developed and developing world.
Pub.: 18 Nov '05, Pinned: 31 Aug '17
Abstract: The advent of genome-scale models of metabolism has laid the foundation for the development of computational procedures for suggesting genetic manipulations that lead to overproduction. In this work, the computational OptKnock framework is introduced for suggesting gene deletion strategies leading to the overproduction of chemicals or biochemicals in E. coli. This is accomplished by ensuring that a drain towards growth resources (i.e., carbon, redox potential, and energy) must be accompanied, due to stoichiometry, by the production of a desired product. Computational results for gene deletions for succinate, lactate, and 1,3-propanediol (PDO) production are in good agreement with mutant strains published in the literature. While some of the suggested deletion strategies are straightforward and involve eliminating competing reaction pathways, many others suggest complex and nonintuitive mechanisms of compensating for the removed functionalities. Finally, the OptKnock procedure, by coupling biomass formation with chemical production, hints at a growth selection/adaptation system for indirectly evolving overproducing mutants.
Pub.: 05 Nov '03, Pinned: 01 Sep '17