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The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast. BIOLOGY 2021; 10:biology10070632. [PMID: 34356487 PMCID: PMC8301174 DOI: 10.3390/biology10070632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Metabolic engineering involves the sustainable production of high-value products. E. coli and yeast, in particular, are used for such processes. Using metabolic engineering, the biosynthetic pathways of these cells are altered to obtain a high production of desired products. Fatty acids (FAs) and their derivatives are products produced using metabolic engineering. However, classical methods used for engineering yeast metabolic pathways for the production of fatty acids and their derivatives face problems such as the low supply of key precursors and product tolerance. This review introduces the different ways FAs are being produced in E. coli and yeast and the genetic manipulations for enhanced production of FAs. The review also summarizes the latest techniques (i.e., CRISPR–Cas and synthetic biology) for developing FA-producing yeast cell factories. Abstract Metabolic engineering is a cutting-edge field that aims to produce simple, readily available, and inexpensive biomolecules by applying different genetic engineering and molecular biology techniques. Fatty acids (FAs) play an important role in determining the physicochemical properties of membrane lipids and are precursors of biofuels. Microbial production of FAs and FA-derived biofuels has several advantages in terms of sustainability and cost. Conventional yeast Saccharomyces cerevisiae is one of the models used for FA synthesis. Several genetic manipulations have been performed to enhance the citrate accumulation and its conversation into acetyl-CoA, a precursor for FA synthesis. Success has been achieved in producing different chemicals, including FAs and their derivatives, through metabolic engineering. However, several hurdles such as slow growth rate, low oleaginicity, and cytotoxicity are still need to be resolved. More robust research needs to be conducted on developing microbes capable of resisting diverse environments, chemicals, and cost-effective feed requirements. Redesigning microbes to produce FAs with cutting-edge synthetic biology and CRISPR techniques can solve these problems. Here, we reviewed the technological progression of metabolic engineering techniques and genetic studies conducted on S. cerevisiae, making it suitable as a model organism and a great candidate for the production of biomolecules, especially FAs.
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Cloutier M, Xiang D, Gao P, Kochian LV, Zou J, Datla R, Wang E. Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642938. [PMID: 33889166 PMCID: PMC8056077 DOI: 10.3389/fpls.2021.642938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed metabolism and to identify underpinning genetic targets for engineering the traits associated with seed oil composition and content. Here, we present a dynamic model, using an Ordinary Differential Equations model and integrated time-course gene expression data, to describe metabolic networks during Arabidopsis thaliana seed development. Through in silico perturbation of genes, targets were predicted in seed oil traits. Validation and supporting evidence were obtained for several of these predictions using published reports in the scientific literature. Furthermore, we investigated two predicted targets using omics datasets for both gene expression and metabolites from the seed embryo, and demonstrated the applicability of this network-based model. This work highlights that integration of dynamic gene expression atlases generates informative models which can be explored to dissect metabolic pathways and lead to the identification of causal genes associated with seed oil traits.
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Affiliation(s)
- Mathieu Cloutier
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edwin Wang
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
- Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Vanhercke T, Dyer JM, Mullen RT, Kilaru A, Rahman MM, Petrie JR, Green AG, Yurchenko O, Singh SP. Metabolic engineering for enhanced oil in biomass. Prog Lipid Res 2019; 74:103-129. [PMID: 30822461 DOI: 10.1016/j.plipres.2019.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023]
Abstract
The world is hungry for energy. Plant oils in the form of triacylglycerol (TAG) are one of the most reduced storage forms of carbon found in nature and hence represent an excellent source of energy. The myriad of applications for plant oils range across foods, feeds, biofuels, and chemical feedstocks as a unique substitute for petroleum derivatives. Traditionally, plant oils are sourced either from oilseeds or tissues surrounding the seed (mesocarp). Most vegetative tissues, such as leaves and stems, however, accumulate relatively low levels of TAG. Since non-seed tissues constitute the majority of the plant biomass, metabolic engineering to improve their low-intrinsic TAG-biosynthetic capacity has recently attracted significant attention as a novel, sustainable and potentially high-yielding oil production platform. While initial attempts predominantly targeted single genes, recent combinatorial metabolic engineering strategies have focused on the simultaneous optimization of oil synthesis, packaging and degradation pathways (i.e., 'push, pull, package and protect'). This holistic approach has resulted in dramatic, seed-like TAG levels in vegetative tissues. With the first proof of concept hurdle addressed, new challenges and opportunities emerge, including engineering fatty acid profile, translation into agronomic crops, extraction, and downstream processing to deliver accessible and sustainable bioenergy.
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Affiliation(s)
- Thomas Vanhercke
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia.
| | - John M Dyer
- USDA-ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, USA
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - Md Mahbubur Rahman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - James R Petrie
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia; Folear, Goulburn, NSW, Australia
| | - Allan G Green
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Olga Yurchenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Surinder P Singh
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
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Liang MH, Jiang JG. Characterization and nitrogen deficiency response of ATP-citrate lyase from unicellular alga Dunaliella tertiolecta. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Tan KWM, Lee YK. The dilemma for lipid productivity in green microalgae: importance of substrate provision in improving oil yield without sacrificing growth. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:255. [PMID: 27895709 PMCID: PMC5120525 DOI: 10.1186/s13068-016-0671-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 05/02/2023]
Abstract
Rising oil prices and concerns over climate change have resulted in more emphasis on research into renewable biofuels from microalgae. Unlike plants, green microalgae have higher biomass productivity, will not compete with food and agriculture, and do not require fertile land for cultivation. However, microalgae biofuels currently suffer from high capital and operating costs due to low yields and costly extraction methods. Microalgae grown under optimal conditions produce large amounts of biomass but with low neutral lipid content, while microalgae grown in nutrient starvation accumulate high levels of neutral lipids but are slow growing. Producing lipids while maintaining high growth rates is vital for biofuel production because high biomass productivity increases yield per harvest volume while high lipid content decreases the cost of extraction per unit product. Therefore, there is a need for metabolic engineering of microalgae to constitutively produce high amounts of lipids without sacrificing growth. Substrate availability is a rate-limiting step in balancing growth and fatty acid (FA) production because both biomass and FA synthesis pathways compete for the same substrates, namely acetyl-CoA and NADPH. In this review, we discuss the efforts made for improving biofuel production in plants and microorganisms, the challenges faced in achieving lipid productivity, and the important role of precursor supply for FA synthesis. The main focus is placed on the enzymes which catalyzed the reactions supplying acetyl-CoA and NADPH.
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Affiliation(s)
- Kenneth Wei Min Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545 Singapore
| | - Yuan Kun Lee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545 Singapore
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Zhang H, Zhang L, Chen H, Chen YQ, Chen W, Song Y, Ratledge C. Enhanced lipid accumulation in the yeast Yarrowia lipolytica by over-expression of ATP:citrate lyase from Mus musculus. J Biotechnol 2015; 192 Pt A:78-84. [PMID: 25450640 DOI: 10.1016/j.jbiotec.2014.10.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/15/2014] [Accepted: 10/01/2014] [Indexed: 12/18/2022]
Abstract
Yarrowia lipolytica can accumulate large amounts of storage lipids and has considerable potential for the production of polyunsaturated fatty acids and other lipids for biofuels. When the nitrogen source is exhausted in the medium, the key intermediate, citrate, is converted to acetyl-CoA by ATP:citrate lyase (ACL) for lipid accumulation. However, in this yeast most of the citrate is also secreted into the culture medium. To increase the endogenous substrate (acetyl-CoA) level for lipid biosynthesis, the acl gene from Mus musculus was over-expressed in Y. lipolytica with mono-copy integration vector pINA1312sp and multi-copy integration vector pINA1292sp. This increased the lipid content from 7.3% to between 11% and 23% (w/w) of the cell dry weight. Cell growth was only slightly affected. Multi-copy integration transformants had higher lipid contents than mono-copy integration transformants; the lipid content of the transformants was consistent with the copy number of acl gene integrated. Over-expression of ACL had no significant effect on fatty acid profile of the yeast. These results suggested that ACL is an important acetyl-CoA producer and plays a vital role in lipid accumulation in oleaginous yeast Y. lipolytica.
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Hegde K, Chandra N, Sarma SJ, Brar SK, Veeranki VD. Genetic Engineering Strategies for Enhanced Biodiesel Production. Mol Biotechnol 2015; 57:606-24. [DOI: 10.1007/s12033-015-9869-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Dey P, Mall N, Chattopadhyay A, Chakraborty M, Maiti MK. Enhancement of lipid productivity in oleaginous Colletotrichum fungus through genetic transformation using the yeast CtDGAT2b gene under model-optimized growth condition. PLoS One 2014; 9:e111253. [PMID: 25375973 PMCID: PMC4222912 DOI: 10.1371/journal.pone.0111253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/27/2014] [Indexed: 01/17/2023] Open
Abstract
Oleaginous fungi are of special interest among microorganisms for the production of lipid feedstocks as they can be cultured on a variety of substrates, particularly waste lingocellulosic materials, and few fungal strains are reported to accumulate inherently higher neutral lipid than bacteria or microalgae. Previously, we have characterized an endophytic filamentous fungus Colletotrichum sp. DM06 that can produce total lipid ranging from 34% to 49% of its dry cell weight (DCW) upon growing with various carbon sources and nutrient-stress conditions. In the present study, we report on the genetic transformation of this fungal strain with the CtDGAT2b gene, which encodes for a catalytically efficient isozyme of type-2 diacylglycerol acyltransferase (DGAT) from oleaginous yeast Candida troplicalis SY005. Besides the increase in size of lipid bodies, total lipid titer by the transformed Colletotrichum (lipid content ∼73% DCW) was found to be ∼1.7-fold more than the wild type (lipid content ∼38% DCW) due to functional activity of the CtDGAT2b transgene when grown under standard condition of growth without imposition of any nutrient-stress. Analysis of lipid fractionation revealed that the neutral lipid titer in transformants increased up to 1.8-, 1.6- and 1.5-fold compared to the wild type when grown under standard, nitrogen stress and phosphorus stress conditions, respectively. Lipid titer of transformed cells was further increased to 1.7-fold following model-based optimization of culture conditions. Taken together, ∼2.9-fold higher lipid titer was achieved in Colletotrichum fungus due to overexpression of a rate-limiting crucial enzyme of lipid biosynthesis coupled with prediction-based bioprocess optimization.
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Affiliation(s)
- Prabuddha Dey
- Adv. Lab. for Plant Genetic Engineering, Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Nikunj Mall
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Atrayee Chattopadhyay
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Monami Chakraborty
- Adv. Lab. for Plant Genetic Engineering, Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mrinal K. Maiti
- Adv. Lab. for Plant Genetic Engineering, Advanced Technology Development Center, Indian Institute of Technology Kharagpur, Kharagpur, India
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
- * E-mail:
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Sunaga Y, Maeda Y, Yabuuchi T, Muto M, Yoshino T, Tanaka T. Chloroplast-targeting protein expression in the oleaginous diatom Fistulifera solaris JPCC DA0580 toward metabolic engineering. J Biosci Bioeng 2014; 119:28-34. [PMID: 25043335 DOI: 10.1016/j.jbiosc.2014.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/12/2014] [Accepted: 06/13/2014] [Indexed: 01/12/2023]
Abstract
The chloroplast plays critical roles in lipid metabolism of microalgae, thus it is recognized as an attractive target of metabolic engineering to enhance biofuel production. It has been well known that recombinant protein expression in microalgal chloroplasts needs specific signal sequence which governs the transition manner of nuclear-encoded polypeptides within the subcellular compartments. However certain microalgae, including diatoms, have complex membrane systems surrounding the chloroplast, and thus chloroplast-targeting protein expression with the signal sequence has rarely been demonstrated except for a few model non-oleaginous diatoms. In this study, we performed recombinant green fluorescence protein (GFP) expression and transportation into the chloroplast of the oleaginous marine diatom, Fistulifera solaris JPCC DA0580. The signal sequence of ATP synthetase gamma subunit, which was predicted to localize in the chloroplast according to a bioinformatics analysis pipeline, was employed as a key factor of this technique. As a result, specific localization of GFP in the chloroplast was observed. It would be useful to engineer the lipid synthesis pathways existing in the chloroplast. Furthermore, intensive gathering of GFP in the rod-like structure was also detected, which has not been observed in model diatom studies. As comparing with electron microscopic observation, the structure was estimated to be a pyrenoid.
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Affiliation(s)
- Yoshihiko Sunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan; Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), 5, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Takashi Yabuuchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaki Muto
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan; Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), 5, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan; Japan Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), 5, Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan.
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Geng Z, Zhu W, Su H, Zhao Y, Zhang KQ, Yang J. Recent advances in genes involved in secondary metabolite synthesis, hyphal development, energy metabolism and pathogenicity in Fusarium graminearum (teleomorph Gibberella zeae). Biotechnol Adv 2014; 32:390-402. [DOI: 10.1016/j.biotechadv.2013.12.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 11/11/2013] [Accepted: 12/16/2013] [Indexed: 01/01/2023]
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Allen DK, Young JD. Carbon and nitrogen provisions alter the metabolic flux in developing soybean embryos. PLANT PHYSIOLOGY 2013; 161:1458-75. [PMID: 23314943 PMCID: PMC3585609 DOI: 10.1104/pp.112.203299] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 01/09/2013] [Indexed: 05/19/2023]
Abstract
Soybean (Glycine max) seeds store significant amounts of their biomass as protein, levels of which reflect the carbon and nitrogen received by the developing embryo. The relationship between carbon and nitrogen supply during filling and seed composition was examined through a series of embryo-culturing experiments. Three distinct ratios of carbon to nitrogen supply were further explored through metabolic flux analysis. Labeling experiments utilizing [U-(13)C5]glutamine, [U-(13)C4]asparagine, and [1,2-(13)C2]glucose were performed to assess embryo metabolism under altered feeding conditions and to create corresponding flux maps. Additionally, [U-(14)C12]sucrose, [U-(14)C6]glucose, [U-(14)C5]glutamine, and [U-(14)C4]asparagine were used to monitor differences in carbon allocation. The analyses revealed that: (1) protein concentration as a percentage of total soybean embryo biomass coincided with the carbon-to-nitrogen ratio; (2) altered nitrogen supply did not dramatically impact relative amino acid or storage protein subunit profiles; and (3) glutamine supply contributed 10% to 23% of the carbon for biomass production, including 9% to 19% of carbon to fatty acid biosynthesis and 32% to 46% of carbon to amino acids. Seed metabolism accommodated different levels of protein biosynthesis while maintaining a consistent rate of dry weight accumulation. Flux through ATP-citrate lyase, combined with malic enzyme activity, contributed significantly to acetyl-coenzyme A production. These fluxes changed with plastidic pyruvate kinase to maintain a supply of pyruvate for amino and fatty acids. The flux maps were independently validated by nitrogen balancing and highlight the robustness of primary metabolism.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetic Research Unit, St. Louis, MO 63132, USA.
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Tang X, Feng H, Chen WN. Metabolic engineering for enhanced fatty acids synthesis in Saccharomyces cerevisiae. Metab Eng 2013; 16:95-102. [PMID: 23353549 DOI: 10.1016/j.ymben.2013.01.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 01/04/2013] [Accepted: 01/09/2013] [Indexed: 01/23/2023]
Abstract
Microbial production of biofuel has attracted significant attention in recent years. The fatty acids are important precursors for the production of fuels and chemicals, and its biosynthesis is initiated by the conversion of acetyl-CoA to malonyl-CoA which requires acetyl-CoA as key substrate. Herein, the yeast Saccharomyces cerevisiae was proposed to be metabolically engineered for cytosol acetyl-CoA enhancement for fatty acid synthesis. By gene disruption strategy, idh1 and idh2 genes involved in citrate turnover in tricarboxylic acid cycle (TCA cycle) were disrupted and the citrate production level was increased to 4- and 5-times in mutant yeast strains. In order to convert accumulated citrate to cytosol acetyl-CoA, a heterologous ATP-citrate lyase (ACL) was overexpressed in yeast wild type and idh1,2 disrupted strains. The wild type strain expressing acl mainly accumulated saturated fatty acids: C14:0, C16:0 and C18:0 at levels about 20%, 14% and 27%, respectively. Additionally, the idh1,2 disrupted strains expressing acl mainly accumulated unsaturated fatty acids. Specifically in Δidh1 strain expressing acl, 80% increase in C16:1 and 60% increase in C18:1 was detected. In Δidh2 strain expressing acl, 60% increase in C16:1 and 45% increase in C18:1 was detected. In Δidh1/2 strain expressing acl, there was 92% increase in C16:1 and 77% increase in C18:1, respectively. The increased fatty acids from our study may well be potential substrates for the production of hydrocarbon molecules as potential biofuels.
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Affiliation(s)
- Xiaoling Tang
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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Lin H, Wang Q, Shen Q, Zhan J, Zhao Y. Genetic engineering of microorganisms for biodiesel production. Bioengineered 2012; 4:292-304. [PMID: 23222170 DOI: 10.4161/bioe.23114] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Biodiesel, as one type of renewable energy, is an ideal substitute for petroleum-based diesel fuel and is usually made from triacylglycerides by transesterification with alcohols. Biodiesel production based on microbial fermentation aiming to establish more efficient, less-cost and sustainable biodiesel production strategies is under current investigation by various start-up biotechnology companies and research centers. Genetic engineering plays a key role in the transformation of microbes into the desired cell factories with high efficiency of biodiesel production. Here, we present an overview of principal microorganisms used in the microbial biodiesel production and recent advances in metabolic engineering for the modification required. Overexpression or deletion of the related enzymes for de novo synthesis of biodiesel is highlighted with relevant examples.
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Affiliation(s)
- Hui Lin
- Institute of Microbiology; College of Life Sciences; Zhejiang University; Hangzhou, China; Institute of Plant Science; College of Life Sciences; Zhejiang University; Hangzhou, China
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Ferreira SJ, Sonnewald U. The mode of sucrose degradation in potato tubers determines the fate of assimilate utilization. FRONTIERS IN PLANT SCIENCE 2012; 3:23. [PMID: 22639642 PMCID: PMC3355675 DOI: 10.3389/fpls.2012.00023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/20/2012] [Indexed: 05/10/2023]
Abstract
Cytosolic (U-IN-2) or apoplasmic (U-IN-1) targeting of yeast invertase in potato tubers leads to a reduction in sucrose and an increase in glucose content, but specific phenotypical changes are dependent on the subcellular targeting of the enzyme. Cytosolic expression leads to a more severe phenotype with the most striking aspects being reduced starch content and increased respiration. Despite extensive research, the regulatory mechanisms leading to these changes remain obscure. Recent technological advancements regarding potato transcriptional and genomic research presented us with the opportunity to revisit these lines and perform detailed gene expression analysis, in combination with extensive metabolic profiling, to identify regulatory networks underlying the observed changes. Our results indicate that in both genotypes reduced UDP-glucose production is associated with a reduced expression of cell wall biosynthetic genes. In addition, U-IN-1 tubers are characterized by elevated expression of senescence-associated genes, coupled to reduced expression of genes related to photosynthesis and the cytoskeleton. We provide evidence that increased respiration, observed specifically in U-IN-2 tubers, might be due to sugar signaling via released trehalose-6-phosphate inhibition of the SnRK1 complex. In both genotypes, expression of the plastidic glucose-6-phosphate transporter (GPT) is significantly down-regulated. This leads to a shift in the cytosolic to plastidic glucose-6-phosphate ratio and hence might limit starch synthesis but also the oxidative pentose phosphate pathway. This might explain the observed changes in several additional plastid localized pathways, most notably reduced expression of fatty acid biosynthetic genes and an accumulation of shikimate. Interestingly, a strict negative correlation between invertase and GPT expression could be observed in a wide range of potato tubers. This reciprocal regulation may be part of a more general switch controlling energy versus storage metabolism, suggesting that the fate of assimilate utilization is coordinated at the level of sucrose degradation.
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Affiliation(s)
- Stephanus J. Ferreira
- Biochemistry Division, Department Biology, Friedrich-Alexander-University Erlangen-NurembergErlangen, Germany
| | - Uwe Sonnewald
- Biochemistry Division, Department Biology, Friedrich-Alexander-University Erlangen-NurembergErlangen, Germany
- *Correspondence: Uwe Sonnewald, Biochemistry Division, Department Biology, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstrasse 5, Erlangen 91058, Germany. e-mail:
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Miao Y, Ding Y, Sun QY, Xu ZF, Jiang L. Plant bioreactors for pharmaceuticals. Biotechnol Genet Eng Rev 2011; 25:363-80. [PMID: 21412362 DOI: 10.5661/bger-25-363] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plant bioreactors are attractive expression systems for economic production of pharmaceuticals. Various plant expression systems or platforms have been tested with certain degrees of success over the past years. However, further development and improvement are needed for more effective plant bioreactors. In this review we first summarize recent progress in various plant bioreactor expression systems and then focus on discussing protein compartmentation to unique organelles and various strategies for developing better plant bioreactors.
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Affiliation(s)
- Yansong Miao
- Department of Biology and Molecular Biotechnology Program, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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16
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Courchesne NMD, Parisien A, Wang B, Lan CQ. Enhancement of lipid production using biochemical, genetic and transcription factor engineering approaches. J Biotechnol 2009; 141:31-41. [PMID: 19428728 DOI: 10.1016/j.jbiotec.2009.02.018] [Citation(s) in RCA: 257] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 02/15/2009] [Accepted: 02/20/2009] [Indexed: 01/03/2023]
Abstract
This paper compares three possible strategies for enhanced lipid overproduction in microalgae: the biochemical engineering (BE) approaches, the genetic engineering (GE) approaches, and the transcription factor engineering (TFE) approaches. The BE strategy relies on creating a physiological stress such as nutrient-starvation or high salinity to channel metabolic fluxes to lipid accumulation. The GE strategy exploits our understanding to the lipid metabolic pathway, especially the rate-limiting enzymes, to create a channelling of metabolites to lipid biosynthesis by overexpressing one or more key enzymes in recombinant microalgal strains. The TFE strategy is an emerging technology aiming at enhancing the production of a particular metabolite by means of overexpressing TFs regulating the metabolic pathways involved in the accumulation of target metabolites. Currently, BE approaches are the most established in microalgal lipid production. The TFE is a very promising strategy because it may avoid the inhibitive effects of the BE approaches and the limitation of "secondary bottlenecks" as commonly observed in the GE approaches. However, it is still a novel concept to be investigated systematically.
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Fu SX, Cheng H, Qi C. Microarray analysis of gene expression in seeds of Brassica napus planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m) with different oil content. Mol Biol Rep 2009; 36:2375-86. [PMID: 19219639 DOI: 10.1007/s11033-009-9460-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Accepted: 02/02/2009] [Indexed: 10/21/2022]
Abstract
The regulation of seed oil synthesis in rapeseed is largely unknown. In this study, Arabidopsis microarray was used to analyze the gene differential expression of the immature seeds 30 days after flowering of a high oil Brassica napus, H105, whose oil content was 46.04 +/- 1.42, 53.94 +/- 1.35 and 53.09 +/- 1.35% when planted in Nanjing (altitude: 8.9 m), Xining (altitude: 2261.2 m) and Lhasa (altitude: 3658 m), respectively. Transcript levels of 363 genes and 421 genes were altered twofold or more for H105 planted in Xining and Lhasa compared to that in Nanjing, respectively. Together, there were 53 common up-regulated and 42 common down-regulated expression transcripts shared by H105 planted in Xining and Lhasa compared to that in Nanjing. Some important genes, such as sucrose synthase, pyruvate kinase and 6-phosphogluconate dehydrogenase which related to sugar metabolism were identified common up-regulated in higher oil content H105. These results revealed the expressional disciplinarian of correlative genes, and provided important information of the molecular genetic mechanism of oil content difference of rapeseed. In addition, these differential expression genes could be suitable as targets for genetic improvement of seed oil content.
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Affiliation(s)
- San-Xiong Fu
- Nanjing Sub-Center (Rapeseed) of National Center of Oilseeds Crop Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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Metabolic Engineering of the Content and Fatty Acid Composition of Vegetable Oils. BIOENGINEERING AND MOLECULAR BIOLOGY OF PLANT PATHWAYS 2008. [DOI: 10.1016/s1755-0408(07)01007-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Zhang Y, Adams IP, Ratledge C. Malic enzyme: the controlling activity for lipid production? Overexpression of malic enzyme in Mucor circinelloides leads to a 2.5-fold increase in lipid accumulation. MICROBIOLOGY-SGM 2007; 153:2013-2025. [PMID: 17600047 DOI: 10.1099/mic.0.2006/002683-0] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Malic enzyme (ME; NADP(+)-dependent; EC 1 . 1 . 1 . 40) has been postulated to be the rate-limiting step for fatty acid biosynthesis in oleaginous fungi in which the extent of lipid accumulation is below the maximum possible. The genes encoding the isoform of ME involved in fatty acid synthesis were identified in Mucor circinelloides and Mortierella alpina, two commercially useful oil-producing fungi, using degenerate primers. Both showed high similarity with ME genes from other micro-organisms. The whole-length ME gene from each source was cloned into a leucine auxotroph of Mc. circinelloides and placed under the control of the constitutive glyceraldehyde-3-phosphate dehydrogenase gene (gpd1) promoter. After confirming correct expression of the ME genes, the two recombinant strains were grown in fully controlled, submerged-culture bioreactors using a high C : N ratio medium for lipid accumulation. Activities of ME were increased by two- to threefold and the lipid contents of the cells, in both recombinants, were increased from 12 % of the biomass to 30 %. Simultaneously, the degree of fatty acid desaturation increased slightly. Thus, increased expression of the ME gene leads to both increased biosynthesis of fatty acids and formation of unsaturated fatty acids, including gamma-linolenic acid (18 : 3 n-6). At the end of lipid accumulation (96 h), ME activity in the recombinant strains had ceased, as it had done in the parent wild-type cells, indicating that additional, but unknown, controls over its activity must be in place to account for this loss of activity: this may be due to the presence of a specific ME-cleaving enzyme. The hypothesis that the rate-limiting step of fatty acid biosynthesis is therefore the supply of NADPH, as generated specifically and solely by ME, is therefore considerably strengthened by these results.
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Affiliation(s)
- Ying Zhang
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Ian P Adams
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
| | - Colin Ratledge
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
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Li RJ, Wang HZ, Mao H, Lu YT, Hua W. Identification of differentially expressed genes in seeds of two near-isogenic Brassica napus lines with different oil content. PLANTA 2006; 224:952-62. [PMID: 16575595 DOI: 10.1007/s00425-006-0266-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Accepted: 03/09/2006] [Indexed: 05/08/2023]
Abstract
The regulation of seed oil synthesis in rapeseed is largely unknown. In this study, we compared the gene expression during seed development between two lines of Brassica napus with a 10% difference in oil content. We isolated the immature seeds 15 and 25 days after flowering at periods preceding and including the major accumulation of storage oils and proteins. The differentially expressed gene clones between the two rape lines were isolated by subtractive suppression hybridization (SSH). All SSH clones were arrayed and screened by dot blot hybridization, followed by RT-PCR analysis for selected clones. A total of 217 cDNA clones corresponding to 30 genes were found to have a high expression in seeds with high oil content. Six genes were highly expressed in seeds with low oil content. Northern blot and enzyme activity analysis demonstrated a change in expression pattern of several genes. The results provide information on gene-encoding factors responsible for the regulation of oil synthesis. The possible role of these genes in seeds is discussed. The genes in this study may be suitable as novel targets for genetic improvement of seed oil content and may also provide molecular markers for studies of rape breeding.
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Affiliation(s)
- Rong-Jun Li
- Institute of Oil Crops Research, Chinese Academy of Agriculture Sciences, Wuhan 430062, China
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Ratledge C, Wynn JP. The biochemistry and molecular biology of lipid accumulation in oleaginous microorganisms. ADVANCES IN APPLIED MICROBIOLOGY 2003; 51:1-51. [PMID: 12236054 DOI: 10.1016/s0065-2164(02)51000-5] [Citation(s) in RCA: 531] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Colin Ratledge
- Lipid Research Centre, Department of Biological Sciences, University of Hull, HU6 7RX, United Kingdom
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Abstract
Non-green plastids are important sites for the biosynthesis of starch and fatty acids, which are essential for plant development and reproduction, and have a significant role in human nutrition. Unlike chloroplasts, all the metabolites for these processes in non-green plastids have to be imported via specific transport proteins. Recent advances in unravelling the molecular structures and substrate specificities of the transporters connecting the biochemical pathways between cytosol and stroma now make it possible to develop models for metabolic fluxes in these pathways. The basic principle of adapting the transport capacities of the plastid envelope to the physiological needs of the plant is the variable production of closely related transporters with overlapping substrate specificities.
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Affiliation(s)
- Karsten Fischer
- University of Cologne, Botanical Institute, Cologne, Germany.
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Adams IP, Dack S, Dickinson FM, Ratledge C. The distinctiveness of ATP:citrate lyase from Aspergillus nidulans. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:36-41. [PMID: 12009400 DOI: 10.1016/s0167-4838(02)00276-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATP:citrate lyase (ACL), an important enzyme in lipid synthesis, has been purified from Aspergillus nidulans to a specific activity of 19.6 micromol min(-1) mg(-1), almost twice that of any other purified ACL and shown to be distinct from any previously purified ACL. The enzyme is a 371+/-31 kDa hexamer of 3 alpha, 3 beta proteins, unlike the 4 alpha tetramer found in rats or yeasts. The molecular weights of the alpha and beta protein subunits were determined by SDS-PAGE to be 70 and 55 kDa. ACL in A. nidulans (unlike Aspergillus niger) appears to be regulated by the carbon source present in the media. In crude extracts, it was found at high activity (88 micromol min(-1) mg protein(-1)) in glucose-grown cells but only at low activity (10 micromol min(-1) mg protein(-1)) in acetate-grown cells.
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Affiliation(s)
- Ian P Adams
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK.
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Abstract
The de novo synthesis of fatty acids in plants occurs in the plastids through the activity of fatty acid synthetase. The synthesis of the malonyl-coenzyme A that is required for acyl-chain elongation requires the import of metabolites from the cytosol and their subsequent metabolism. Early studies had implicated acetate as the carbon source for plastidial fatty acid synthesis but more recent experiments have provided data that argue against this. A range of cytosolic metabolites including glucose 6-phosphate, malate, phosphoenolpyruvate and pyruvate support high rates of fatty acid synthesis by isolated plastids, the relative utilisation of which depends upon the plant species and the organ from which the plastids are isolated. The import of these metabolites occurs via specific transporters on the plastid envelope and recent advances in the understanding of the role of these transporters are discussed. Chloroplasts are able to generate the reducing power and ATP required for fatty acid synthesis by capture of light energy in the reactions of photosynthetic electron transport. Regulation of chloroplast fatty acid synthesis is mediated by the response of acetyl-CoA carboxylase to the redox state of the plastid, which ensures that the carbon metabolism is linked to the energy status. The regulation of fatty acid synthesis in plastids of heterotrophic cells is much less well understood and is of particular interest in the tissues that accumulate large amounts of the storage oil, triacylglycerol. In these heterotrophic cells the plastids import ATP and oxidise imported carbon sources to produce the required reducing power. The sequencing of the genome of Arabidopsis thaliana has now enabled a number of aspects of plant fatty acid synthesis to be re-addressed, particularly those areas in which in vitro biochemical analysis had provided equivocal answers. Examples of such aspects and future opportunities for our understanding of plant fatty acid synthesis are presented and discussed.
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Affiliation(s)
- Stephen Rawsthorne
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Colney, NR4 7UH, Norwich, UK.
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Wynn JP, Hamid AA, Li Y, Ratledge C. Biochemical events leading to the diversion of carbon into storage lipids in the oleaginous fungi Mucor circinelloides and Mortierella alpina. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2857-2864. [PMID: 11577164 DOI: 10.1099/00221287-147-10-2857] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The biochemical events associated with the onset of lipid accumulation in Mucor circinelloides and Mortierella alpina, under conditions of nitrogen-limited growth, have been elucidated; they differ in key aspects from those described in oleaginous yeasts. The NAD+:isocitrate dehydrogenases of Mc. circinelloides and Mort. alpina were not absolutely dependent on AMP for activity. Furthermore, changes in the cellular adenine nucleotide pools and energy charge were different from those reported for oleaginous yeasts. In Mc. circinelloides ATP, ADP and AMP concentrations all decreased by 50% after nitrogen limitation, leading to a constant energy charge at the expense of the size of the total adenylate pool. Pyruvate carboxylase in Mc. circinelloides was cytosolic, having implications for the organization of lipid synthesis in filamentous fungi. As a result of the data obtained, a revised and more concerted mechanism for the initiation of storage lipid accumulation is put forward for filamentous fungi.
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Affiliation(s)
- James P Wynn
- Centre for Advanced Lipid Research, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK1
| | - Adil A Hamid
- Department of Microbiology, Universitii Kebangsaan, Malaysia, 43600 Bangi, Salangor Darul Ehsan, Malaysia2
| | - Yonghua Li
- Centre for Advanced Lipid Research, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK1
| | - Colin Ratledge
- Centre for Advanced Lipid Research, Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK1
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Rangasamy D, Ratledge C. Compartmentation of ATP:citrate lyase in plants. PLANT PHYSIOLOGY 2000; 122:1225-30. [PMID: 10759519 PMCID: PMC58958 DOI: 10.1104/pp.122.4.1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/1999] [Accepted: 12/16/1999] [Indexed: 05/20/2023]
Abstract
Extracts prepared from young leaves of Pea (Pisum sativum), tobacco (Nicotiana tabacum), rape (Brassica napus), and spinach (Spinacia oleracea) all contained ATP:citrate lyase (ACL) activity, which was most active in rape leaflets (130 nmol min(-1) g fresh weight). In rape and spinach, ACL activity was predominantly localized in the plastids (between about 78% and 90% of the total activity), whereas in pea and tobacco, distribution was mainly cytosolic (about 85% and 78%, respectively, of the total). These distributions were calculated from the relative distributions of plastid and cytosol marker enzymes. Cross-reactivity between plant and rat ACL antibody was carried out by immunoblot analysis and, in rape and spinach, showed that a 120-kD protein, presumably indicating homomeric ACL proteins, was present in both cytosolic and plastidic fractions. In pea, two cross-reacting proteins were detected, the major material being in the cytosol fraction. Therefore, ACL occurs both in the cytosol and plastids of higher plants, but the distribution of activity changes according to the species. The plastidic ACL is proposed to function for the supply of acetyl-coenzyme A for lipid biosynthesis de novo, whereas the cytosolic ACL may provide acetyl-coenzyme A for the mevalonate pathway or fatty acid elongation.
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Affiliation(s)
- D Rangasamy
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, United Kingdom
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