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Sreenikethanam A, Raj S, J RB, Gugulothu P, Bajhaiya AK. Genetic Engineering of Microalgae for Secondary Metabolite Production: Recent Developments, Challenges, and Future Prospects. Front Bioeng Biotechnol 2022; 10:836056. [PMID: 35402414 PMCID: PMC8984019 DOI: 10.3389/fbioe.2022.836056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 12/19/2022] Open
Abstract
Microalgae are highly diverse photosynthetic organisms with higher growth rate and simple nutritional requirements. They are evolved with an efficiency to adapt to a wide range of environmental conditions, resulting in a variety of genetic diversity. Algae accounts for nearly half of global photosynthesis, which makes them a crucial player for CO2 sequestration. In addition, they have metabolic capacities to produce novel secondary metabolites of pharmaceutical, nutraceutical and industrial applications. Studies have explored the inherent metabolic capacities of microalgae with altered growth conditions for the production of primary and secondary metabolites. However, the production of the targeted metabolites at higher rates is not guaranteed just with the inherent genetic potentials. The strain improvement using genetic engineering is possible hope to overcome the conventional methods of culture condition improvements for metabolite synthesis. Although the advanced gene editing tools are available, the gene manipulation of microalgae remains relatively unexplored. Among the performed gene manipulations studies, most of them focus on primary metabolites with limited focus on secondary metabolite production. The targeted genes can be overexpressed to enhance the production of the desired metabolite or redesigning them using the synthetic biology. A mutant (KOR1) rich in carotenoid and lipid content was developed in a recent study employing mutational breeding in microalgae (Kato, Commun. Biol, 2021, 4, 450). There are lot of challenges in genetic engineering associated with large algal diversity but the numerous applications of secondary metabolites make this field of research very vital for the biotech industries. This review, summarise all the genetic engineering studies and their significance with respect to secondary metabolite production from microalgae. Further, current genetic engineering strategies, their limitations and future strategies are also discussed.
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Affiliation(s)
- Arathi Sreenikethanam
- Algal Biotechnology Lab, Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thirvarur, India
| | - Subhisha Raj
- Algal Biotechnology Lab, Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thirvarur, India
| | - Rajesh Banu J
- Department of Biotechnology, Central University of Tamil Nadu, Thirvarur, India
| | | | - Amit K Bajhaiya
- Algal Biotechnology Lab, Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Thirvarur, India
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2
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A critical perspective on the scope of interdisciplinary approaches used in fourth-generation biofuel production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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3
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赵 宇. Applications of Systems Biology in Bioremediation. INTERNATIONAL JOURNAL OF ECOLOGY 2021. [DOI: 10.12677/ije.2021.104062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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Fayyaz M, Chew KW, Show PL, Ling TC, Ng IS, Chang JS. Genetic engineering of microalgae for enhanced biorefinery capabilities. Biotechnol Adv 2020; 43:107554. [PMID: 32437732 DOI: 10.1016/j.biotechadv.2020.107554] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
Microalgae-based bioproducts are in limelight because of their promising future, novel characteristics, the current situation of population needs, and rising prices of rapidly depleting energy resources. Algae-based products are considered as clean sustainable energy and food resources. At present, they are not commercialized due to their high production cost and low yield. In recent years, novel genome editing tools like RNAi, ZNFs, TALENs, and CRISPR/Cas9 are used to enhance the quality and quantity of the desired products. Genetic and metabolic engineering are frequently applied because of their rapid and precise results than random mutagenesis. Omic approaches help enhance biorefinery capabilities and are now in the developing stage for algae. The future is very bright for transgenic algae with increased biomass yield, carbon dioxide uptake rate, accumulating high-value compounds, reduction in cultivation, and production costs, thus reaching the goal in the global algal market and capital flow. However, microalgae are primary producers and any harmful exposure to the wild strains can affect the entire ecosystem. Therefore, strict regulation and monitoring are required to assess the potential risks before introducing genetically modified microalgae into the natural ecosystem.
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Affiliation(s)
- Mehmooda Fayyaz
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Kit Wayne Chew
- School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900 Sepang, Selangor, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Tau Chuan Ling
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan.
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6
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Nagappan S, Tsai PC, Devendran S, Alagarsamy V, Ponnusamy VK. Enhancement of biofuel production by microalgae using cement flue gas as substrate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:17571-17586. [PMID: 31512119 DOI: 10.1007/s11356-019-06425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
The cement industry generates a substantial amount of gaseous pollutants that cannot be treated efficiently and economically using standard techniques. Microalgae, a promising bioremediation and biodegradation agent used as feedstock for biofuel production, can be used for the biotreatment of cement flue gas. In specific, components of cement flue gas such as carbon dioxide, nitrogen, and sulfur oxides are shown to serve as nutrients for microalgae. Microalgae also have the capacity to sequestrate heavy metals present in cement kiln dust, adding further benefits. This work provides an extensive overview of multiple approaches taken in the inclusion of microalgae biofuel production in the cement sector. In addition, factors influencing the production of microalgal biomass are also described in such an integrated plant. In addition, process limitations such as the adverse impact of flue gas on medium pH, exhaust gas toxicity, and efficient delivery of carbon dioxide to media are also discussed. Finally, the article concludes by proposing the future potential for incorporating the microalgae biofuel plant into the cement sector.
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Affiliation(s)
- Senthil Nagappan
- Department of Biotechnology, Sri Venkateswara College of Engineering (Autonomous - Affiliated to Anna University), Sriperumbudur, Tamil Nadu, 602 117, India
| | - Pei-Chien Tsai
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan 1st Road, Sanmin District, Kaohsiung City, 807, Taiwan
| | - Saravanan Devendran
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Vardhini Alagarsamy
- Department of Biotechnology, Sri Venkateswara College of Engineering (Autonomous - Affiliated to Anna University), Sriperumbudur, Tamil Nadu, 602 117, India
| | - Vinoth Kumar Ponnusamy
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, No. 100, Shiquan 1st Road, Sanmin District, Kaohsiung City, 807, Taiwan.
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung City, 807, Taiwan.
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Sahoo S, Mahapatra SR, Das N, Parida BK, Rath S, Misra N, Suar M. Functional elucidation of hypothetical proteins associated with lipid accumulation: Prioritizing genetic engineering targets for improved algal biofuel production. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101887] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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8
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Valorization of microalgae biomass as a potential source of high-value sugars and polyalcohols. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Kato Y, Fujihara Y, Vavricka CJ, Chang JS, Hasunuma T, Kondo A. Light/dark cycling causes delayed lipid accumulation and increased photoperiod-based biomass yield by altering metabolic flux in oleaginous Chlamydomonas sp. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:39. [PMID: 30828384 PMCID: PMC6383270 DOI: 10.1186/s13068-019-1380-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Light/dark cycling is an inevitable outdoor culture condition for microalgal biofuel production; however, the influence of this cycling on cellular lipid production has not been clearly established. The general aim of this study was to determine the influence of light/dark cycling on microalgal biomass production and lipid accumulation. To achieve this goal, specific causative mechanisms were investigated using a metabolomics approach. Laboratory scale photoautotrophic cultivations of the oleaginous green microalga Chlamydomonas sp. JSC4 were performed under continuous light (LL) and light/dark (LD) conditions. RESULTS Lipid accumulation and carbohydrate degradation were delayed under the LD condition compared with that under the LL condition. Metabolomic analysis revealed accumulation of phosphoenolpyruvate and decrease of glycerol 3-phosphate under the LD condition, suggesting that the imbalance of these metabolites is a source of delayed lipid accumulation. When accounting for light dosage, biomass yield under the LD condition was significantly higher than that under the LL condition. Dynamic metabolic profiling showed higher levels of lipid/carbohydrate anabolism (including production of 3-phosphoglycerate, fructose 6-phosphate, glucose 6-phosphate, phosphoenolpyruvate and acetyl-CoA) from CO2 under the LD condition, indicating higher CO2 fixation than that of the LL condition. CONCLUSIONS Photoperiods define lipid accumulation and biomass production, and light/dark cycling was determined as a critical obstacle for lipid production in JSC4. Conversions of phosphoenolpyruvate to pyruvate and 3-phosphoglycerate to glycerol 3-phosphate are the candidate rate-limiting steps responsible for delayed lipid accumulation. The accumulation of substrates including ribulose 5-phosphate could be explained by the close relationship of increased biomass yield with enhanced CO2 fixation. The present study investigated the influence of light/dark cycling on lipid production by direct comparison with continuous illumination for the first time, and revealed underlying metabolic mechanisms and candidate metabolic rate-limiting steps during light/dark cycling. These findings suggest promising targets to metabolically engineer improved lipid production.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Yusuke Fujihara
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Christopher J. Vavricka
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 701 Taiwan
- Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, 701 Taiwan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
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Behera B, Acharya A, Gargey IA, Aly N, P B. Bioprocess engineering principles of microalgal cultivation for sustainable biofuel production. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biteb.2018.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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11
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Li N, Zhang Y, Meng H, Li S, Wang S, Xiao Z, Chang P, Zhang X, Li Q, Guo L, Igarashi Y, Luo F. Characterization of Fatty Acid Exporters involved in fatty acid transport for oil accumulation in the green alga Chlamydomonas reinhardtii. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:14. [PMID: 30651755 PMCID: PMC6330502 DOI: 10.1186/s13068-018-1332-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/06/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND In the past few decades, microalgae biofuel has become one of the most interesting sources of renewable energy. However, the higher cost of microalgae biofuel compared to that of petroleum prevented microalgae biofuel production. Therefore, the research on increasing lipid productivity from microalgae becomes more important. The lipid production source, triacylglycerol biosynthesis in microalgae requires short chain fatty acids as substrates, which are synthesized in chloroplasts. However, the transport mechanism of fatty acids from microalgae chloroplasts to cytosol remains unknown. RESULTS cDNAs from two homologs of the Arabidopsis fatty acid exporter 1 (FAX1) were cloned from Chlamydomonas reinhardtii and were named crfax1 and crfax2. Both CrFAXs were involved in fatty acid transport, and their substrates were mainly C16 and C18 fatty acids. Overexpression of both CrFAXs increased the accumulation of the total lipid content in algae cells, and the fatty acid compositions were changed under normal TAP or nitrogen deprivation conditions. Overexpression of both CrFAXs also increased the chlorophyll content. The MGDG content was decreased but the TAG, DAG, DGDG and other lipid contents were increased in CrFAXs overexpression strains. CONCLUSION These results reveal that CrFAX1 and CrFAX2 were involved in mediating fatty acid export for lipids biosynthesis in C. reinhardtii. In addition, overexpression of both CrFAXs obviously increased the intracellular lipid content, especially the triacylglycerol content in microalgae, which provides a potential technology for the production of more biofuels using microalgae.
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Affiliation(s)
- Nannan Li
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Yan Zhang
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Hongjun Meng
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Shengting Li
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Shufeng Wang
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Zhongchun Xiao
- Academy of Agricultural Science, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Peng Chang
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Xiaohui Zhang
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yasuo Igarashi
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
| | - Feng Luo
- Research Center of Bioremediation and Bioenergy, College of Resources and Environment, Southwest University, Beibei, Chongqing, 400715 People’s Republic of China
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12
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Naghshbandi MP, Tabatabaei M, Aghbashlo M, Aftab MN, Iqbal I. Metabolic Engineering of Microalgae for Biofuel Production. Methods Mol Biol 2019; 1980:153-172. [PMID: 30666564 DOI: 10.1007/7651_2018_205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Microalgae are considered as promising cell factories for the production of various types of biofuels, including bioethanol, biodiesel, and biohydrogen by using carbon dioxide and sunlight. In spite of unique advantages of these microorganisms, the commercialization of microalgal biofuels has been hindered by poor economic features. Metabolic engineering is among the most promising strategies put forth to overcome this challenge. In this chapter, metabolic pathways involved in lipid and hydrogen production by microalgae are reviewed and discussed. Moreover, metabolic and genetic engineering approaches investigated for improving the rate of lipid (as a feedstock for biodiesel production) and biohydrogen synthesis are presented. Finally, genetic engineering tools and approaches employed for engineering microalgal metabolic pathways are elaborated. A thorough step-by-step protocol for reconstructing the metabolic pathway of various microorganisms including microalgae is also presented.
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Affiliation(s)
- Mohammad Pooya Naghshbandi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Meisam Tabatabaei
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran. .,Biofuel Research Team (BRTeam), Karaj, Iran.
| | - Mortaza Aghbashlo
- Department of Mechanical Engineering of Agricultural Machinery, Faculty of Agricultural Engineering and Technology, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | - Muhammad Nauman Aftab
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Irfana Iqbal
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
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13
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Sun XM, Ren LJ, Zhao QY, Ji XJ, Huang H. Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:272. [PMID: 30305845 PMCID: PMC6171298 DOI: 10.1186/s13068-018-1275-9] [Citation(s) in RCA: 163] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/26/2018] [Indexed: 05/04/2023]
Abstract
Microalgae have drawn great attention as promising sustainable source of lipids and carotenoids. Their lipid and carotenoids accumulation machinery can be trigged by the stress conditions such as nutrient limitation or exposure to the damaging physical factors. However, stressful conditions often adversely affect microalgal growth and cause oxidative damage to the cells, which can eventually reduce the yield of the desired products. To overcome these limitations, two-stage cultivation strategies and supplementation of growth-promoting agents have traditionally been utilized, but developing new highly adapted strains is theoretically the simplest strategy. In addition to genetic engineering, adaptive laboratory evolution (ALE) is frequently used to develop beneficial phenotypes in industrial microorganisms during long-term selection under specific stress conditions. In recent years, many studies have gradually introduced ALE as a powerful tool to improve the biological properties of microalgae, especially for improving the production of lipid and carotenoids. In this review, strategies for the manipulation of stress in microalgal lipids and carotenoids production are summarized and discussed. Furthermore, this review summarizes the overall state of ALE technology, including available selection pressures, methods, and their applications in microalgae for the improved production of lipids and carotenoids.
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Affiliation(s)
- Xiao-Man Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816 People’s Republic of China
| | - Lu-Jing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, People’s Republic of China
| | - Quan-Yu Zhao
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816 People’s Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, People’s Republic of China
| | - He Huang
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816 People’s Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing, 210009 People’s Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing, People’s Republic of China
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14
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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15
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Tack ILMM, Nimmegeers P, Akkermans S, Logist F, Van Impe JFM. A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli. PLoS One 2018; 13:e0202565. [PMID: 30157229 PMCID: PMC6114798 DOI: 10.1371/journal.pone.0202565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
Over the last decades, predictive microbiology has made significant advances in the mathematical description of microbial spoiler and pathogen dynamics in or on food products. Recently, the focus of predictive microbiology has shifted from a (semi-)empirical population-level approach towards mechanistic models including information about the intracellular metabolism in order to increase model accuracy and genericness. However, incorporation of this subpopulation-level information increases model complexity and, consequently, the required run time to simulate microbial cell and population dynamics. In this paper, results of metabolic flux balance analyses (FBA) with a genome-scale model are used to calibrate a low-complexity linear model describing the microbial growth and metabolite secretion rates of Escherichia coli as a function of the nutrient and oxygen uptake rate. Hence, the required information about the cellular metabolism (i.e., biomass growth and secretion of cell products) is selected and included in the linear model without incorporating the complete intracellular reaction network. However, the applied FBAs are only representative for microbial dynamics under specific extracellular conditions, viz., a neutral medium without weak acids at a temperature of 37℃. Deviations from these reference conditions lead to metabolic shifts and adjustments of the cellular nutrient uptake or maintenance requirements. This metabolic dependency on extracellular conditions has been taken into account in our low-complex metabolic model. In this way, a novel approach is developed to take the synergistic effects of temperature, pH, and undissociated acids on the cell metabolism into account. Consequently, the developed model is deployable as a tool to describe, predict and control E. coli dynamics in and on food products under various combinations of environmental conditions. To emphasize this point,three specific scenarios are elaborated: (i) aerobic respiration without production of weak acid extracellular metabolites, (ii) anaerobic fermentation with secretion of mixed acid fermentation products into the food environment, and (iii) respiro-fermentative metabolic regimes in between the behaviors at aerobic and anaerobic conditions.
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Affiliation(s)
| | | | - Simen Akkermans
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Filip Logist
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
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16
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Chia SR, Chew KW, Show PL, Yap YJ, Ong HC, Ling TC, Chang JS. Analysis of Economic and Environmental Aspects of Microalgae Biorefinery for Biofuels Production: A Review. Biotechnol J 2018; 13:e1700618. [DOI: 10.1002/biot.201700618] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/30/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Shir Reen Chia
- Faculty of Engineering; Department of Mechanical Engineering; University of Malaya; Kuala Lumpur 50603 Malaysia
- Bioseparation Research Group; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
| | - Kit Wayne Chew
- Bioseparation Research Group; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
- Faculty of Engineering; Department of Chemical and Environmental Engineering; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
| | - Pau Loke Show
- Bioseparation Research Group; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
- Faculty of Engineering; Department of Chemical and Environmental Engineering; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
| | - Yee Jiun Yap
- Bioseparation Research Group; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
- Faculty of Engineering; Department of Applied Mathematics; University of Nottingham Malaysia Campus; Semenyih 43500 Selangor Malaysia
| | - Hwai Chyuan Ong
- Faculty of Engineering; Department of Mechanical Engineering; University of Malaya; Kuala Lumpur 50603 Malaysia
| | - Tau Chuan Ling
- Institute of Biological Sciences; University of Malaya; Kuala Lumpur 50603 Malaysia
| | - Jo-Shu Chang
- Department of Chemical Engineering; National Cheng Kung University; Tainan 701 Taiwan
- Research Center for Energy Technology and Strategy; National Cheng Kung University; Tainan 701 Taiwan
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17
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Su Y, Yi Z, Björnsdóttir SH, Brynjolfsson S, Fu W. Adaptive Laboratory Evolution for Enhanced Carotenoid Production in Microalgae. Methods Mol Biol 2018; 1852:117-126. [PMID: 30109628 DOI: 10.1007/978-1-4939-8742-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In order to produce natural pigments with competitive prices, algal strains employed in industrial production need to be improved for increasing the productivity of valuable metabolites, thereby reducing the overall production cost. Adaptive laboratory evolution (ALE) is a traditional method for strain improvement, which has been effectively utilized in bacteria and fungi. With the growing interest in algal biotechnology, attempts have recently been put forward to improve microalgal strains with ALE approach. This chapter describes a stepwise adaptive evolution strategy that enhances carotenoid yield from microalgae.
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Affiliation(s)
- Yixi Su
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Zhiqian Yi
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Snædís Huld Björnsdóttir
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Sigurdur Brynjolfsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Weiqi Fu
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland.
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18
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Jagadevan S, Banerjee A, Banerjee C, Guria C, Tiwari R, Baweja M, Shukla P. Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:185. [PMID: 29988523 PMCID: PMC6026345 DOI: 10.1186/s13068-018-1181-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/20/2018] [Indexed: 05/03/2023]
Abstract
In the wake of the uprising global energy crisis, microalgae have emerged as an alternate feedstock for biofuel production. In addition, microalgae bear immense potential as bio-cell factories in terms of producing key chemicals, recombinant proteins, enzymes, lipid, hydrogen and alcohol. Abstraction of such high-value products (algal biorefinery approach) facilitates to make microalgae-based renewable energy an economically viable option. Synthetic biology is an emerging field that harmoniously blends science and engineering to help design and construct novel biological systems, with an aim to achieve rationally formulated objectives. However, resources and tools used for such nuclear manipulation, construction of synthetic gene network and genome-scale reconstruction of microalgae are limited. Herein, we present recent developments in the upcoming field of microalgae employed as a model system for synthetic biology applications and highlight the importance of genome-scale reconstruction models and kinetic models, to maximize the metabolic output by understanding the intricacies of algal growth. This review also examines the role played by microalgae as biorefineries, microalgal culture conditions and various operating parameters that need to be optimized to yield biofuel that can be economically competitive with fossil fuels.
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Affiliation(s)
- Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004 India
| | - Avik Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004 India
| | - Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004 India
| | - Chandan Guria
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004 India
| | - Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
- Enzyme and Microbial Biochemistry Lab, Department of Chemistry, Indian Institute of Technology, Hauz-Khas, New Delhi 110016 India
| | - Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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19
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Ng I, Tan S, Kao P, Chang Y, Chang J. Recent Developments on Genetic Engineering of Microalgae for Biofuels and Bio‐Based Chemicals. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600644] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/24/2017] [Indexed: 12/15/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
- Research Center for Energy Technology and StrategyNational Cheng Kung UniversityTainan70101Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
| | - Pei‐Hsun Kao
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
| | - Yu‐Kaung Chang
- Graduate School of Biochemical EngineeringMing Chi University of TechnologyNew Taipei City24301Taiwan
| | - Jo‐Shu Chang
- Department of Chemical EngineeringNational Cheng Kung UniversityTainan70101Taiwan
- Research Center for Energy Technology and StrategyNational Cheng Kung UniversityTainan70101Taiwan
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20
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Banerjee A, Banerjee C, Negi S, Chang JS, Shukla P. Improvements in algal lipid production: a systems biology and gene editing approach. Crit Rev Biotechnol 2017; 38:369-385. [DOI: 10.1080/07388551.2017.1356803] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Avik Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | - Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, India
| | | | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Pratyoosh Shukla
- Department of Microbiology, Enzyme Technology and Protein Bioinformatics Laboratory, Maharshi Dayanand University, Rohtak, India
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21
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Proteomic approaches in microalgae: perspectives and applications. 3 Biotech 2017; 7:197. [PMID: 28667637 DOI: 10.1007/s13205-017-0831-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
Biofuels are the promising sources which are produced by various microalgae or in the form of metabolic by-products from organic or food waste products. Microalgae have been widely reported for the production of biofuels since these have a high storage of lipids as triacylglycerides, which can mainly be converted into biofuels. Recently, products such as biodiesel, bioethanol and biogas have renewed the interest toward the microalgae. The proteomics alone will not pave the way toward finding an ideal alga which will fulfill the current energy demands, but a combined approach of proteomics, genomics and bioinformatics can be pivotal for a sustainable solution. The present review emphasizes various technologies currently involved in algal proteomics for the efficient production of biofuels.
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Kumar R, Biswas K, Singh PK, Singh PK, Elumalai S, Shukla P, Pabbi S. Lipid production and molecular dynamics simulation for regulation of accD gene in cyanobacteria under different N and P regimes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:94. [PMID: 28428819 PMCID: PMC5393026 DOI: 10.1186/s13068-017-0776-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/05/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microalgae grown under different nutrient deficient conditions present a good source of natural lipids with applications for several types of biofuels. The expression of acetyl-CoA carboxylase gene can further provide an insight to the mechanisms leading to enhanced lipid production under such stresses. In this study, two nutrients viz. nitrogen and phosphorus were modulated to see its effect on lipid productivity in selected cyanobacteria and its correlation with Accase followed by molecular dynamics simulation. RESULTS Selected cyanobacteria viz. Oscillatoria sp. (SP8), Anabaena sp. (SP12), Anabaena sp. (SP13), Microcoleus sp. (SP18), and Nostoc sp. (SP20) varied in their ability to accumulate lipids which ranged from a lowest of 0.13% in Anabaena sp. (SP13) to the maximum of 7.24% in Microcoleus sp. (SP18). Microcoleus sp. (SP18) also recorded highest lipid accumulation at both N (6 mM NaNO3) and P (0.20 mM K2HPO4) limiting conditions. The overall expression of accD was found to be upregulated in both Oscillatoria sp. (SP8) and Microcoleus sp. (SP18) for all nitrogen concentrations but was differentially regulated with both positive and negative induction under phosphorus stress conditions. Maximum induction was observed in Microcoleus sp. (SP18) at 0.20 mM K2HPO4. The obtained 3D structure of SP8 protein (21.8 kDa) showed six alpha helices, while SP18 protein (16.7 kDa) exhibited four alpha helices and four beta sheets. The phi (ϕ)/psi(ψ) angles of the amino acid residues observed in Ramachandran plot analysis showed that both SP8 and SP18 proteins were highly stable with more than 90% amino acids in allowed regions. The molecular dynamics simulation results also indicated the stability of ligand-bound protein complexes. CONCLUSION It has been demonstrated that cyanobacterial isolates are affected differently by nutrient limitation leading to variation in their lipid productivity. The same has been revealed by the behavior of accD gene expression which was regulated more by nutrients concentrations rather than the organism. However, the ligand-bound protein complexes were stable throughout MD simulations.
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Affiliation(s)
- Roshan Kumar
- Centre for Conservation and Utilisation of Blue Green Algae, Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Department of Plant Biology and Biotechnology, Presidency College, Chennai, 600005 India
| | - Koushik Biswas
- Department of Biotechnology, Shri JJT University, Jhunjhunu, Rajasthan 333001 India
| | - Puneet Kumar Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Pankaj Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012 India
| | - Sanniyasi Elumalai
- Department of Plant Biology and Biotechnology, Presidency College, Chennai, 600005 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae, Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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23
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Metabolic pathways for lipid synthesis under nitrogen stress in Chlamydomonas and Nannochloropsis. Biotechnol Lett 2016; 39:1-11. [DOI: 10.1007/s10529-016-2216-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
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24
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Banerjee C, Dubey KK, Shukla P. Metabolic Engineering of Microalgal Based Biofuel Production: Prospects and Challenges. Front Microbiol 2016; 7:432. [PMID: 27065986 PMCID: PMC4815533 DOI: 10.3389/fmicb.2016.00432] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/17/2016] [Indexed: 12/14/2022] Open
Abstract
The current scenario in renewable energy is focused on development of alternate and sustainable energy sources, amongst which microalgae stands as one of the promising feedstock for biofuel production. It is well known that microalgae generate much larger amounts of biofuels in a shorter time than other sources based on plant seeds. However, the greatest challenge in a transition to algae-based biofuel production is the various other complications involved in microalgal cultivation, its harvesting, concentration, drying and lipid extraction. Several green microalgae accumulate lipids, especially triacylglycerols (TAGs), which are main precursors in the production of lipid. The various aspects on metabolic pathway analysis of an oleaginous microalgae i.e., Chlamydomonas reinhardtii have elucidated some novel metabolically important genes and this enhances the lipid production in this microalgae. Adding to it, various other aspects in metabolic engineering using OptFlux and effectual bioprocess design also gives an interactive snapshot of enhancing lipid production which ultimately improvises the oil yield. This article reviews the current status of microalgal based technologies for biofuel production, bioreactor process design, flux analysis and it also provides various strategies to increase lipids accumulation via metabolic engineering.
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Affiliation(s)
- Chiranjib Banerjee
- Department of Environmental Science and Engineering, Indian School of Mines Dhanbad, India
| | - Kashyap K Dubey
- Department of Biotechnology, University Institute of Engineering and Technology, Maharshi Dayanand University Rohtak, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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