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Chen J, Yang J, Du H, Aslam M, Wang W, Chen W, Li T, Liu Z, Liu X. Laminarin, a Major Polysaccharide in Stramenopiles. Mar Drugs 2021; 19:576. [PMID: 34677475 PMCID: PMC8541152 DOI: 10.3390/md19100576] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 01/09/2023] Open
Abstract
During the processes of primary and secondary endosymbiosis, different microalgae evolved to synthesis different storage polysaccharides. In stramenopiles, the main storage polysaccharides are β-1,3-glucan, or laminarin, in vacuoles. Currently, laminarin is gaining considerable attention due to its application in the food, cosmetic and pharmaceuticals industries, and also its importance in global biogeochemical cycles (especially in the ocean carbon cycle). In this review, the structures, composition, contents, and bioactivity of laminarin were summarized in different algae. It was shown that the general features of laminarin are species-dependence. Furthermore, the proposed biosynthesis and catabolism pathways of laminarin, functions of key genes, and diel regulation of laminarin were also depicted and comprehensively discussed for the first time. However, the complete pathways, functions of genes, and diel regulatory mechanisms of laminarin require more biomolecular studies. This review provides more useful information and identifies the knowledge gap regarding the future studies of laminarin and its applications.
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Affiliation(s)
- Jichen Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Jianchao Yang
- Yantai Academy of Agricultural Sciences, Yantai 265500, China;
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Muhmmad Aslam
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Wanna Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Tangcheng Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
| | - Zhengyi Liu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China;
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Institute of Marine Sciences, Shantou University, Shantou 515063, China; (J.C.); (H.D.); (M.A.); (W.W.); (W.C.); (T.L.)
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 510000, China
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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Vavitsas K, Kugler A, Satta A, Hatzinikolaou DG, Lindblad P, Fewer DP, Lindberg P, Toivari M, Stensjö K. Doing synthetic biology with photosynthetic microorganisms. PHYSIOLOGIA PLANTARUM 2021; 173:624-638. [PMID: 33963557 DOI: 10.1111/ppl.13455] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.
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Affiliation(s)
- Konstantinos Vavitsas
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
| | - Dimitris G Hatzinikolaou
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, Zografou Campus, Athens, Greece
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Mervi Toivari
- VTT, Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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CRISPR/Cas9 disruption of glucan synthase in Nannochloropsis gaditana attenuates accumulation of β-1,3-glucose oligomers. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Defrel G, Marsaud N, Rifa E, Martins F, Daboussi F. Identification of Loci Enabling Stable and High-Level Heterologous Gene Expression. Front Bioeng Biotechnol 2021; 9:734902. [PMID: 34660556 PMCID: PMC8517075 DOI: 10.3389/fbioe.2021.734902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
Efficient and reliable genome engineering technologies have yet to be developed for diatoms. The delivery of DNA in diatoms results in the random integration of multiple copies, quite often leading to heterogeneous gene activity, as well as host instability. Transgenic diatoms are generally selected on the basis of transgene expression or high enzyme activity, without consideration of the copy number or the integration locus. Here, we propose an integrated pipeline for the diatom, Phaeodactylum tricornutum, that accurately quantifies transgene activity using a β-glucuronidase assay and the number of transgene copies integrated into the genome through Droplet Digital PCR (ddPCR). An exhaustive and systematic analysis performed on 93 strains indicated that 42% of them exhibited high β-glucuronidase activity. Though most were attributed to high transgene copy numbers, we succeeded in isolating single-copy clones, as well as sequencing the integration loci. In addition to demonstrating the impact of the genomic integration site on gene activity, this study identifies integration sites for stable transgene expression in Phaeodactylum tricornutum.
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Affiliation(s)
- Gilles Defrel
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Marsaud
- Toulouse Biotechnology Institute (TBI), Plateforme Genome et Transcriptome (GeT-Biopuces) Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Etienne Rifa
- Toulouse Biotechnology Institute (TBI), Plateforme Genome et Transcriptome (GeT-Biopuces) Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Frédéric Martins
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), UMR1297, INSERM, UPS, Toulouse, France
- Plateforme Genome et Transcriptome (GeT), Genopole Toulouse, Toulouse, France
| | - Fayza Daboussi
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Toulouse White Biotechnology (TWB), INSA, Toulouse, France
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Potential for Biomass Production and Remediation by Cultivation of the Marine Model Diatom Phaeodactylum tricornutum in Oil Field Produced Wastewater Media. WATER 2021. [DOI: 10.3390/w13192700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
While oilfield produced water (PW) is one of the largest, unclaimed wastewater streams of the oil industry, it could potentially be used as a cultivation medium for microalgae. Microalgae could help with the remediation of this water while also delivering biomass that can be transformed into valuable byproducts such as biofuels. The coupling of these two purposes is expected to cut production costs of biofuels while aiding environmental protection. In this study, we compared the cultivation capacity of the marine model diatom Phaeodactylum tricornutum in media at varying salinities and in media composed of PW from two oilfields in the Central Valley of California that differed drastically in the concentration of inorganic and organic constituents. Specifically, we measured the carrying capacity of these media, the maximum growth rates of P. tricornutum, its cellular lipid accumulation capacity, and its capacity to remediate the most polluted PW source. Our study shows that P. tricornutum can successfully adjust to the tested cultivation media through processes of short-term acclimation and long-term adaptation. Furthermore, the cultivation of P. tricornutum in the most heavily polluted PW source led to significant increases in cell yield and improved photosynthetic capacity during the stationary phase, which could be attributed chiefly to the higher levels of nitrate present in this PW source. Chemical water analyses also demonstrated the capability of P. tricornutum to remediate major nutrient content and potentially harmful elements like fluorine and copper. Because P. tricornutum is amenable to advanced genetic engineering, which could be taken advantage of to improve its cultivation resilience and productivity in an economic setting, we propose this study as a step towards essential follow-up studies that will identify the genetic regulation behind its growth in oilfield PW media and its remediation of the PW constituents.
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Maréchal E. Grand Challenges in Microalgae Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:764573. [PMID: 34630500 PMCID: PMC8495258 DOI: 10.3389/fpls.2021.764573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
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Sirohi R, Joun J, Choi HI, Gaur VK, Sim SJ. Algal glycobiotechnology: omics approaches for strain improvement. Microb Cell Fact 2021; 20:163. [PMID: 34419059 PMCID: PMC8379821 DOI: 10.1186/s12934-021-01656-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/12/2021] [Indexed: 12/18/2022] Open
Abstract
Microalgae has the capability to replace petroleum-based fuels and is a promising option as an energy feedstock because of its fast growth, high photosynthetic capacity and remarkable ability to store energy reserve molecules in the form of lipids and starch. But the commercialization of microalgae based product is difficult due to its high processing cost and low productivity. Higher accumulation of these molecules may help to cut the processing cost. There are several reports on the use of various omics techniques to improve the strains of microalgae for increasing the productivity of desired products. To effectively use these techniques, it is important that the glycobiology of microalgae is associated to omics approaches to essentially give rise to the field of algal glycobiotechnology. In the past few decades, lot of work has been done to improve the strain of various microalgae such as Chlorella, Chlamydomonas reinhardtii, Botryococcus braunii etc., through genome sequencing and metabolic engineering with major focus on significantly increasing the productivity of biofuels, biopolymers, pigments and other products. The advancements in algae glycobiotechnology have highly significant role to play in innovation and new developments for the production algae-derived products as above. It would be highly desirable to understand the basic biology of the products derived using -omics technology together with biochemistry and biotechnology. This review discusses the potential of different omic techniques (genomics, transcriptomics, proteomics, metabolomics) to improve the yield of desired products through algal strain manipulation.
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Affiliation(s)
- Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Jaemin Joun
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Hong Ii Choi
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea
| | - Vivek Kumar Gaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226 001, India
| | - Sang Jun Sim
- Department of Chemical & Biological Engineering, Korea University, Seoul, 136713, Republic of Korea.
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Zhang K, Zhou Z, Li J, Wang J, Yu L, Lin S. SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum. Commun Biol 2021; 4:797. [PMID: 34172821 PMCID: PMC8233357 DOI: 10.1038/s42003-021-02284-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 06/01/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphorus (P) is an essential nutrient for marine phytoplankton. Maintaining intracellular P homeostasis against environmental P variability is critical for phytoplankton, but how they achieve this is poorly understood. Here we identify a SPX gene and investigate its role in Phaeodactylum tricornutum. SPX knockout led to significant increases in the expression of phosphate transporters, alkaline phosphatases (the P acquisition machinery) and phospholipid hydrolases (a mechanism to reduce P demand). These demonstrate that SPX is a negative regulator of both P uptake and P-stress responses. Furthermore, we show that SPX regulation of P uptake and metabolism involves a phosphate starvation response regulator (PHR) as an intermediate. Additionally, we find the SPX related genes exist and operate across the phytoplankton phylogenetic spectrum and in the global oceans, indicating its universal importance in marine phytoplankton. This study lays a foundation for better understanding phytoplankton adaptation to P variability in the future changing oceans.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China.
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, China.
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Lu Y, Gu X, Lin H, Melis A. Engineering microalgae: transition from empirical design to programmable cells. Crit Rev Biotechnol 2021; 41:1233-1256. [PMID: 34130561 DOI: 10.1080/07388551.2021.1917507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Domesticated microalgae hold great promise for the sustainable provision of various bioresources for human domestic and industrial consumption. Efforts to exploit their potential are far from being fully realized due to limitations in the know-how of microalgal engineering. The associated technologies are not as well developed as those for heterotrophic microbes, cyanobacteria, and plants. However, recent studies on microalgal metabolic engineering, genome editing, and synthetic biology have immensely helped to enhance transformation efficiencies and are bringing new insights into this field. Therefore, this article, summarizes recent developments in microalgal biotechnology and examines the prospects for generating specialty and commodity products through the processes of metabolic engineering and synthetic biology. After a brief examination of empirical engineering methods and vector design, this article focuses on quantitative transformation cassette design, elaborates on target editing methods and emerging digital design of algal cellular metabolism to arrive at high yields of valuable products. These advances have enabled a transition of manners in microalgal engineering from single-gene and enzyme-based metabolic engineering to systems-level precision engineering, from cells created with genetically modified (GM) tags to that without GM tags, and ultimately from proof of concept to tangible industrial applications. Finally, future trends are proposed in microalgal engineering, aiming to establish individualized transformation systems in newly identified species for strain-specific specialty and commodity products, while developing sophisticated universal toolkits in model algal species.
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Affiliation(s)
- Yandu Lu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Xinping Gu
- State Key Laboratory of Marine Resource Utilization in the South China Sea, College of Oceanology, Hainan University, Haikou, China
| | - Hanzhi Lin
- Institute of Marine & Environmental Technology, Center for Environmental Science, University of Maryland, College Park, MD, USA
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Pancha I, Takaya K, Tanaka K, Imamura S. The Unicellular Red Alga Cyanidioschyzon merolae, an Excellent Model Organism for Elucidating Fundamental Molecular Mechanisms and Their Applications in Biofuel Production. PLANTS 2021; 10:plants10061218. [PMID: 34203949 PMCID: PMC8232737 DOI: 10.3390/plants10061218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022]
Abstract
Microalgae are considered one of the best resources for the production of biofuels and industrially important compounds. Various models have been developed to understand the fundamental mechanism underlying the accumulation of triacylglycerols (TAGs)/starch and to enhance its content in cells. Among various algae, the red alga Cyanidioschyzonmerolae has been considered an excellent model system to understand the fundamental mechanisms behind the accumulation of TAG/starch in the microalga, as it has a smaller genome size and various biotechnological methods are available for it. Furthermore, C. merolae can grow and survive under high temperature (40 °C) and low pH (2–3) conditions, where most other organisms would die, thus making it a choice alga for large-scale production. Investigations using this alga has revealed that the target of rapamycin (TOR) kinase is involved in the accumulation of carbon-reserved molecules, TAGs, and starch. Furthermore, detailed molecular mechanisms of the role of TOR in controlling the accumulation of TAGs and starch were uncovered via omics analyses. Based on these findings, genetic engineering of the key gene and proteins resulted in a drastic increment of the amount of TAGs and starch. In addition to these studies, other trials that attempted to achieve the TAG increment in C. merolae have been summarized in this article.
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Affiliation(s)
- Imran Pancha
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh 522502, India
- Correspondence: (I.P.); (S.I.); Tel.: +81-422-59-6179 (S.I.)
| | - Kazuhiro Takaya
- NTT Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, 3-9-11 Midori-cho, Musashino-shi, Tokyo 180-8585, Japan;
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama-shi, Kanagawa 226-8503, Japan;
| | - Sousuke Imamura
- NTT Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, 3-9-11 Midori-cho, Musashino-shi, Tokyo 180-8585, Japan;
- Correspondence: (I.P.); (S.I.); Tel.: +81-422-59-6179 (S.I.)
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Sittmann J, Bae M, Mevers E, Li M, Quinn A, Sriram G, Clardy J, Liu Z. Bacterial diketopiperazines stimulate diatom growth and lipid accumulation. PLANT PHYSIOLOGY 2021; 186:1159-1170. [PMID: 33620482 PMCID: PMC8195512 DOI: 10.1093/plphys/kiab080] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/10/2023]
Abstract
Diatoms are photosynthetic microalgae that fix a significant fraction of the world's carbon. Because of their photosynthetic efficiency and high-lipid content, diatoms are priority candidates for biofuel production. Here, we report that sporulating Bacillus thuringiensis and other members of the Bacillus cereus group, when in co-culture with the marine diatom Phaeodactylum tricornutum, significantly increase diatom cell count. Bioassay-guided purification of the mother cell lysate of B. thuringiensis led to the identification of two diketopiperazines (DKPs) that stimulate both P. tricornutum growth and increase its lipid content. These findings may be exploited to enhance P. tricornutum growth and microalgae-based biofuel production. As increasing numbers of DKPs are isolated from marine microbes, the work gives potential clues to bacterial-produced growth factors for marine microalgae.
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Affiliation(s)
- John Sittmann
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Munhyung Bae
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Emily Mevers
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Andrew Quinn
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Rawat J, Gupta PK, Pandit S, Prasad R, Pande V. Current perspectives on integrated approaches to enhance lipid accumulation in microalgae. 3 Biotech 2021; 11:303. [PMID: 34194896 DOI: 10.1007/s13205-021-02851-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022] Open
Abstract
In recent years, research initiatives on renewable bioenergy or biofuels have been gaining momentum, not only due to fast depletion of finite reserves of fossil fuels but also because of the associated concerns for the environment and future energy security. In the last few decades, interest is growing concerning microalgae as the third-generation biofuel feedstock. The CO2 fixation ability and conversion of it into value-added compounds, devoid of challenging food and feed crops, make these photosynthetic microorganisms an optimistic producer of biofuel from an environmental point of view. Microalgal-derived fuels are currently being considered as clean, renewable, and promising sustainable biofuel. Therefore, most research targets to obtain strains with the highest lipid productivity and a high growth rate at the lowest cultivation costs. Different methods and strategies to attain higher biomass and lipid accumulation in microalgae have been extensively reported in the previous research, but there are fewer inclusive reports that summarize the conventional methods with the modern techniques for lipid enhancement and biodiesel production from microalgae. Therefore, the current review focuses on the latest techniques and advances in different cultivation conditions, the effect of different abiotic and heavy metal stress, and the role of nanoparticles (NPs) in the stimulation of lipid accumulation in microalgae. Techniques such as genetic engineering, where particular genes associated with lipid metabolism, are modified to boost lipid synthesis within the microalgae, the contribution of "Omics" in metabolic pathway studies. Further, the contribution of CRISPR/Cas9 system technique to the production of microalgae biofuel is also briefly described.
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Affiliation(s)
- Jyoti Rawat
- Department of Biotechnology, Sir J. C. Bose Technical Campus Bhimtal, Kumaun University, Nainital, Uttarakhand 263136 India
| | - Piyush Kumar Gupta
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310 India
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Knowledge Park III, Greater Noida, Uttar Pradesh 201310 India
| | - Ram Prasad
- Department of Botany, Mahatma Gandhi Central University, Motihari, Bihar 845801 India
| | - Veena Pande
- Department of Biotechnology, Sir J. C. Bose Technical Campus Bhimtal, Kumaun University, Nainital, Uttarakhand 263136 India
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Galas L, Burel C, Schapman D, Ropitaux M, Bernard S, Bénard M, Bardor M. Comparative Structural and Functional Analyses of the Fusiform, Oval, and Triradiate Morphotypes of Phaeodactylum tricornutum Pt3 Strain. FRONTIERS IN PLANT SCIENCE 2021; 12:638181. [PMID: 33912207 PMCID: PMC8072121 DOI: 10.3389/fpls.2021.638181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/16/2021] [Indexed: 05/24/2023]
Abstract
The diatom Phaeodactylum tricornutum is a marine unicellular microalga that exists under three main morphotypes: oval, fusiform, and triradiate. Previous works have demonstrated that the oval morphotype of P. tricornutum Pt3 strain presents specific metabolic features. Here, we compared the cellular organization of the main morphotypes of the diatom P. tricornutum Pt3 strain through transmission electron and advanced light microscopies. The three morphotypes share similarities including spectral characteristics of the plastid, the location of the nucleus, the organization of mitochondria around the plastid as well as the existence of both a F-actin cortex, and an intracellular network of F-actin. In contrast, compared to fusiform and triradiate cells, oval cells spontaneously release proteins more rapidly. In addition, comparison of whole transcriptomes of oval versus fusiform or triradiate cells revealed numerous differential expression of positive and negative regulators belonging to the complex dynamic secretory machinery. This study highlights the specificities occurring within the oval morphotype underlying that the oval cells secrete proteins more rapidly.
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Affiliation(s)
- Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Carole Burel
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Damien Schapman
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Marc Ropitaux
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Sophie Bernard
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Magalie Bénard
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Muriel Bardor
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
- Institut Universitaire de France, Paris, France
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Villanova V, Singh D, Pagliardini J, Fell D, Le Monnier A, Finazzi G, Poolman M. Boosting Biomass Quantity and Quality by Improved Mixotrophic Culture of the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2021; 12:642199. [PMID: 33897733 PMCID: PMC8063856 DOI: 10.3389/fpls.2021.642199] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are photoautotrophic unicellular algae and are among the most abundant, adaptable, and diverse marine phytoplankton. They are extremely interesting not only for their ecological role but also as potential feedstocks for sustainable biofuels and high-value commodities such as omega fatty acids, because of their capacity to accumulate lipids. However, the cultivation of microalgae on an industrial scale requires higher cell densities and lipid accumulation than those found in nature to make the process economically viable. One of the known ways to induce lipid accumulation in Phaeodactylum tricornutum is nitrogen deprivation, which comes at the expense of growth inhibition and lower cell density. Thus, alternative ways need to be explored to enhance the lipid production as well as biomass density to make them sustainable at industrial scale. In this study, we have used experimental and metabolic modeling approaches to optimize the media composition, in terms of elemental composition, organic and inorganic carbon sources, and light intensity, that boost both biomass quality and quantity of P. tricornutum. Eventually, the optimized conditions were scaled-up to 2 L photobioreactors, where a better system control (temperature, pH, light, aeration/mixing) allowed a further improvement of the biomass capacity of P. tricornutum to 12 g/L.
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Affiliation(s)
- Valeria Villanova
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
- Fermentalg SA, Libourne, France
| | - Dipali Singh
- Microbes in the Food Chain, Quadram Institute Biosciences, Norwich Research Park, Norwich, United Kingdom
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - David Fell
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
| | | | - Giovanni Finazzi
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Interdisciplinary Research Institute of Grenoble, CEA Grenoble, Grenoble, France
| | - Mark Poolman
- Cell System Modelling Group, Oxford Brookes University, Oxford, United Kingdom
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Jin X, Gong S, Yang B, Wu J, Li T, Wu H, Wu H, Xiang W. Transcriptomic analysis for phosphorus limitation-induced β-glucans accumulation in Chlorella sorokiniana SCSIO 46784 during the early phase of growth. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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68
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Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
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Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
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69
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Characterisation of novel regulatory sequences compatible with modular assembly in the diatom Phaeodactylum tricornutum. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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70
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Bonneure E, De Baets A, De Decker S, Van den Berge K, Clement L, Vyverman W, Mangelinckx S. Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe. Int J Mol Sci 2021; 22:1037. [PMID: 33494376 PMCID: PMC7865345 DOI: 10.3390/ijms22031037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
As a major group of algae, diatoms are responsible for a substantial part of the primary production on the planet. Pennate diatoms have a predominantly benthic lifestyle and are the most species-rich diatom group, with members of the raphid clades being motile and generally having heterothallic sexual reproduction. It was recently shown that the model species Seminavis robusta uses multiple sexual cues during mating, including cyclo(l-Pro-l-Pro) as an attraction pheromone. Elaboration of the pheromone-detection system is a key aspect in elucidating pennate diatom life-cycle regulation that could yield novel fundamental insights into diatom speciation. This study reports the synthesis and bio-evaluation of seven novel pheromone analogs containing small structural alterations to the cyclo(l-Pro-l-Pro) pheromone. Toxicity, attraction, and interference assays were applied to assess their potential activity as a pheromone. Most of our analogs show a moderate-to-good bioactivity and low-to-no phytotoxicity. The pheromone activity of azide- and diazirine-containing analogs was unaffected and induced a similar mating behavior as the natural pheromone. These results demonstrate that the introduction of confined structural modifications can be used to develop a chemical probe based on the diazirine- and/or azide-containing analogs to study the pheromone-detection system of S. robusta.
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Affiliation(s)
- Eli Bonneure
- Department of Green Chemistry and Technology—SynBioC, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (E.B.); (A.D.B.)
| | - Amber De Baets
- Department of Green Chemistry and Technology—SynBioC, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (E.B.); (A.D.B.)
| | - Sam De Decker
- Department of Biology—Protistology and Aquatic Ecology, Faculty of Sciences, Ghent University, Krijgslaan 281/S8, 9000 Ghent, Belgium; (S.D.D.); (W.V.)
| | - Koen Van den Berge
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281/S9, 9000 Ghent, Belgium; (K.V.d.B.); (L.C.)
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281/S9, 9000 Ghent, Belgium; (K.V.d.B.); (L.C.)
| | - Wim Vyverman
- Department of Biology—Protistology and Aquatic Ecology, Faculty of Sciences, Ghent University, Krijgslaan 281/S8, 9000 Ghent, Belgium; (S.D.D.); (W.V.)
| | - Sven Mangelinckx
- Department of Green Chemistry and Technology—SynBioC, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium; (E.B.); (A.D.B.)
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71
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Annunziata R, Balestra C, Marotta P, Ruggiero A, Manfellotto F, Benvenuto G, Biffali E, Ferrante MI. An optimised method for intact nuclei isolation from diatoms. Sci Rep 2021; 11:1681. [PMID: 33462289 PMCID: PMC7813820 DOI: 10.1038/s41598-021-81238-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 12/22/2020] [Indexed: 01/21/2023] Open
Abstract
Due to their abundance in the oceans, their extraordinary biodiversity and the increasing use for biotech applications, the study of diatom biology is receiving more and more attention in the recent years. One of the limitations in developing molecular tools for diatoms lies in the peculiar nature of their cell wall, that is made of silica and organic molecules and that hinders the application of standard methods for cell lysis required, for example, to extract organelles. In this study we present a protocol for intact nuclei isolation from diatoms that was successfully applied to three different species: two pennates, Pseudo-nitzschia multistriata and Phaeodactylum tricornutum, and one centric diatom species, Chaetoceros diadema. Intact nuclei were extracted by treatment with acidified NH4F solution combined to low intensity sonication pulses and separated from cell debris via FAC-sorting upon incubation with SYBR Green. Microscopy observations confirmed the integrity of isolated nuclei and high sensitivity DNA electrophoresis showed that genomic DNA extracted from isolated nuclei has low degree of fragmentation. This protocol has proved to be a flexible and versatile method to obtain intact nuclei preparations from different diatom species and it has the potential to speed up applications such as epigenetic explorations as well as single cell ("single nuclei") genomics, transcriptomics and proteomics in different diatom species.
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Affiliation(s)
| | | | - Pina Marotta
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | | | | | | | - Elio Biffali
- Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
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72
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Abstract
TALENs (Transcription Activator-Like EndoNuclease) are molecular scissors designed to recognize and introduce a double-strand break at a specific genome locus. They represent tools of interest in the frame of genome edition. Upon cleavage, two different pathways lead to DNA repair: Non-homologous End Joining (NHEJ) repair, leading to efficient introduction of short insertion/deletion mutations which can disrupt translational reading frame and Homology Recombination (HR)-directed repair that occurs when exogenous DNA is supplied. Here we introduce how to use TALENs in the oleaginous yeast Yarrowia lipolytica by presenting a step-by-step method allowing to knock out or to introduce in vivo a point mutation in a gene of Yarrowia lipolytica. This chapter describes the material required, the transformation procedure, and the screening process.
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Affiliation(s)
- Coraline Rigouin
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Christian Croux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | - Fayza Daboussi
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Florence Bordes
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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73
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Yang L, Zhang Y. Effects of atrazine and its two major derivatives on the photosynthetic physiology and carbon sequestration potential of a marine diatom. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111359. [PMID: 32961490 DOI: 10.1016/j.ecoenv.2020.111359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
As one of the most commonly used and frequently detected herbicides in the coastal seawater, the ecotoxicity of atrazine to phytoplankton has been well demonstrated. However, little attention has been paid to the ecotoxicity of its two major hydrolysates (desisopropylatrazine (DIA) and desethylatrazine (DEA)), which are also widely distributed in natural seawater. Here we present a comprehensive analysis of the photosynthetic physiology and chromophoric dissolved organic matter (CDOM) characteristics of the diatom Phaeodactylum tricornutum Pt-1 (CCMP 2561) under atrazine, DIA and DEA stress, respectively. The results showed that both atrazine and the two derivatives had significant negative effects on the concentration of chlorophyll a, maximum quantum efficiency (Fv/Fm) and relative electron transport rates (rETR) of P. tricornutum Pt-1. Furthermore, the CDOM pattern released by P. tricornutum Pt-1 cells also changed significantly after 7-day exposure. Compared with the control group, the fluorescence intensity (3D-EEM spectra) of protein-like components was obviously lower, while that of the humic acid-like components was higher. The findings of this study indicate that the ecotoxicity of atrazine might have been underestimated in previous investigations: both atrazine and its two major derivatives are not only phototoxic to microalgae but also influence the carbon sequestration potential in the coastal seawater.
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Affiliation(s)
- Liqiang Yang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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74
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Cunha C, Lopes J, Paulo J, Faria M, Kaufmann M, Nogueira N, Ferreira A, Cordeiro N. The effect of microplastics pollution in microalgal biomass production: A biochemical study. WATER RESEARCH 2020; 186:116370. [PMID: 32906034 DOI: 10.1016/j.watres.2020.116370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/03/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Microplastics (MPs) are widely spread throughout aquatic systems and water bodies. Given that water quality is one of the most important parameters in the microalgal-based industry, it is critical to assess the biochemical impact of short- and long-term exposure to MPs pollution. Here, the microalga Phaeodactylum tricornutum was exposed to water contaminated with 0.5 and 50 mg L-1 of polystyrene (PS) and/or polymethyl methacrylate (PMMA). Results show that the microalgal cultures exposed to lower concentrations of PS displayed a growth enhancement of up to 73% in the first stage (days 3-9) of the exponential growth phase. Surprisingly, and despite the fact that long-term exposure to MPs contamination did not impair microalgal growth, a steep decrease in biomass production (of up to 82%) was observed. The production of photosynthetic pigments was shown to be pH-correlated during the full growth cycle, but cell density-independent in later stages of culturing. The extracellular carbohydrates production exhibited a major decrease during long-term exposure. Still, the production of extracellular proteins was not affected by the presence of MPs. This pilot laboratory-scale study shows that the microalgal exposure to water contaminated with MPs disturbs its biochemical equilibrium in a time-dependent manner, decreasing biomass production. Thus, microalgal industry-related consequences derived from the use of MPs-contaminated water are a plausible possibility.
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Affiliation(s)
- César Cunha
- LB3 - Faculty of Science and Engineering, University of Madeira, 9000-390 Funchal, Portugal
| | - Joana Lopes
- LB3 - Faculty of Science and Engineering, University of Madeira, 9000-390 Funchal, Portugal
| | - Jorge Paulo
- LB3 - Faculty of Science and Engineering, University of Madeira, 9000-390 Funchal, Portugal
| | - Marisa Faria
- LB3 - Faculty of Science and Engineering, University of Madeira, 9000-390 Funchal, Portugal; Oceanic Observatory of Madeira, ARDITI, Madeira Tecnopolo, 9020-105 Funchal, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Manfred Kaufmann
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal; Marine Biology Station of Funchal, Faculty of Life Sciences, University of Madeira, 9000-107 Funchal, Portugal
| | - Natacha Nogueira
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal; Mariculture Center of Calheta, Fisheries Directorate, 9370-133 Calheta, Portugal
| | - Artur Ferreira
- CICECO - Aveiro Institute of Materials and Águeda School of Technology and Management, University of Aveiro, 3754-909 Águeda, Portugal
| | - Nereida Cordeiro
- LB3 - Faculty of Science and Engineering, University of Madeira, 9000-390 Funchal, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
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75
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Kurita T, Moroi K, Iwai M, Okazaki K, Shimizu S, Nomura S, Saito F, Maeda S, Takami A, Sakamoto A, Ohta H, Sakuma T, Yamamoto T. Efficient and multiplexable genome editing using Platinum TALENs in oleaginous microalga, Nannochloropsis oceanica NIES-2145. Genes Cells 2020; 25:695-702. [PMID: 32888368 DOI: 10.1111/gtc.12805] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/25/2022]
Abstract
Algae accumulate large amounts of lipids produced by photosynthesis, and these lipids are expected to be utilized as feedstocks for sustainable new energies, known as biodiesels. Nannochloropsis species are eukaryotic microalgae that produce high levels of lipids. However, since the production costs of algal biodiesels are higher than those of fossil fuels, the improved productivity of algal lipids by molecular breeding of algae is required for practical use. In the present study, we developed a highly efficient genome-editing system involving Platinum transcription activator-like effector nucleases (TALENs) in Nannochloropsis oceanica. Platinum TALENs codon-optimized for N. oceanica were synthesized, and their DNA-binding activity was confirmed by single-strand annealing assays in human HEK293T cells. All-in-one expression vectors for Platinum TALEN targeting the nitrate reductase gene, NoNR, and acyltransferase gene, LPAT1, were transfected into Nannochloropsis species. The introduction of each Platinum TALEN revealed high genome-editing efficiency with no detectable off-target mutations at the candidate sites in N. oceanica. By simultaneously introducing TALENs targeting two genes, we obtained double mutant strains. The loss-of-function phenotype of NoNR was also confirmed. These findings will provide an essential technology for molecular breeding in Nannochloropsis species.
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Affiliation(s)
- Tomokazu Kurita
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Keishi Moroi
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Masako Iwai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kumiko Okazaki
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shinsuke Shimizu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Seiji Nomura
- Mazda Motor Corporation, Fuchu-cho, Hiroshima, Japan
| | | | | | | | - Atsushi Sakamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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76
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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77
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Ho SH, Zhang C, Tao F, Zhang C, Chen WH. Microalgal Torrefaction for Solid Biofuel Production. Trends Biotechnol 2020; 38:1023-1033. [DOI: 10.1016/j.tibtech.2020.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/19/2022]
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78
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Demir I, Besson A, Guiraud P, Formosa-Dague C. Towards a better understanding of microalgae natural flocculation mechanisms to enhance flotation harvesting efficiency. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 82:1009-1024. [PMID: 33055392 DOI: 10.2166/wst.2020.177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In microalgae harvesting, flocculation is usually a compulsory preliminary step to further separation by sedimentation or flotation. For some microalgae species, and under certain growth conditions, flocculation can occur naturally. Natural flocculation presents many advantages as it does not require the addition of any flocculants to the culture medium and shows high efficiency rate. But because natural flocculation is so specific to the species and conditions, and thanks to the knowledge accumulated over the last years on flocculation mechanisms, researchers have developed strategies to induce this natural harvesting. In this review, we first decipher at the molecular scale the underlying mechanisms of natural flocculation and illustrate them by selected studies from the literature. Then we describe the developed strategies to induce natural flocculation that include the use of biopolymers, chemically modified or not, or involve mixed species cultures. But all these strategies need the addition of external compounds or microorganism which can present some issues. Thus alternative directions to completely eliminate the need for an external molecule, through genetic engineering of microalgae strains, are presented and discussed in the third part of this review.
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Affiliation(s)
- Irem Demir
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France and TBI-INSA de Toulouse, 135 avenue de Rangeuil 31077 Toulouse Cedex 4, France E-mail:
| | - Alexandre Besson
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France and TBI-INSA de Toulouse, 135 avenue de Rangeuil 31077 Toulouse Cedex 4, France E-mail:
| | - Pascal Guiraud
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France and TBI-INSA de Toulouse, 135 avenue de Rangeuil 31077 Toulouse Cedex 4, France E-mail:
| | - Cécile Formosa-Dague
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France and TBI-INSA de Toulouse, 135 avenue de Rangeuil 31077 Toulouse Cedex 4, France E-mail:
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79
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Slattery SS, Wang H, Giguere DJ, Kocsis C, Urquhart BL, Karas BJ, Edgell DR. Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing. Sci Rep 2020; 10:13879. [PMID: 32807825 PMCID: PMC7431573 DOI: 10.1038/s41598-020-70769-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
The model diatom Phaeodactylum tricornutum is an attractive candidate for synthetic biology applications. Development of auxotrophic strains of P. tricornutum would provide alternative selective markers to commonly used antibiotic resistance genes. Here, using CRISPR/Cas9, we show successful editing of genes in the uracil, histidine, and tryptophan biosynthetic pathways. Nanopore long-read sequencing indicates that editing events are characterized by the occurrence of large deletions of up to ~ 2.7 kb centered on the editing site. The uracil and histidine-requiring phenotypes can be complemented by plasmid-based copies of the intact genes after curing of the Cas9-editing plasmid. Growth of uracil auxotrophs on media supplemented with 5-fluoroorotic acid and uracil results in loss of the complementing plasmid, providing a facile method for plasmid curing with potential applications in strain engineering and CRISPR editing. Metabolomic characterization of uracil auxotrophs revealed changes in cellular orotate concentrations consistent with partial or complete loss of orotate phosphoribosyltransferase activity. Our results expand the range of P. tricornutum auxotrophic strains and demonstrate that auxotrophic complementation markers provide a viable alternative to traditionally used antibiotic selection markers. Plasmid-based auxotrophic markers should expand the range of genome engineering applications and provide a means for biocontainment of engineered P. tricornutum strains.
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Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Helen Wang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Csanad Kocsis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bradley L Urquhart
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada.
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80
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Sethi D, Butler TO, Shuhaili F, Vaidyanathan S. Diatoms for Carbon Sequestration and Bio-Based Manufacturing. BIOLOGY 2020; 9:E217. [PMID: 32785088 PMCID: PMC7464044 DOI: 10.3390/biology9080217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Carbon dioxide (CO2) is a major greenhouse gas responsible for climate change. Diatoms, a natural sink of atmospheric CO2, can be cultivated industrially in autotrophic and mixotrophic modes for the purpose of CO2 sequestration. In addition, the metabolic diversity exhibited by this group of photosynthetic organisms provides avenues to redirect the captured carbon into products of value. These include lipids, omega-3 fatty acids, pigments, antioxidants, exopolysaccharides, sulphated polysaccharides, and other valuable metabolites that can be produced in environmentally sustainable bio-manufacturing processes. To realize the potential of diatoms, expansion of our knowledge of carbon supply, CO2 uptake and fixation by these organisms, in conjunction with ways to enhance metabolic routing of the fixed carbon to products of value is required. In this review, current knowledge is explored, with an evaluation of the potential of diatoms for carbon capture and bio-based manufacturing.
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Affiliation(s)
- Deepak Sethi
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK; (F.S.); (S.V.)
| | - Thomas O. Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK; (F.S.); (S.V.)
| | - Faqih Shuhaili
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK; (F.S.); (S.V.)
- School of Bioprocess Engineering, Universiti Malaysia Perlis (UniMAP), Arau 02600, Perlis, Malaysia
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 3JD, UK; (F.S.); (S.V.)
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81
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Launay H, Huang W, Maberly SC, Gontero B. Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates. FRONTIERS IN PLANT SCIENCE 2020; 11:1033. [PMID: 32765548 PMCID: PMC7378808 DOI: 10.3389/fpls.2020.01033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.
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Affiliation(s)
- Hélène Launay
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
| | - Wenmin Huang
- BIP, Aix Marseille Univ CNRS, BIP UMR 7281, Marseille, France
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Stephen C. Maberly
- UK Centre for Ecology & Hydrology, Lake Ecosystems Group, Lancaster Environment Centre, Lancaster, United Kingdom
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82
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Seo S, Kim J, Lee JW, Nam O, Chang KS, Jin E. Enhanced pyruvate metabolism in plastids by overexpression of putative plastidial pyruvate transporter in Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:120. [PMID: 32670407 PMCID: PMC7350735 DOI: 10.1186/s13068-020-01760-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/02/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The development of microalgal strains for enhanced biomass and biofuel production has received increased attention. Moreover, strain development via metabolic engineering for commercial production is being considered as the most efficient strategy. Pyruvate is an essential metabolite in the cells and plays an essential role in amino acid biosynthesis and de novo fatty acid biosynthesis in plastids. Although pyruvate can be a valuable target for metabolic engineering, its transporters have rarely been studied in microalgae. In this study, we aimed to identify the plastidial pyruvate transporter of Phaeodactylum tricornutum and utilize it for strain development. RESULTS We identified putative pyruvate transporter localized in the plastid membrane of Phaeodactylum tricornutum. Transformants overexpressing the pyruvate transporter were generated to increase the influx of pyruvate into plastids. Overexpression of a plastidial pyruvate transporter in P. tricornutum resulted in enhanced biomass (13.6% to 21.9%), lipid contents (11% to 30%), and growth (3.3% to 8.0%) compared to those of wild type during one-stage cultivation. CONCLUSION To regulate the pyruvate influx and its metabolism in plastids, we generated transformants overexpressing the putative plastidial pyruvate transporter in P. tricornutum. They showed that its overexpression for compartmentalizing pyruvate in plastids could be an attractive strategy for the effective production of biomass and lipids with better growth, via enhanced pyruvate metabolism in plastids.
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Affiliation(s)
- Seungbeom Seo
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Joon Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Jun-Woo Lee
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Onyou Nam
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Kwang Suk Chang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
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83
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George J, Kahlke T, Abbriano RM, Kuzhiumparambil U, Ralph PJ, Fabris M. Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology. Front Bioeng Biotechnol 2020; 8:513. [PMID: 32582656 PMCID: PMC7290003 DOI: 10.3389/fbioe.2020.00513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Diatoms are photosynthetic microeukaryotes that dominate phytoplankton populations and have increasing applicability in biotechnology. Uncovering their complex biology and elevating strains to commercial standards depends heavily on robust genetic engineering tools. However, engineering microalgal genomes predominantly relies on random integration of transgenes into nuclear DNA, often resulting in detrimental “position-effects” such as transgene silencing, integration into transcriptionally-inactive regions, and endogenous sequence disruption. With the recent development of extrachromosomal transgene expression via independent episomes, it is timely to investigate both strategies at the phenotypic and genomic level. Here, we engineered the model diatom Phaeodactylum tricornutum to produce the high-value heterologous monoterpenoid geraniol, which, besides applications as fragrance and insect repellent, is a key intermediate of high-value pharmaceuticals. Using high-throughput phenotyping we confirmed the suitability of episomes for synthetic biology applications and identified superior geraniol-yielding strains following random integration. We used third generation long-read sequencing technology to generate a complete analysis of all transgene integration events including their genomic locations and arrangements associated with high-performing strains at a genome-wide scale with subchromosomal detail, never before reported in any microalga. This revealed very large, highly concatenated insertion islands, offering profound implications on diatom functional genetics and next generation genome editing technologies, and is key for developing more precise genome engineering approaches in diatoms, including possible genomic safe harbour locations to support high transgene expression for targeted integration approaches. Furthermore, we have demonstrated that exogenous DNA is not integrated inadvertently into the nuclear genome of extrachromosomal-expression clones, an important characterisation of this novel engineering approach that paves the road to synthetic biology applications.
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Affiliation(s)
- Jestin George
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Raffaela M Abbriano
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | | | - Peter J Ralph
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Michele Fabris
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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84
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Gholami P, Khataee A, Bhatnagar A. Environmentally superior cleaning of diatom frustules using sono-Fenton process: Facile fabrication of nanoporous silica with homogeneous morphology and controlled size. ULTRASONICS SONOCHEMISTRY 2020; 64:105044. [PMID: 32146334 DOI: 10.1016/j.ultsonch.2020.105044] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
Existing techniques for the preparation of silica structures from diatom cells include cleaning of frustules through baking at high temperature and oxidant cleaning using concentrated sulfuric acid, hydrogen peroxide, nitric acid, or sodium dodecyl sulfate (SDS)/ethylenediaminetetraacetic acid (EDTA). In this study, sono-Fenton (SF) process was examined to prepare nanoporous silica through cleaning diatom frustules, while preserving their structural features. Single colonies of Cyclotella sp. were cultivated in batch mode f/2-enriched seawater. Combination of Fenton process with ultrasonication was found to be more efficient than the sum of individual processes in the removal of organic compounds from Cyclotella sp. structure. The optimized amounts of operational parameters were determined as suspension pH of 3, diatom cell density of 4.8 × 105 cell mL-1, H2O2 concentration of 60 mM, Fe2+ concentration of 15 mM, ultrasound irradiation power of 400 W and the temperature of 45 °C. The results of energy-dispersive X-ray spectroscopy (EDX) and thermal gravimetry (TG) analyses proved that organic materials covering the cell wall were significantly removed from the frustules through SF process. Scanning electron microscopy (SEM) images showed that after SF treatment, silica nanostructures were produced having uniform pores less than 15 nm in diameter. N2 adsorption-desorption isotherms demonstrated that almost non-porous structure of diatom frustules became mesoporous during removing the organic matrix. Lipids, amino acids, carbohydrates and organic acids or their oxidized products were identified using GC-MS analysis as the main organic compounds released from diatom cells to the solution after SF treatment. Treated frustules exhibited adsorption capability of 91.2 mg/g for Methylene Blue, which was almost 2.5 times higher than that of untreated frustules (34.8 mg/g).
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Affiliation(s)
- Peyman Gholami
- Research Laboratory of Advanced Water and Wastewater Treatment Processes, Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, 51666-16471 Tabriz, Iran; Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Alireza Khataee
- Research Laboratory of Advanced Water and Wastewater Treatment Processes, Department of Applied Chemistry, Faculty of Chemistry, University of Tabriz, 51666-16471 Tabriz, Iran; Department of Materials Science and Nanotechnology Engineering, Faculty of Engineering, Near East University, 99138, Nicosia, TRNC, Mersin 10, Turkey; Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam.
| | - Amit Bhatnagar
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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85
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Dourou M, Dritsas P, Baeshen MN, Elazzazy A, Al-Farga A, Aggelis G. High-added value products from microalgae and prospects of aquaculture wastewaters as microalgae growth media. FEMS Microbiol Lett 2020; 367:5837083. [PMID: 32407478 DOI: 10.1093/femsle/fnaa081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Abstract
Aquaculture plays an important role in human nutrition and economic development but is often expanded to the detriment of the natural environment. Several research projects, aimed at cultivating microalgae in aquaculture wastewaters (AWWs) to reduce organic loads and minerals, along with the production of microalgal cell mass and metabolic products, are underway. Microalgal cell mass is of high nutritional value and is regarded as a candidate to replace, partially at least, the fish meal in the fish feed. Also, microalgal cell mass is considered as a feedstock in the bio-fuel manufacture, as well as a source of high-added value metabolic products. The production of these valuable products can be combined with the reuse of AWWs in the light of environmental concerns related with the aquaculture sector. Many research papers published in the last decade demonstrate that plenty of microalgae species are able to efficiently grow in AWWs, mainly derived from fish and shrimp farms, and produce valuable metabolites reducing the AWW pollutant load. We conclude that bio-remediation of AWWs combining with the production of microalgae cell mass and specific metabolites is probably the most convenient and economical solution for AWWs management and can contribute to the sustainable growth of the aquaculture.
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Affiliation(s)
- Marianna Dourou
- Unit of Microbiology, Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Panagiotis Dritsas
- Unit of Microbiology, Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Mohamed N Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, 23218 Jeddah, Saudi Arabia
| | - Ahmed Elazzazy
- Department of Biology, Faculty of Science, University of Jeddah, 23218 Jeddah, Saudi Arabia
- Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical and Drug Industries, National Research Centre, Dokki, 12622 Giza, Egypt
| | - Ammar Al-Farga
- Department of Biology, Faculty of Science, University of Jeddah, 23218 Jeddah, Saudi Arabia
| | - George Aggelis
- Unit of Microbiology, Division of Genetics, Cell and Developmental Biology, Department of Biology, University of Patras, 26504 Patras, Greece
- Department of Biology, Faculty of Science, University of Jeddah, 23218 Jeddah, Saudi Arabia
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86
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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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87
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Nawaly H, Tsuji Y, Matsuda Y. Rapid and precise genome editing in a marine diatom, Thalassiosira pseudonana by Cas9 nickase (D10A). ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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88
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Patel A, Karageorgou D, Rova E, Katapodis P, Rova U, Christakopoulos P, Matsakas L. An Overview of Potential Oleaginous Microorganisms and Their Role in Biodiesel and Omega-3 Fatty Acid-Based Industries. Microorganisms 2020; 8:E434. [PMID: 32204542 PMCID: PMC7143722 DOI: 10.3390/microorganisms8030434] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Microorganisms are known to be natural oil producers in their cellular compartments. Microorganisms that accumulate more than 20% w/w of lipids on a cell dry weight basis are considered as oleaginous microorganisms. These are capable of synthesizing vast majority of fatty acids from short hydrocarbonated chain (C6) to long hydrocarbonated chain (C36), which may be saturated (SFA), monounsaturated (MUFA), or polyunsaturated fatty acids (PUFA), depending on the presence and number of double bonds in hydrocarbonated chains. Depending on the fatty acid profile, the oils obtained from oleaginous microorganisms are utilized as feedstock for either biodiesel production or as nutraceuticals. Mainly microalgae, bacteria, and yeasts are involved in the production of biodiesel, whereas thraustochytrids, fungi, and some of the microalgae are well known to be producers of very long-chain PUFA (omega-3 fatty acids). In this review article, the type of oleaginous microorganisms and their expertise in the field of biodiesel or omega-3 fatty acids, advances in metabolic engineering tools for enhanced lipid accumulation, upstream and downstream processing of lipids, including purification of biodiesel and concentration of omega-3 fatty acids are reviewed.
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Affiliation(s)
- Alok Patel
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Dimitra Karageorgou
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Emma Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Petros Katapodis
- Laboratory of Biotechnology, Department of Biological Applications and Technologies, University of Ioannina, Ioannina 45110, Greece; (D.K.); (P.K.)
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental, and Natural Resources Engineering, Luleå University of Technology, SE-971 87 Luleå, Sweden; (A.P.); (E.R.); (U.R.); (P.C.)
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Ryu AJ, Kang NK, Jeon S, Hur DH, Lee EM, Lee DY, Jeong BR, Chang YK, Jeong KJ. Development and characterization of a Nannochloropsis mutant with simultaneously enhanced growth and lipid production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:38. [PMID: 32158502 PMCID: PMC7057510 DOI: 10.1186/s13068-020-01681-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/13/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND The necessity to develop high lipid-producing microalgae is emphasized for the commercialization of microalgal biomass, which is environmentally friendly and sustainable. Nannochloropsis are one of the best industrial microalgae and have been widely studied for their lipids, including high-value polyunsaturated fatty acids (PUFAs). Many reports on the genetic and biological engineering of Nannochloropsis to improve their growth and lipid contents have been published. RESULTS We performed insertional mutagenesis in Nannochloropsis salina, and screened mutants with high lipid contents using fluorescence-activated cell sorting (FACS). We isolated a mutant, Mut68, which showed improved growth and a concomitant increase in lipid contents. Mut68 exhibited 53% faster growth rate and 34% higher fatty acid methyl ester (FAME) contents after incubation for 8 days, resulting in a 75% increase in FAME productivity compared to that in the wild type (WT). By sequencing the whole genome, we identified the disrupted gene in Mut68 that encoded trehalose-6-phosphate (T6P) synthase (TPS). TPS is composed of two domains: TPS domain and T6P phosphatase (TPP) domain, which catalyze the initial formation of T6P and dephosphorylation to trehalose, respectively. Mut68 was disrupted at the TPP domain in the C-terminal half, which was confirmed by metabolic analyses revealing a great reduction in the trehalose content in Mut68. Consistent with the unaffected N-terminal TPS domain, Mut68 showed moderate increase in T6P that is known for regulation of sugar metabolism, growth, and lipid biosynthesis. Interestingly, the metabolic analyses also revealed a significant increase in stress-related amino acids, including proline and glutamine, which may further contribute to the Mut68 phenotypes. CONCLUSION We have successfully isolated an insertional mutant showing improved growth and lipid production. Moreover, we identified the disrupted gene encoding TPS. Consistent with the disrupted TPP domain, metabolic analyses revealed a moderate increase in T6P and greatly reduced trehalose. Herein, we provide an excellent proof of concept that the selection of insertional mutations via FACS can be employed for the isolation of mutants with improved growth and lipid production. In addition, trehalose and genes encoding TPS will provide novel targets for chemical and genetic engineering, in other microalgae and organisms as well as Nannochloropsis.
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Affiliation(s)
- Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Nam Kyu Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Present Address: Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Dong Hoon Hur
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Eun Mi Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Do Yup Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Byeong-ryool Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Present Address: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919 Korea
- Present Address: Single-Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Qingdao, 266101 Shandong China
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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Barolo L, Abbriano RM, Commault AS, George J, Kahlke T, Fabris M, Padula MP, Lopez A, Ralph PJ, Pernice M. Perspectives for Glyco-Engineering of Recombinant Biopharmaceuticals from Microalgae. Cells 2020; 9:E633. [PMID: 32151094 PMCID: PMC7140410 DOI: 10.3390/cells9030633] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Microalgae exhibit great potential for recombinant therapeutic protein production, due to lower production costs, immunity to human pathogens, and advanced genetic toolkits. However, a fundamental aspect to consider for recombinant biopharmaceutical production is the presence of correct post-translational modifications. Multiple recent studies focusing on glycosylation in microalgae have revealed unique species-specific patterns absent in humans. Glycosylation is particularly important for protein function and is directly responsible for recombinant biopharmaceutical immunogenicity. Therefore, it is necessary to fully characterise this key feature in microalgae before these organisms can be established as industrially relevant microbial biofactories. Here, we review the work done to date on production of recombinant biopharmaceuticals in microalgae, experimental and computational evidence for N- and O-glycosylation in diverse microalgal groups, established approaches for glyco-engineering, and perspectives for their application in microalgal systems. The insights from this review may be applied to future glyco-engineering attempts to humanize recombinant therapeutic proteins and to potentially obtain cheaper, fully functional biopharmaceuticals from microalgae.
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Affiliation(s)
- Lorenzo Barolo
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Audrey S. Commault
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Jestin George
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
- CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD 4001, Australia
| | - Matthew P. Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo NSW 2007, Sydney, Australia;
| | - Angelo Lopez
- Department of Chemistry, University of York, York, YO10 5DD, UK;
| | - Peter J. Ralph
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
| | - Mathieu Pernice
- Climate Change Cluster, University of Technology Sydney, Broadway Campus, Ultimo NSW 2007, Sydney, Australia; (R.M.A.); (A.S.C.); (J.G.); (T.K.); (M.F.); (P.J.R.)
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Ng I, Keskin BB, Tan S. A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria. Biotechnol J 2020; 15:e1900228. [DOI: 10.1002/biot.201900228] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Indexed: 12/13/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Batuhan Birol Keskin
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
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92
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Wang B, Jia J. Photoprotection mechanisms of Nannochloropsis oceanica in response to light stress. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101784] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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93
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Rastogi A, Vieira FRJ, Deton-Cabanillas AF, Veluchamy A, Cantrel C, Wang G, Vanormelingen P, Bowler C, Piganeau G, Hu H, Tirichine L. A genomics approach reveals the global genetic polymorphism, structure, and functional diversity of ten accessions of the marine model diatom Phaeodactylum tricornutum. THE ISME JOURNAL 2020; 14:347-363. [PMID: 31624346 PMCID: PMC6976637 DOI: 10.1038/s41396-019-0528-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/24/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022]
Abstract
Diatoms emerged in the Mesozoic period and presently constitute one of the main primary producers in the world's ocean and are of a major economic importance. In the current study, using whole genome sequencing of ten accessions of the model diatom Phaeodactylum tricornutum, sampled at broad geospatial and temporal scales, we draw a comprehensive landscape of the genomic diversity within the species. We describe strong genetic subdivisions of the accessions into four genetic clades (A-D) with constituent populations of each clade possessing a conserved genetic and functional makeup, likely a consequence of the limited dispersal of P. tricornutum in the open ocean. We further suggest dominance of asexual reproduction across all the populations, as implied by high linkage disequilibrium. Finally, we show limited yet compelling signatures of genetic and functional convergence inducing changes in the selection pressure on many genes and metabolic pathways. We propose these findings to have significant implications for understanding the genetic structure of diatom populations in nature and provide a framework to assess the genomic underpinnings of their ecological success and impact on aquatic ecosystems where they play a major role. Our work provides valuable resources for functional genomics and for exploiting the biotechnological potential of this model diatom species.
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Affiliation(s)
- Achal Rastogi
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Corteva Agriscience™, The V Ascendas, Atria Block, 12th Floor, Madhapur, Hyderabad, 500081, India
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Alaguraj Veluchamy
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Biological and Environmental Sciences and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Catherine Cantrel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China
| | - Pieter Vanormelingen
- Department of Biology, Research Group Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281/S8 9000, Gent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Gwenael Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, 430072, Wuhan, China.
| | - Leila Tirichine
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France.
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94
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Butler T, Kapoore RV, Vaidyanathan S. Phaeodactylum tricornutum: A Diatom Cell Factory. Trends Biotechnol 2020; 38:606-622. [PMID: 31980300 DOI: 10.1016/j.tibtech.2019.12.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.
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Affiliation(s)
- Thomas Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK
| | - Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK; Present address: Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK.
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95
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Poliner E, Clark E, Cummings C, Benning C, Farre EM. A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. ALGAL RES 2020. [DOI: 10.1016/j.algal.2019.101664] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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96
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Mathieu-Rivet E, Mati-Baouche N, Walet-Balieu ML, Lerouge P, Bardor M. N- and O-Glycosylation Pathways in the Microalgae Polyphyletic Group. FRONTIERS IN PLANT SCIENCE 2020; 11:609993. [PMID: 33391324 PMCID: PMC7773692 DOI: 10.3389/fpls.2020.609993] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/23/2020] [Indexed: 05/15/2023]
Abstract
The term microalga refers to various unicellular and photosynthetic organisms representing a polyphyletic group. It gathers numerous species, which can be found in cyanobacteria (i.e., Arthrospira) as well as in distinct eukaryotic groups, such as Chlorophytes (i.e., Chlamydomonas or Chlorella) and Heterokonts (i.e., diatoms). This phylogenetic diversity results in an extraordinary variety of metabolic pathways, offering large possibilities for the production of natural compounds like pigments or lipids that can explain the ever-growing interest of industrials for these organisms since the middle of the last century. More recently, several species have received particular attention as biofactories for the production of recombinant proteins. Indeed, microalgae are easy to grow, safe and cheap making them attractive alternatives as heterologous expression systems. In this last scope of applications, the glycosylation capacity of these organisms must be considered as this post-translational modification of proteins impacts their structural and biological features. Although these mechanisms are well known in various Eukaryotes like mammals, plants or insects, only a few studies have been undertaken for the investigation of the protein glycosylation in microalgae. Recently, significant progresses have been made especially regarding protein N-glycosylation, while O-glycosylation remain poorly known. This review aims at summarizing the recent data in order to assess the state-of-the art knowledge in glycosylation processing in microalgae.
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Affiliation(s)
| | | | | | - Patrice Lerouge
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Muriel Bardor
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576, CNRS, Université de Lille, Lille, France
- *Correspondence: Muriel Bardor,
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97
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Sasaki M, Takagi A, Ota S, Kawano S, Sasaki D, Asayama M. Coproduction of lipids and extracellular polysaccharides from the novel green alga Parachlorella sp. BX1.5 depending on cultivation conditions. ACTA ACUST UNITED AC 2019; 25:e00392. [PMID: 31871922 PMCID: PMC6909058 DOI: 10.1016/j.btre.2019.e00392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 12/22/2022]
Abstract
A novel strain of microalga Parachlorella sp. BX1.5 was isolated and its unique properties of producing lipids and extracellular polysaccharides (EPS) characterized. The cells could extracellularly produce a large amount of acidic EPS, when cultured in nitrogen-deficient BG110 medium (BG11–N) with 2 % CO2-air supply. The main component of intracellularly accumulated lipids was triacylglycerol (TAG), depending on the different cultivation conditions of BG11, BG11–N, BG11–P (phosphate depleted), and BG11–N–P (nitrogen and phosphate depleted). Fatty-methyl-esters (FAMEs), methyl-esterification of total lipids, consisted of abundant saturated C16 and unsaturated C18 fatty acids under the culture conditions. Cell spot assays on BG11 plates revealed the resistance of cells to pH 2–11, high temperatures of 50–70 °C, ultraviolet irradiation, and drought, under different culture conditions, thereby suggesting the biological significance of lipid and EPS accumulation. The prospects of BX1.5 as a dual producer has also been discussed for biorefineries.
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Affiliation(s)
- Mitsuki Sasaki
- College of Agriculture, Ibaraki University, 3-21-1 Ami, Ibaraki, 300-0393, Japan
| | - Akari Takagi
- College of Agriculture, Ibaraki University, 3-21-1 Ami, Ibaraki, 300-0393, Japan
| | - Shuhei Ota
- Department of Integrated Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shigeyuki Kawano
- Department of Integrated Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
- Future Center Initiative, The University of Tokyo, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan
| | - Daisaku Sasaki
- BioX Chemical Industries Co. Ltd., 2-20-11 Inokuchidai, Nishi-ku, Hiroshima 733-0844, Japan
| | - Munehiko Asayama
- College of Agriculture, Ibaraki University, 3-21-1 Ami, Ibaraki, 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Fuchu, Tokyo, 183-8509, Japan
- Corresponding author at: College of Agriculture, Ibaraki University, 3-21-1 Ami, Ibaraki, 300-0393, Japan.
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98
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Sun XM, Ren LJ, Zhao QY, Zhang LH, Huang H. Application of chemicals for enhancing lipid production in microalgae-a short review. BIORESOURCE TECHNOLOGY 2019; 293:122135. [PMID: 31540787 DOI: 10.1016/j.biortech.2019.122135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 05/05/2023]
Abstract
Microalgae have attracted great attention as a promising sustainable resource for biofuel production. In studies aiming to improve lipid accumulation, many key enzymes involved in lipid biosynthesis were identified and confirmed, but genetic engineering remains a challenge in most species of microalgae. In an alternative approach, various chemical modulators can be used to directly regulate the lipid biosynthesis pathway, with similar effects to gene overexpression and interference approaches, including improving the precursor supply and blocking competing pathways. The produced lipid can be protected from being converted into other metabolites by the chemicals such as lipase inhibitors. In addition, a few chemicals were also demonstrated to greatly influence cell growth and lipid accumulation by indirect regulation of the lipid biosynthesis pathway, such as increasing cell permeability or regulating oxidative stress. Thus, adding chemical modulators can be a useful alternative strategy for improving lipid accumulation in large-scale cultivation of microalgae.
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Affiliation(s)
- Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu Province, China
| | - Lu-Jing Ren
- Jiangsu National Synergetic Innovation Center for Advanced Materials, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, School of Pharmacy, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
| | - Quan-Yu Zhao
- Jiangsu National Synergetic Innovation Center for Advanced Materials, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, School of Pharmacy, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
| | - Li-Hui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu Province, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu Province, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, School of Pharmacy, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, China
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Yang L, Li H, Zhang Y, Jiao N. Environmental risk assessment of triazine herbicides in the Bohai Sea and the Yellow Sea and their toxicity to phytoplankton at environmental concentrations. ENVIRONMENT INTERNATIONAL 2019; 133:105175. [PMID: 31629173 DOI: 10.1016/j.envint.2019.105175] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/04/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Herbicides have been increasingly used worldwide and a large amount of herbicide residue eventually enters the ocean via groundwater or surface run-off every year. However, the global coastal pollution status of herbicides and their negative impact on marine life (especially phytoplankton) in natural environmental concentrations are poorly understood except for few special environments (e.g. the Great Barrier Reef, Australia). Our field investigation of the distribution of ten triazine herbicides in the Bohai Sea and the Yellow Sea of China revealed that the concentrations of triazine herbicides exceeded the "No Observed Effect Concentrations" for phytoplankton. Their total concentrations could be as high as 6.61 nmol L-1. Based on the concentration addition model, the toxicity of herbicide homologues is usually cumulative, and the combined toxicity of these ten triazine herbicides could cause 13.2% inhibition on the chlorophyll a fluorescence intensity of a representative diatom species Phaeodactylum tricornutum Pt-1, which corresponds roughly to the toxicity of atrazine in an equivalent concentration of 14.08 nmol L-1. Atrazine in this equivalent-effect concentration could greatly inhibit the growth of cells, the maximum quantum efficiency of photosystem II (Fv/Fm), and nutrient absorption of Phaeodactylum tricornutum Pt-1. Transcriptome analysis revealed that multiple metabolic pathways (Calvin cycle, tricarboxylic acid (TCA) cycle, glycolysis/gluconeogenesis, etc.) related with photosynthesis and carbon metabolism were greatly disturbed, which might ultimately influence the primary productivity of coastal waters. Moreover, with the values of its bioaccumulation factor ranging from 69.6 to 118.9, atrazine was found to be accumulated in algal cells, which indicates that herbicide pollution might eventually affect the marine food web and even threaten the seafood safety of human beings.
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Affiliation(s)
- Liqiang Yang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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Antonacci A, Scognamiglio V. Biotechnological Advances in the Design of Algae-Based Biosensors. Trends Biotechnol 2019; 38:334-347. [PMID: 31706693 DOI: 10.1016/j.tibtech.2019.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/25/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023]
Abstract
In addition to their use in biomass production and bioremediation, algae have been extensively exploited in biosensing applications. Algae-based biosensors have demonstrated potential for sensitive, sustainable, and multiplexed detection of analytes of agroenvironmental and security interest. Their advantages include the availability of different algal bioreceptors including whole cells and their photosynthetic subcomponents, their potential to be integrated into dual transduction miniaturized devices, and the opportunity for continuous environmental monitoring. Despite obstacles including limited stability and selectivity, algae-based biosensing is a realistic prospect that has some recent effective applications. Strategic exploitation of cutting-edge technologies including materials science, nanotechnology, microfluidics, and genome editing will help to achieve the full potential of algae-based sensors.
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Affiliation(s)
- Amina Antonacci
- Institute of Crystallography (IC-CNR), Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015 Monterotondo, Italy.
| | - Viviana Scognamiglio
- Institute of Crystallography (IC-CNR), Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015 Monterotondo, Italy.
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