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Cornejo-Corona I, Boland DJ, Devarenne TP. Method for isolation of high molecular weight genomic DNA from Botryococcus biomass. PLoS One 2024; 19:e0301680. [PMID: 39046949 PMCID: PMC11268603 DOI: 10.1371/journal.pone.0301680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/19/2024] [Indexed: 07/27/2024] Open
Abstract
The development of high molecular weight (HMW) genomic DNA (gDNA) extraction protocols for non-model species is essential to fully exploit long-read sequencing technologies in order to generate genome assemblies that can help answer complex questions about these organisms. Obtaining enough high-quality HMW gDNA can be challenging for these species, especially for tissues rich in polysaccharides such as biomass from species within the Botryococcus genus. The existing protocols based on column-based DNA extraction and biochemical lysis kits can be inefficient and may not be useful due to variations in biomass polysaccharide content. We developed an optimized protocol for the efficient extraction of HMW gDNA from Botryococcus biomass for use in long-read sequencing technologies. The protocol utilized an initial wash step with sorbitol to remove polysaccharides and yielded HMW gDNA concentrations up to 220 ng/μL with high purity. We then demonstrated the suitability of the HMW gDNA isolated from this protocol for long-read sequencing on the Oxford Nanopore PromethION platform for three Botryococcus species. Our protocol can be used as a standard for efficient HMW gDNA extraction in microalgae rich in polysaccharides and may be adapted for other challenging species.
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Affiliation(s)
- Ivette Cornejo-Corona
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Devon J. Boland
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Timothy P. Devarenne
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Wang WN, Li T, Li Y, Zhang Y, Wu HL, Xiang WZ, Li AF. Exopolysaccharides from the Energy Microalga Strain Botryococcus braunii: Purification, Characterization, and Antioxidant Activity. Foods 2022; 11:foods11010110. [PMID: 35010236 PMCID: PMC8750022 DOI: 10.3390/foods11010110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 11/26/2022] Open
Abstract
Botryococcus braunii, a prestigious energy microalga, has recently received widespread attention because it can secrete large amounts of exopolysaccharides (EPS) with potential applications in food, cosmetics, and nutraceuticals. Unfortunately, the insufficiency of research on the bioactivity and structure–activity relationship of B. braunii EPS has impeded the downstream applications. In the present study, alcohol precipitation, deproteinization, and DEAE-cellulose column chromatography were used to extract and purify B. braunii SCS-1905 EPS. It was found that B. braunii SCS-1905 EPS were high-molecular-weight heteropolysaccharides containing uronic acid (7.43–8.83%), protein (2.30–4.04%), and sulfate groups (1.52–1.95%). Additionally, the EPS primarily comprised galactose (52.34–54.12%), glucose (34.60–35.53%), arabinose (9.41–10.32%), and minor amounts of fucose (1.80–1.99%), with the presence of a pyranose ring linked by a β-configurational glycosidic bond. Notably, the antioxidant activity of crude exopolysaccharides (CEPS) was stronger, and the half maximal inhibitory concentration (IC50) for ABTS and hydroxyl radicals was significantly lower than that of deproteinized exopolysaccharides (DEPS). Overall, this study indicated a potential application of B. braunii SCS-1905 EPS as a natural antioxidant. In summary, B. braunii EPS could be used as a potential feedstock for the production of antioxidant health foods.
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Affiliation(s)
- Wei-Nan Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.-N.W.); (T.L.); (H.-L.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.-N.W.); (T.L.); (H.-L.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yi Li
- Engineering Research Center for Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, China; (Y.L.); (Y.Z.)
| | - Ying Zhang
- Engineering Research Center for Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, China; (Y.L.); (Y.Z.)
| | - Hua-Lian Wu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.-N.W.); (T.L.); (H.-L.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Wen-Zhou Xiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Institution of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (W.-N.W.); (T.L.); (H.-L.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (W.-Z.X.); (A.-F.L.); Tel.: +86-20-89023223 (W.-Z.X.); +86-20-85224366 (A.-F.L.)
| | - Ai-Fen Li
- Engineering Research Center for Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou 510632, China; (Y.L.); (Y.Z.)
- Correspondence: (W.-Z.X.); (A.-F.L.); Tel.: +86-20-89023223 (W.-Z.X.); +86-20-85224366 (A.-F.L.)
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Ross IL, Shah S, Hankamer B, Amiralian N. Microalgal nanocellulose - opportunities for a circular bioeconomy. TRENDS IN PLANT SCIENCE 2021; 26:924-939. [PMID: 34144878 DOI: 10.1016/j.tplants.2021.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Over 3 billion years, photosynthetic algae have evolved complex uses for cellulose, the most abundant polymer worldwide. A major cell-wall component of lignocellulosic plants, seaweeds, microalgae, and bacteria, cellulose can be processed to nanocellulose, a promising nanomaterial with novel properties. The structural diversity of macro- and microalgal nanocelluloses opens opportunities to couple low-impact biomass production with novel, green-chemistry processing to yield valuable, sustainable nanomaterials for a multitude of applications ranging from novel wound dressings to organic solar cells. We review the origins of algal cellulose and the applications and uses of nanocellulose, and highlight the potential for microalgae as a nanocellulose source. Given the limited state of current knowledge, we identify research challenges and strategies to help to realise this potential.
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Affiliation(s)
- Ian L Ross
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Sarah Shah
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Nasim Amiralian
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.
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Structure of the polysaccharide sheath from the B race of the green microalga Botryococcus braunii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Cheng P, Okada S, Zhou C, Chen P, Huo S, Li K, Addy M, Yan X, Ruan RR. High-value chemicals from Botryococcus braunii and their current applications - A review. BIORESOURCE TECHNOLOGY 2019; 291:121911. [PMID: 31383389 DOI: 10.1016/j.biortech.2019.121911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Botryococcus braunii is known for its high yield of extracellular hydrocarbons and polysaccharides. Hydrocarbons, especially botryococcenes and squalene can be used as not only fuels but also alternative feedstock for other fossil-based products. Exopolysaccharides excreted from B. braunii can be used as scaffolds for polyesters production, and have a notable potential for synthesis of nanoparticles. B. braunii is also a rich source of carotenoids, especially the unique secondary carotenoids such as botryoxanthins that have never been found in other microalgae. The morphology, physiology, and outer cell walls of B. braunii are complex. Understanding the colony structure shall provide insights into the mechanism of cell growth and chemicals secretion. It is possible to improve the production economics of the alga with advanced culture systems. Moreover, investigation of metabolic pathways for B. braunii may help us understand their regulation and provide valuable information for strain selection and optimal production of high-value chemicals.
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Affiliation(s)
- Pengfei Cheng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Shigeru Okada
- Department of Aquatic Biosciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Chengxu Zhou
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Paul Chen
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Shuhao Huo
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Kun Li
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Min Addy
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Roger R Ruan
- Department of Bioproducts and Biosystems Engineering, University of Minnesota-Twin Cities, Saint Paul, MN 55108, USA.
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