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Reyes-Weiss DS, Bligh M, Rhein-Knudsen N, Hehemann JH, Liebeke M, Westereng B, Horn SJ. Application of MALDI-MS for characterization of fucoidan hydrolysates and screening of endo-fucoidanase activity. Carbohydr Polym 2024; 340:122317. [PMID: 38858030 DOI: 10.1016/j.carbpol.2024.122317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/12/2024]
Abstract
Brown macroalgae synthesize large amounts of fucoidans, sulfated fucose-containing polysaccharides, in the ocean. Fucoidans are of importance for their recently discovered contribution to marine carbon dioxide sequestration and due to their potential applications in biotechnology and biomedicine. However, fucoidans have high intra- and intermolecular diversity that challenges assignment of structure to biological function and the development of applications. Fucoidan-active enzymes may be used to simplify this diversity by producing defined oligosaccharides more applicable for structural refinement, characterization, and structure to function assignment for example via bioassays. In this study, we combined MALDI mass spectrometry with biocatalysis to show that the endo-fucoidanases P5AFcnA and Wv323 can produce defined oligosaccharide structures directly from unrefined macroalgal biomass. P5AFcnA released oligosaccharides from seven commercial fucoidan extracts in addition to unrefined biomass of three macroalgae species indicating a broadly applicable approach reproducible across 10 species. Both MALDI-TOF/TOF and AP-MALDI-Orbitrap systems were used, demonstrating that the approach is not instrument-specific and exploiting their combined high-throughput and high-resolution capabilities. Overall, the combination of MALDI-MS and endo-fucoidanase assays offers high-throughput evaluation of fucoidan samples and also enables extraction of defined oligosaccharides of known structure from unrefined seaweed biomass.
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Affiliation(s)
- Diego S Reyes-Weiss
- Department of Chemistry, Biotechnology, and Life Science, Norwegian University of Life Sciences (NMBU), Christian Magnus Falsens vei 18, 1433 Ås, Norway
| | - Margot Bligh
- University of Bremen, MARUM Centre for Marine Environmental Sciences, Leobener Str. 8, D-28359 Bremen, Germany; Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Nanna Rhein-Knudsen
- Department of Chemistry, Biotechnology, and Life Science, Norwegian University of Life Sciences (NMBU), Christian Magnus Falsens vei 18, 1433 Ås, Norway
| | - Jan-Hendrik Hehemann
- University of Bremen, MARUM Centre for Marine Environmental Sciences, Leobener Str. 8, D-28359 Bremen, Germany; Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany; University of Kiel, Institute for Human Nutrition and Food Science, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Bjørge Westereng
- Department of Chemistry, Biotechnology, and Life Science, Norwegian University of Life Sciences (NMBU), Christian Magnus Falsens vei 18, 1433 Ås, Norway
| | - Svein Jarle Horn
- Department of Chemistry, Biotechnology, and Life Science, Norwegian University of Life Sciences (NMBU), Christian Magnus Falsens vei 18, 1433 Ås, Norway.
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2
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Chen G, Dong S, Zhang Y, Shen J, Liu G, Chen F, Li X, Xue C, Cui Q, Feng Y, Chang Y. Structural investigation of Fun168A unraveling the recognition mechanism of endo-1,3-fucanase towards sulfated fucan. Int J Biol Macromol 2024; 271:132622. [PMID: 38795894 DOI: 10.1016/j.ijbiomac.2024.132622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/05/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
BACKGROUND Sulfated fucan has gained interest due to its various physiological activities. Endo-1,3-fucanases are valuable tools for investigating the structure and establishing structure-activity relationships of sulfated fucan. However, the substrate recognition mechanism of endo-1,3-fucanases towards sulfated fucan remains unclear, limiting the application of endo-1,3-fucanases in sulfated fucan research. SCOPE AND APPROACH This study presented the first crystal structure of endo-1,3-fucanase (Fun168A) and its complex with the tetrasaccharide product, utilizing X-ray diffraction techniques. The novel subsite specificity of Fun168A was identified through glycomics and nuclear magnetic resonance (NMR). KEY FINDINGS AND CONCLUSIONS The structure of Fun168A was determined at 1.92 Å. Residues D206 and E264 acted as the nucleophile and general acid/base, respectively. Notably, Fun168A strategically positioned a series of polar residues at the subsites ranging from -2 to +3, enabling interactions with the sulfate groups of sulfated fucan through salt bridges or hydrogen bonds. Based on the structure of Fun168A and its substrate recognition mechanisms, the novel subsite specificities at the -2 and +2 subsites of Fun168A were identified. Overall, this study provided insight into the structure and substrate recognition mechanism of endo-1,3-fucanase for the first time and offered a valuable tool for further research and development of sulfated fucan.
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Affiliation(s)
- Guangning Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Fangyi Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Xinyu Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China.
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3
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Macdonald JFH, Pérez-García P, Schneider YKH, Blümke P, Indenbirken D, Andersen JH, Krohn I, Streit WR. Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation. Sci Rep 2024; 14:10237. [PMID: 38702505 PMCID: PMC11068906 DOI: 10.1038/s41598-024-60978-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Enzymatic degradation of algae cell wall carbohydrates by microorganisms is under increasing investigation as marine organic matter gains more value as a sustainable resource. The fate of carbon in the marine ecosystem is in part driven by these degradation processes. In this study, we observe the microbiome dynamics of the macroalga Fucus vesiculosus in 25-day-enrichment cultures resulting in partial degradation of the brown algae. Microbial community analyses revealed the phylum Pseudomonadota as the main bacterial fraction dominated by the genera Marinomonas and Vibrio. More importantly, a metagenome-based Hidden Markov model for specific glycosyl hydrolyses and sulphatases identified Bacteroidota as the phylum with the highest potential for cell wall degradation, contrary to their low abundance. For experimental verification, we cloned, expressed, and biochemically characterised two α-L-fucosidases, FUJM18 and FUJM20. While protein structure predictions suggest the highest similarity to a Bacillota origin, protein-protein blasts solely showed weak similarities to defined Bacteroidota proteins. Both enzymes were remarkably active at elevated temperatures and are the basis for a potential synthetic enzyme cocktail for large-scale algal destruction.
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Affiliation(s)
- Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Pablo Pérez-García
- Institute for General Microbiology, Molecular Microbiology, Kiel University, Kiel, Germany
| | - Yannik K-H Schneider
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Patrick Blümke
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Hamburg, Germany
| | - Jeanette H Andersen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
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4
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Shen J, Zheng L, Zhang Y, Chen G, Mei X, Chang Y, Xue C. Discovery of a catalytic domain defines a new glycoside hydrolase family containing endo-1,3-fucanase. Carbohydr Polym 2024; 323:121442. [PMID: 37940306 DOI: 10.1016/j.carbpol.2023.121442] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023]
Abstract
Sulfated fucans are important marine polysaccharides with various bioactivities. Fucanases are desirable tools for the structural elucidations and oligosaccharides preparation of sulfated fucans. Herein, a gene with unknown function was screened from a sulfated fucan utilization locus in genome of marine bacterium Wenyingzhuangia aestuarii OF219 with the assistance of a machine learning approach on the structural biology. An undefined catalytic domain that presented in this gene was further cloned and expressed in Escherichia coli. Utilizing a sulfated fucan tetrasaccharide with definite structure as substrate, the endo-acting cleavage point of expressed protein (named Fun187A) was identified as the α-l-1,3-glycosidic bond between Fucp and Fucp(2OSO3-). Fun187A demonstrated a novel cleavage specificity, that is the subsite -1 could tolerate α-l-Fucp, and the subsite +1 could tolerate α-l-Fucp(2OSO3-). A homologue of Fun187A was also validated to display the endo-1,3-fucanse activity. The sequence novelty of Fun187A and its homologue defines a new glycoside hydrolase family, GH187.
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Affiliation(s)
- Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Long Zheng
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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5
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Silchenko AS, Taran IV, Usoltseva RV, Zvyagintsev NV, Zueva AO, Rubtsov NK, Lembikova DE, Nedashkovskaya OI, Kusaykin MI, Isaeva MP, Ermakova SP. The Discovery of the Fucoidan-Active Endo-1→4-α-L-Fucanase of the GH168 Family, Which Produces Fucoidan Derivatives with Regular Sulfation and Anticoagulant Activity. Int J Mol Sci 2023; 25:218. [PMID: 38203394 PMCID: PMC10778895 DOI: 10.3390/ijms25010218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Sulfated polysaccharides of brown algae, fucoidans, are known for their anticoagulant properties, similar to animal heparin. Their complex and irregular structure is the main bottleneck in standardization and in defining the relationship between their structure and bioactivity. Fucoidan-active enzymes can be effective tools to overcome these problems. In the present work, we identified the gene fwf5 encoding the fucoidan-active endo-fucanase of the GH168 family in the marine bacterium Wenyingzhuangia fucanilytica CZ1127T. The biochemical characteristics of the recombinant fucanase FWf5 were investigated. Fucanase FWf5 was shown to catalyze the endo-type cleavage of the 1→4-O-glycosidic linkages between 2-O-sulfated α-L-fucose residues in fucoidans composed of the alternating 1→3- and 1→4-linked residues of sulfated α-L-fucose. This is the first report on the endo-1→4-α-L-fucanases (EC 3.2.1.212) of the GH168 family. The endo-fucanase FWf5 was used to selectively produce high- and low-molecular-weight fucoidan derivatives containing either regular alternating 2-O- and 2,4-di-O-sulfation or regular 2-O-sulfation. The polymeric 2,4-di-O-sulfated fucoidan derivative was shown to have significantly greater in vitro anticoagulant properties than 2-O-sulfated derivatives. The results have demonstrated a new type specificity among fucanases of the GH168 family and the prospects of using such enzymes to obtain standard fucoidan preparations with regular sulfation and high anticoagulant properties.
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Affiliation(s)
- Artem S. Silchenko
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Ilya V. Taran
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Roza V. Usoltseva
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Nikolay V. Zvyagintsev
- Laboratory of Physical and Chemical Research Methods, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia
| | - Anastasiya O. Zueva
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Nikita K. Rubtsov
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Dana E. Lembikova
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Olga I. Nedashkovskaya
- Laboratory of Microbiology, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia;
| | - Mikhail I. Kusaykin
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
| | - Marina P. Isaeva
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia;
| | - Svetlana P. Ermakova
- Laboratory of Enzyme Chemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-Let Vladivostoku, 690022 Vladivostok, Russia (R.V.U.); (A.O.Z.); (N.K.R.); (D.E.L.); (M.I.K.)
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6
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Mikkelsen MD, Tran VHN, Meier S, Nguyen TT, Holck J, Cao HTT, Van TTT, Thinh PD, Meyer AS, Morth JP. Structural and functional characterization of the novel endo-α(1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae. Acta Crystallogr D Struct Biol 2023; 79:1026-1043. [PMID: 37877949 PMCID: PMC10619423 DOI: 10.1107/s2059798323008732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
Fucoidanases (EC 3.2.1.-) catalyze the hydrolysis of glycosidic bonds between fucose residues in fucoidans. Fucoidans are a compositionally and structurally diverse class of fucose-containing sulfated polysaccharides that are primarily found in brown seaweeds. Here, the structural characterization of a novel endo-α(1,4)-fucoidanase, Mef1, from the marine bacterium Muricauda eckloniae is presented, showing sequence similarity to members of glycoside hydrolase family 107. Using carbohydrate polyacrylamide gel electrophoresis and nuclear magnetic resonance analyses, it is shown that the fucoidanase Mef1 catalyzes the cleavage of α(1,4)-linkages between fucose residues sulfated on C2 in the structure [-3)-α-L-Fucp2S-(1,4)-α-L-Fucp2S-(1-]n in fucoidan from Fucus evanescens. Kinetic analysis of Mef1 activity by Fourier transform infrared spectroscopy revealed that the specific Mef1 fucoidanase activity (Uf) on F. evanescens fucoidan was 0.1 × 10-3 Uf µM-1. By crystal structure determination of Mef1 at 1.8 Å resolution, a single-domain organization comprising a (β/α)8-barrel domain was determined. The active site was in an extended, positively charged groove that is likely to be designed to accommodate the binding of the negatively charged, sulfated fucoidan substrate. The active site of Mef1 comprises the amino acids His270 and Asp187, providing acid/base and nucleophile groups, respectively, for the hydrolysis of glycosidic bonds in the fucoidan backbone. Electron densities were identified for two possible Ca2+ ions in the enzyme, one of which is partially exposed to the active-site groove, while the other is very tightly coordinated. A water wire was discovered leading from the exterior of the Mef1 enzyme into the active site, passing the tightly coordinated Ca2+ site.
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Affiliation(s)
- Maria Dalgaard Mikkelsen
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Vy Ha Nguyen Tran
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Thuan Thi Nguyen
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, NhaTrang 650000, Vietnam
| | - Tran Thi Thanh Van
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, NhaTrang 650000, Vietnam
| | - Pham Duc Thinh
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, NhaTrang 650000, Vietnam
| | - Anne S. Meyer
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Jens Preben Morth
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
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7
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Zueva AO, Silchenko AS, Rasin AB, Malyarenko OS, Kusaykin MI, Kalinovsky AI, Ermakova SP. Production of high- and low-molecular weight fucoidan fragments with defined sulfation patterns and heightened in vitro anticancer activity against TNBC cells using novel endo-fucanases of the GH107 family. Carbohydr Polym 2023; 318:121128. [PMID: 37479440 DOI: 10.1016/j.carbpol.2023.121128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/23/2023]
Abstract
Fucoidans are complex fucose-containing sulfated polysaccharides with pronounced anticancer effects. Their structure-anticancer activity relationships are difficult to determine due to fucoidans' complex, often irregularities-including structures. Fucoidan-active enzymes can be used for this propose. We have investigated two new recombinant endo-fucanases FWf3 and FWf4 from the marine bacterium Wenyingzhuangia fucanilytica CZ1127T that belong to the 107 family of glycoside hydrolases (GH). Both enzymes cleaved α-(1→4)-glycosidic bonds but in fucoidan fragments with different sulfation patterns. FWf3 is the first characterized endo-fucanase that cleaves glycosidic bonds between 2O- and 2,4diO-sulfated L-fucose residues. The obtained endo-fucanases were used to produce low- and high-molecular weight fucoidan derivatives with different sulfate group locations. Low- and high-molecular weight fucoidan derivatives rich with 2,4diO-sulfation were shown to inhibit MDA-MB-231 cell colony formation more efficiently than the native fucoidan and the derivatives sulfated otherwise. Such derivatives effectively suppressed the mitochondrial membrane potential of MDA-MB-231 cells and reduced the expression of the glucose transporter 1 (GLUT1). Co-treatment of MDA-MB-231 cells with the fucoidan derivatives and oligomycin (an OXPHOS inhibitor) resulted in a synergistic anticancer effect. The data obtained demonstrate, that fucoidan and its 2,4diO-sulfated derivatives can be an effective adjunct in TNBC therapy targeting cell metabolism.
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Affiliation(s)
- Anastasiya O Zueva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation
| | - Artem S Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation.
| | - Anton B Rasin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation
| | - Olesya S Malyarenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation
| | - Mikhail I Kusaykin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation
| | - Anatoly I Kalinovsky
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation
| | - Svetlana P Ermakova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Enzyme Chemistry, 159 100-Let Vladivostoku Ave., 690022 Vladivostok, Russian Federation.
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8
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Cheong KL, Zhang Y, Li Z, Li T, Ou Y, Shen J, Zhong S, Tan K. Role of Polysaccharides from Marine Seaweed as Feed Additives for Methane Mitigation in Ruminants: A Critical Review. Polymers (Basel) 2023; 15:3153. [PMID: 37571046 PMCID: PMC10420924 DOI: 10.3390/polym15153153] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Given the increasing concerns regarding greenhouse gas emissions associated with livestock production, the need to discover effective strategies to mitigate methane production in ruminants is clear. Marine algal polysaccharides have emerged as a promising research avenue because of their abundance and sustainability. Polysaccharides, such as alginate, laminaran, and fucoidan, which are extracted from marine seaweeds, have demonstrated the potential to reduce methane emissions by influencing the microbial populations in the rumen. This comprehensive review extensively examines the available literature and considers the effectiveness, challenges, and prospects of using marine seaweed polysaccharides as feed additives. The findings emphasise that marine algal polysaccharides can modulate rumen fermentation, promote the growth of beneficial microorganisms, and inhibit methanogenic archaea, ultimately leading to decreases in methane emissions. However, we must understand the long-term effects and address the obstacles to practical implementation. Further research is warranted to optimise dosage levels, evaluate potential effects on animal health, and assess economic feasibility. This critical review provides insights for researchers, policymakers, and industry stakeholders dedicated to advancing sustainable livestock production and methane mitigation.
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Affiliation(s)
- Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Yiyu Zhang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Zhuoting Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Tongtong Li
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Yiqing Ou
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Jiayi Shen
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China; (K.-L.C.)
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf University, Qinzhou 535000, China
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9
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Wang M, Veeraperumal S, Zhong S, Cheong KL. Fucoidan-Derived Functional Oligosaccharides: Recent Developments, Preparation, and Potential Applications. Foods 2023; 12:foods12040878. [PMID: 36832953 PMCID: PMC9956988 DOI: 10.3390/foods12040878] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Oligosaccharides derived from natural resources are attracting increasing attention as both food and nutraceutical products because of their beneficial health effects and lack of toxicity. During the past few decades, many studies have focused on the potential health benefits of fucoidan. Recently, new interest has emerged in fucoidan, partially hydrolysed into fuco-oligosaccharides (FOSs) or low-molecular weight fucoidan, owing to their superior solubility and biological activities compared with fucoidan. There is considerable interest in their development for use in the functional food, cosmetic, and pharmaceutical industries. Therefore, this review summarises and discusses the preparation of FOSs from fucoidan using mild acid hydrolysis, enzymatic depolymerisation, and radical degradation methods, and discusses the advantages and disadvantages of hydrolysis methods. Several purification steps performed to obtain FOSs (according to the latest reports) are also reviewed. Moreover, the biological activities of FOS that are beneficial to human health are summarised based on evidence from in vitro and in vivo studies, and the possible mechanisms for the prevention or treatment of various diseases are discussed.
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Affiliation(s)
- Min Wang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
- Postgraduate College, Guangdong Ocean University, Zhanjiang 524088, China
| | | | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
- Correspondence: (S.Z.); (K.-L.C.)
| | - Kit-Leong Cheong
- Department of Biology, Shantou University, Shantou 515063, China
- Correspondence: (S.Z.); (K.-L.C.)
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10
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Lozada M, Diéguez MC, García PE, Dionisi HM. Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159392. [PMID: 36240919 DOI: 10.1016/j.scitotenv.2022.159392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.
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Affiliation(s)
- Mariana Lozada
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina.
| | - María C Diéguez
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Patricia E García
- Grupo de Ecología de Sistemas Acuáticos a Escala de Paisaje (GESAP, INIBIOMA-CONICET-UNComa), Bariloche, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental (CESIMAR-CONICET/IBIOMAR-CONICET), Puerto Madryn, Argentina
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11
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Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochem Soc Trans 2022; 50:1607-1617. [DOI: 10.1042/bst20220206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022]
Abstract
A large amount of the human proteome is composed of highly dynamic regions that do not adopt a single static conformation. These regions are defined as intrinsically disordered, and they are found in a third of all eukaryotic proteins. They play instrumental roles in many aspects of protein signaling, but can be challenging to characterize by biophysical methods. Intriguingly, many of these regions can adopt stable secondary structure upon interaction with a variety of binding partners, including proteins, lipids, and ligands. This review will discuss the application of Hydrogen-deuterium exchange mass spectrometry (HDX-MS) as a powerful biophysical tool that is particularly well suited for structural and functional characterization of intrinsically disordered regions in proteins. A focus will be on the theory of hydrogen exchange, and its practical application to identify disordered regions, as well as characterize how they participate in protein–protein and protein–membrane interfaces. A particular emphasis will be on how HDX-MS data can be presented specifically tailored for analysis of intrinsically disordered regions, as well as the technical aspects that are critical to consider when designing HDX-MS experiments for proteins containing intrinsically disordered regions.
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12
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Arai Y, Shingu Y, Yagi H, Suzuki H, Ohshiro T. Occurrence of different fucoidanase genes in Flavobacterium sp. SW and enzyme characterization. J Biosci Bioeng 2022; 134:187-194. [PMID: 35780071 DOI: 10.1016/j.jbiosc.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 10/17/2022]
Abstract
Fucoidans are hetero-sulfated polysaccharides that are widely distributed in brown algae and have been extensively studied for their various biological activities. The structure-function relationship of fucoidans remains unclear but can be studied using fucoidan-degrading enzymes (fucoidanases). Here, we isolated and identified Flavobacterium sp. SW as a microbial strain that can grow on fucoidan from Cladosiphon okamuranus as the sole carbon source. Genomic analysis of this strain revealed the presence of two genes, swfct and swfcn2, that are homologous to fct114 from Luteolibacter algae H18 and fcnA from Psychromonas sp. SW5A, respectively. The gene products were produced in Escherichia coli and showed significantly different specificities for fucoidan. Swfct catalyzed the degradation of deacetylated fucoidan from C. okamuranus, and Swfcn2 degraded fucoidans from Saccharina sculpera and Macrocystis pyrifera. The general properties of Swfct were examined by measuring the amounts of reducing ends produced by the enzymatic reaction, and the enzyme properties of Swfcn2 were evaluated by carbohydrate-polyacrylamide gel electrophoresis. Our findings indicate that one microbial strain can harbor genes encoding two different types of fucoidanases.
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Affiliation(s)
- Yoshihito Arai
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Yunako Shingu
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, Tottori 680-8552, Japan
| | - Hisashi Yagi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Hirokazu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Takashi Ohshiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan.
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13
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Tran VHN, Perna V, Mikkelsen MD, Thi Nguyen T, Thi Dieu Trang V, Baum A, Thi Thuy Cao H, Thi Thanh Van T, Meyer AS. A new FTIR assay for quantitative measurement of endo-fucoidanase activity. Enzyme Microb Technol 2022; 158:110035. [PMID: 35489196 DOI: 10.1016/j.enzmictec.2022.110035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 12/16/2022]
Abstract
Endo-fucoidanases, including EC 3.2.1.211 endo-α-1,3-L-fucanase and EC 3.2.1.212 endo-α-1,4-L-fucanase activities, catalyze depolymerization of fucoidans - a group of bioactive, sulfated fucosyl-polysaccharides found primarily in brown macroalgae (brown seaweeds). Quantitative assessment of endo-fucoidanase activity is critical for characterizing endo-fucoidanase kinetics and for comparing the action of different endo-fucoidanases on different types of fucoidans. However, the current state-of-the-art endo-fucoidanase assay consists of a qualitative assessment based on Carbohydrate-Polyacrylamide Gel Electrophoresis. Here, we report a new quantitative endo-fucoidanase assay based on real time spectral evolution profiling of changes in substrate and product during endo-fucoidanase action using Fourier Transform InfraRed spectroscopy (FTIR) combined with Parallel Factor Analysis (PARAFAC). The FTIR-PARAFAC assay was validated by monitoring the reaction progress of three different microbial endo-fucoidanase enzymes, FcnAΔ229, FFA2 and Fhf1Δ470, on two different fucoidan substrates. The substrates were purified from the brown macroalgae Fucus evanescens and Fucus vesiculosus, respectively. The evolution profiling showed that the strongest spectral change of the fucoidans during enzymatic depolymerization occurred in the spectral range 1220-1260 cm-1, but the profiles differed depending on the substrate and the enzyme used. Spectral changes within 1220-1260 cm-1 are in agreement with the enzymatic depolymerization inducing signature changes in the mid-infrared absorption of sulfated fucosyls as sulfate ester bonds and C-O stretching vibrations absorb in this spectral region. Based on the data obtained, we also introduce an activity unit for endo-fucoidanases: One endo-fucoidanase Unit, Uf, is the amount of enzyme able to catalyze a change in the FTIR-PARAFAC score by 0.01 during 498 s of reaction (8.3 min) on 20 g/L pure fucoidan from F. evanescens at 42 °C, pH 7.4, 100 mM NaCl and 10 mM CaCl2. This new quantitative endo-fucoidanase assay can pave the way for better kinetic characterizations as well as novel explorations of endo-fucoidanases.
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Affiliation(s)
- Vy Ha Nguyen Tran
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam
| | - Valentina Perna
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maria Dalgaard Mikkelsen
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thuan Thi Nguyen
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam
| | - Vo Thi Dieu Trang
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam
| | - Andreas Baum
- Section for Statistics and Data Analysis, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam
| | - Tran Thi Thanh Van
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam
| | - Anne S Meyer
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
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14
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Tran VHN, Nguyen TT, Meier S, Holck J, Cao HTT, Van TTT, Meyer AS, Mikkelsen MD. The Endo-α(1,3)-Fucoidanase Mef2 Releases Uniquely Branched Oligosaccharides from Saccharina latissima Fucoidans. Mar Drugs 2022; 20:305. [PMID: 35621956 PMCID: PMC9147238 DOI: 10.3390/md20050305] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 02/05/2023] Open
Abstract
Fucoidans are complex bioactive sulfated fucosyl-polysaccharides primarily found in brown macroalgae. Endo-fucoidanases catalyze the specific hydrolysis of α-L-fucosyl linkages in fucoidans and can be utilized to tailor-make fucoidan oligosaccharides and elucidate new structural details of fucoidans. In this study, an endo-α(1,3)-fucoidanase encoding gene, Mef2, from the marine bacterium Muricauda eckloniae, was cloned, and the Mef2 protein was functionally characterized. Based on the primary sequence, Mef2 was suggested to belong to the glycosyl hydrolase family 107 (GH107) in the Carbohydrate Active enZyme database (CAZy). The Mef2 fucoidanase showed maximal activity at pH 8 and 35 °C, although it could tolerate temperatures up to 50 °C. Ca2+ was shown to increase the melting temperature from 38 to 44 °C and was furthermore required for optimal activity of Mef2. The substrate specificity of Mef2 was investigated, and Fourier transform infrared spectroscopy (FTIR) was used to determine the enzymatic activity (Units per μM enzyme: Uf/μM) of Mef2 on two structurally different fucoidans, showing an activity of 1.2 × 10-3 Uf/μM and 3.6 × 10-3 Uf/μM on fucoidans from Fucus evanescens and Saccharina latissima, respectively. Interestingly, Mef2 was identified as the first described fucoidanase active on fucoidans from S. latissima. The fucoidan oligosaccharides released by Mef2 consisted of a backbone of α(1,3)-linked fucosyl residues with unique and novel α(1,4)-linked fucosyl branches, not previously identified in fucoidans from S. latissima.
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Affiliation(s)
- Vy Ha Nguyen Tran
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Thuan Thi Nguyen
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Jesper Holck
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Tran Thi Thanh Van
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam; (H.T.T.C.); (T.T.T.V.)
| | - Anne S. Meyer
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
| | - Maria Dalgaard Mikkelsen
- Section for Protein Chemistry and Enzyme Technology, DTU Bioengineering-Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (V.H.N.T.); (T.T.N.); (J.H.)
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15
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Expression and Biochemical Characterization of a Novel Fucoidanase from Flavobacteriumalgicola with the Principal Product of Fucoidan-Derived Disaccharide. Foods 2022; 11:foods11071025. [PMID: 35407112 PMCID: PMC8997789 DOI: 10.3390/foods11071025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
Fucoidan is one of the main polysaccharides of brown algae and echinoderm, which has nutritional and pharmacological functions. Due to the low molecular weight and exposure of more sulfate groups, oligo-fucoidan or fucoidan oligosaccharides have potential for broader applications. In this research, a novel endo-α-1,4-L-fucoidanase OUC-FaFcn1 which can degrade fucoidan into oligo-fucoidan was discovered from the fucoidan-digesting strain Flavobacterium algicola 12,076. OUC-FaFcn1 belongs to glycoside hydrolases (GH) family 107 and shows highest activity at 40 °C and pH 9.0. It can degrade the α-1,4 glycosidic bond, instead of α-1,3 glycosidic bond, of the fucoidan with a random tangent way to generate the principal product of disaccharide, which accounts for 49.4% of the total products. Therefore, OUC-FaFcn1 is a promising bio-catalyst for the preparation of fucoidan-derived disaccharide. These results further enrich the resource library of fucoidanase and provide the basis for the directional preparation of fucoidan-derived oligosaccharide with specific polymerization.
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16
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Ropartz D, Marion L, Fanuel M, Nikolic J, Jam M, Larocque R, Ficko-Blean E, Michel G, Rogniaux H. In-depth structural characterization of oligosaccharides released by GH107 endofucanase MfFcnA reveals enzyme subsite specificity and sulfated fucan substructural features. Glycobiology 2022; 32:276-288. [PMID: 34939127 DOI: 10.1093/glycob/cwab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/16/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
The extracellular matrix of brown algae represents an abundant source of fucose-containing sulfated polysaccharides (FCSPs). FCSPs include sulfated fucans, essentially composed of fucose, and highly heterogeneous fucoidans, comprising various monosaccharides. Despite a range of potentially valuable biological activities, the structures of FCSPs are only partially characterized and enzymatic tools leading to their deconstruction are rare. Previously, the enzyme MfFcnA was isolated from the marine bacterium Mariniflexile fucanivorans and biochemically characterized as an endo-α-1 → 4-l-fucanase, the first member of glycoside hydrolase family 107. Here, MfFcnA was used as an enzymatic tool to deconstruct the structure of the sulfated fucans from Pelvetia canaliculata (Fucales brown alga). Oligofucans released by MfFcnA at different time points were characterized using mass spectrometry coupled with liquid chromatography and tandem mass spectrometry through Charge Transfer Dissociation. This approach highlights a large diversity in the structures released. In particular, the analyses show the presence of species with less than three sulfates per two fucose residues. They also reveal species with monosaccharides other than fucose and the occurrence of laterally branched residues. Precisely, the lateral branching is either in the form of a hexose accompanied by a trisulfated fucose nearby, or of a side chain of fucoses with a pentose as the branching point on the polymer. Overall, the results indicate that the structure of sulfated fucans from P. canaliculata is more complex than expected. They also reveal the interesting capacity of MfFcnA to accommodate different substrates, leading to structurally diverse oligofucan products that potentially could be screened for bioactivities.
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Affiliation(s)
- David Ropartz
- INRAE, UR BIA, la Géraudière, F-44316, Nantes, France
- INRAE, BIBS Facility, la Géraudière, F-44316, Nantes, France
| | - Lery Marion
- INRAE, UR BIA, la Géraudière, F-44316, Nantes, France
- INRAE, BIBS Facility, la Géraudière, F-44316, Nantes, France
| | - Mathieu Fanuel
- INRAE, UR BIA, la Géraudière, F-44316, Nantes, France
- INRAE, BIBS Facility, la Géraudière, F-44316, Nantes, France
| | - Jasna Nikolic
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Place George Teissier, F-29680 Roscoff, France
| | - Murielle Jam
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Place George Teissier, F-29680 Roscoff, France
| | - Robert Larocque
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Place George Teissier, F-29680 Roscoff, France
| | - Elizabeth Ficko-Blean
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Place George Teissier, F-29680 Roscoff, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Place George Teissier, F-29680 Roscoff, France
| | - Helene Rogniaux
- INRAE, UR BIA, la Géraudière, F-44316, Nantes, France
- INRAE, BIBS Facility, la Géraudière, F-44316, Nantes, France
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17
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Huang W, Tan H, Nie S. Beneficial effects of seaweed-derived dietary fiber: Highlights of the sulfated polysaccharides. Food Chem 2022; 373:131608. [PMID: 34815114 DOI: 10.1016/j.foodchem.2021.131608] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
Seaweeds and their derivatives are important bioresources of natural bioactive compounds. Nutritional studies indicate that dietary fibers derived from seaweeds have great beneficial potentials in human health and can be developed as functional food. Moreover, sulfated polysaccharides are more likely to be the main bioactive components which are widely distributed in various species of seaweeds including Phaeophyceae, Rhodophyceae and Chlorophyceae. The catabolism by gut microbiota of the seaweeds-derived dietary fibers (DFs) may be one of the pivotal pathways of their physiological functions. Therefore, in this review, we summarized the latest results of the physiological characteristics of seaweed-derived dietary fiber and highlighted the roles of sulfated polysaccharides in the potential regulatory mechanisms against disorders. Meanwhile, the effects of different types of seaweed-derived dietary fiber on gut microbiota were discussed. The analysis of the structure-function correlations and gut microbiota related mechanisms and will contribute to further better applications in food and biotherapeutics.
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Affiliation(s)
- Wenqi Huang
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Huizi Tan
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, 235 Nanjing East Road, Nanchang 330047, China.
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18
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Nikolić Chenais J, Marion L, Larocque R, Jam M, Jouanneau D, Cladiere L, Le Gall S, Fanuel M, Desban N, Rogniaux H, Ropartz D, Ficko-Blean E, Michel G. Systematic comparison of eight methods for preparation of high purity sulfated fucans extracted from the brown alga Pelvetia canaliculata. Int J Biol Macromol 2022; 201:143-157. [PMID: 34968546 DOI: 10.1016/j.ijbiomac.2021.12.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/12/2022]
Abstract
Sulfated fucans from brown algae are a heterogeneous group of biologically active molecules. To learn more on their structure and to analyze and exploit their biological activities, there is a growing need to develop reliable and cost effective protocols for their preparation. In the present study, a brown alga Pelvetia canaliculata (Linnaeus) was used as a rich source of sulfated fucans. Sulfated fucan preparation methods included neutral and acidic extractions followed by purification with activated charcoal (AC), polyvinylpolypyrrolidone (PVPP), or cetylpyridinium chloride (CPC). Final products were compared in terms of yield, purity, monosaccharide composition and molecular weight. Acidic extractions provided higher yields compared to neutral ones, whereas the AC purification provided sulfated fucan products with the highest purity. Mass spectrometry analyses were done on oligosaccharides produced by the fucanase MfFcnA from the marine bacterium Mariniflexille fucanivorans. This has provided unique insight into enzyme specificity and the structural characteristics of sulfated fucans.
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Affiliation(s)
- Jasna Nikolić Chenais
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Léry Marion
- INRAE, UR BIA, F-44316 Nantes, France; INRAE, BIBS facility, PROBE infrastructure, F-44316 Nantes, France
| | - Robert Larocque
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Murielle Jam
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Lionel Cladiere
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Sophie Le Gall
- INRAE, UR BIA, F-44316 Nantes, France; INRAE, BIBS facility, PROBE infrastructure, F-44316 Nantes, France
| | - Mathieu Fanuel
- INRAE, UR BIA, F-44316 Nantes, France; INRAE, BIBS facility, PROBE infrastructure, F-44316 Nantes, France
| | - Nathalie Desban
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France; INRAE, BIBS facility, PROBE infrastructure, F-44316 Nantes, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France; INRAE, BIBS facility, PROBE infrastructure, F-44316 Nantes, France
| | - Elizabeth Ficko-Blean
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France.
| | - Gurvan Michel
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29688 Roscoff, Bretagne, France.
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19
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Li J, He Z, Liang Y, Peng T, Hu Z. Insights into Algal Polysaccharides: A Review of Their Structure, Depolymerases, and Metabolic Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1749-1765. [PMID: 35124966 DOI: 10.1021/acs.jafc.1c05365] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent years, marine macroalgae with extensive biomass have attracted the attention of researchers worldwide. Furthermore, algal polysaccharides have been widely studied in the food, pharmaceutical, and cosmetic fields because of their various kinds of bioactivities. However, there are immense barriers to their application as a result of their high molecular size, poor solubility, hydrocolloid nature, and low physiological activities. Unique polysaccharides, such as laminarin, alginate, fucoidan, agar, carrageenan, porphyran, ulvan, and other complex structural polysaccharides, can be digested by marine bacteria with many carbohydrate-active enzymes (CAZymes) by breaking down the limitation of glycosidic bonds. However, structural elucidation of algal polysaccharides, metabolic pathways, and identification of potential polysaccharide hydrolases that participate in different metabolic pathways remain major obstacles restricting the efficient utilization of algal oligosaccharides. This review focuses on the structure, hydrolase families, metabolic pathways, and potential applications of seven macroalgae polysaccharides. These results will contribute to progressing our understanding of the structure of algal polysaccharides and their metabolic pathways and will be valuable for clearing the way for the compelling utilization of bioactive oligosaccharides.
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Affiliation(s)
- Jin Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhixiao He
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Yumei Liang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, People's Republic of China
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20
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Trang VTD, Mikkelsen MD, Vuillemin M, Meier S, Cao HTT, Muschiol J, Perna V, Nguyen TT, Tran VHN, Holck J, Van TTT, Khanh HHN, Meyer AS. The Endo-α(1,4) Specific Fucoidanase Fhf2 From Formosa haliotis Releases Highly Sulfated Fucoidan Oligosaccharides. FRONTIERS IN PLANT SCIENCE 2022; 13:823668. [PMID: 35185990 PMCID: PMC8847386 DOI: 10.3389/fpls.2022.823668] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Fucoidanases are endo-fucoidanases (also known as endo-fucanases) that catalyze hydrolysis of α-glycosidic linkages in fucoidans, a family of sulfated fucose-rich polysaccharides primarily found in the cell walls of brown seaweeds. Fucoidanases are promising tools for producing bioactive fucoidan oligosaccharides for a range of biomedical applications. High sulfation degree has been linked to high bioactivity of fucoidans. In this study, a novel fucoidanase, Fhf2, was identified in the genome of the aerobic, Gram-negative marine bacterium Formosa haliotis. Fhf2 was found to share sequence similarity to known endo-α(1,4)-fucoidanases (EC 3.2.1.212) from glycoside hydrolase family 107. A C-terminal deletion mutant Fhf2∆484, devoid of 484 amino acids at the C-terminus, with a molecular weight of approximately 46 kDa, was constructed and found to be more stable than the full-length Fhf2 protein. Fhf2∆484 showed endo-fucoidanase activity on fucoidans from different seaweed species including Fucus evanescens, Fucus vesiculosus, Sargassum mcclurei, and Sargassum polycystum. The highest activity was observed on fucoidan from F. evanescens. The Fhf2∆484 enzyme was active at 20-45°C and at pH 6-9 and had optimal activity at 37°C and pH 8. Additionally, Fhf2∆484 was found to be calcium-dependent. NMR analysis showed that Fhf2∆484 catalyzed hydrolysis of α(1,4) linkages between L-fucosyl moieties sulfated on C2 (similar to Fhf1 from Formosa haliotis), but Fhf2∆484 in addition released oligosaccharides containing a substantial amount of 2,4-disulfated fucose residues. The data thus suggest that the Fhf2∆484 enzyme could be a valuable candidate for producing highly sulfated oligosaccharides applicable for fucoidan bioactivity investigations.
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Affiliation(s)
- Vo Thi Dieu Trang
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Maria Dalgaard Mikkelsen
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marlene Vuillemin
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hang Thi Thuy Cao
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Jan Muschiol
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- Ocean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Valentina Perna
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Thuan Thi Nguyen
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Vy Ha Nguyen Tran
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tran Thi Thanh Van
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Huynh Hoang Nhu Khanh
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, Nha Trang, Vietnam
| | - Anne S. Meyer
- Protein Chemistry and Enzyme Technology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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21
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Marine microbial enzymes for the production of algal oligosaccharides and its bioactive potential for application as nutritional supplements. Folia Microbiol (Praha) 2022; 67:175-191. [PMID: 34997524 DOI: 10.1007/s12223-021-00943-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/20/2021] [Indexed: 01/02/2023]
Abstract
Marine macroalgae have a very high carbohydrate content due to complex algal polysaccharides (APS) like agar, alginate, and ulvan in their cell wall. Despite numerous reports on their biomedical properties, their hydrocolloid nature limits their applications. Algal oligosaccharides (AOS), which are hydrolyzed forms of complex APS, are gaining importance due to their low molecular weight, biocompatibility, bioactivities, safety, and solubility in water that makes it a lucrative alternative. The AOS produced through enzymatic hydrolysis using microbial enzymes have far-reaching applications because of its stereospecific nature. Identification and characterization of novel microorganisms producing APS hydrolyzing enzymes are the major bottlenecks for the efficient production of AOS. This review will discuss the marine microbial enzymes identified for AOS production and the bioactive potential of enzymatically produced AOS. This can improve our understanding of the biotechnological potential of microbial enzymes for the production of AOS and facilitate the sustainable utilization of algal biomass. Enzymatically produced AOS are shown to have bioactivities such as antioxidant, antiglycemic, prebiotic, immunomodulation, antiobesity or antihypercholesterolemia, anti-inflammatory, anticancer, and antimicrobial activity. The myriad of health benefits provided by the AOS is the need of the hour as there is an alarming increase in physiological disorders among a wide range of the global population.
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22
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OUP accepted manuscript. Glycobiology 2022; 32:529-539. [DOI: 10.1093/glycob/cwab132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/14/2022] Open
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23
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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24
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Zhu C, Liu Z, Ren L, Jiao S, Zhang X, Wang Q, Li Z, Du Y, Li JJ. Overexpression and biochemical characterization of a truncated endo-α (1 → 3)-fucoidanase from alteromonas sp. SN-1009. Food Chem 2021; 353:129460. [PMID: 33725543 DOI: 10.1016/j.foodchem.2021.129460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022]
Abstract
Endo-fucoidanases are important in structural analysis of fucoidans and preparation of fuco-oligosaccharides. However their enzymological properties and analysis of degradation products are scarcely investigated. Truncated endo-α (1 → 3)-fucoidanase Fda1 (tFda1B from Alteromonas sp. was overexpressed and characterized, showing highest activity at pH 7.0, 35 °C, and 1.0 M NaCl. Its Km and kcat were 3.88 ± 0.81 mg/mL and 0.82 ± 0.17 min-1. Fe3+ and Mn2+ enhanced activity by 100% and 19.5% respectively. Co2+ and Cu2+ completely inactivated tFda1B, whereas Ni2+, Mg2+, Zn2+, Pb2+, Ca2+, Ba2+ and Li+ decreased activity by 58.8%, 56.0%, 50.6%, 47.7%, 28.9%, 15.6% and 37.5%, respectively. Catalytic residues were identified through structure and sequence alignment, and confirmed by mutagenesis. Degradation products of Kjellmaniella crassifolia fucoidan by tFda1B were characterized by LC-ESI-MS/MS, confirming tFda1B belongs to endo-(1 → 3)-fucoidanases, and backbone of K. crassifolia fucoidan is 1 → 3 fucoside linkage. This endo-α (1 → 3)-fucoidanase would be useful for elucidating fucoidan structures, and be used as a food enzyme.
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Affiliation(s)
- Chenlu Zhu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Zebin Liu
- College of Life Sciences, Capital Normal University, Beijing 10048, China
| | - Lishi Ren
- National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Siming Jiao
- National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Xuebing Zhang
- National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Qiukuan Wang
- National R & D Branch Center for Seaweed Processing, Key Laboratory of Aquatic Product Processing and Utilization of Liaoning Province, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Yuguang Du
- National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jian-Jun Li
- National Key Laboratory of Biochemical Engineering, National Engineering Research Center for Biotechnology (Beijing), Key Laboratory of Biopharmaceutical Production & Formulation Engineering, PLA, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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25
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Hagestad OC, Hou L, Andersen JH, Hansen EH, Altermark B, Li C, Kuhnert E, Cox RJ, Crous PW, Spatafora JW, Lail K, Amirebrahimi M, Lipzen A, Pangilinan J, Andreopoulos W, Hayes RD, Ng V, Grigoriev IV, Jackson SA, Sutton TDS, Dobson ADW, Rämä T. Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. IMA Fungus 2021; 12:21. [PMID: 34372938 PMCID: PMC8351168 DOI: 10.1186/s43008-021-00072-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/25/2021] [Indexed: 11/10/2022] Open
Abstract
Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
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Affiliation(s)
- Ole Christian Hagestad
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway.
| | - Lingwei Hou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands
| | - Jeanette H Andersen
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Espen H Hansen
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Chun Li
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eric Kuhnert
- Institute of Organic Chemistry and BMWZ, Leibniz Universität Hannover, Hanover, Germany
| | - Russell J Cox
- Institute of Organic Chemistry and BMWZ, Leibniz Universität Hannover, Hanover, Germany
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, Netherlands
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Richard D Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Stephen A Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- MaREI Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Thomas D S Sutton
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- MaREI Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Teppo Rämä
- Marbio, The Norwegian College of Fishery Science, Department at Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
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26
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Li Q, Jiang C, Tan H, Zhao X, Li K, Yin H. Characterization of recombinant E. coli expressing a novel fucosidase from Bacillus cereus 2-8 belonging to GH95 family. Protein Expr Purif 2021; 186:105897. [PMID: 33991676 DOI: 10.1016/j.pep.2021.105897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/09/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]
Abstract
Fucoidan oligosaccharides possesses diverse physicochemical and biological activities. Specific glycoside hydrolases are valuable tools for degrading polysaccharides to produce oligosaccharides. In this study, BcFucA, a novel fucosidase belonging to GH95 family from Bacillus cereus 2-8, was cloned into pET21a vector, expressed in E. coli BL21 (DE3) and characterized. The protein consists of 1136 amino acid residues encoded by 3411 bases and has a molecular weight of 125.35 kDa. The optimal temperature and pH of this enzyme are 50 °C and pH 4.0. In addition, this study showed that the unknown function domain (encoding Lys261-Thr681) defined as a linker is quite important for its activity. The obtained novel enzyme BcFucA will contribute to the effective degradation of fucoidan and future industrial applications.
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Affiliation(s)
- Qian Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China; Department of Food Science and Engineering, Dalian Ocean University, Dalian, 116023, China
| | - Chaofeng Jiang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haidong Tan
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China
| | - Xiaoming Zhao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China
| | - Kuikui Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China.
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023, China.
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27
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Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, Willats WGT, Fuchs BM, Teeling H, Becher D, Schweder T, Amann R, Hehemann JH. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun 2021; 12:1150. [PMID: 33608542 PMCID: PMC7896085 DOI: 10.1038/s41467-021-21009-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The formation of sinking particles in the ocean, which promote carbon sequestration into deeper water and sediments, involves algal polysaccharides acting as an adhesive, binding together molecules, cells and minerals. These as yet unidentified adhesive polysaccharides must resist degradation by bacterial enzymes or else they dissolve and particles disassemble before exporting carbon. Here, using monoclonal antibodies as analytical tools, we trace the abundance of 27 polysaccharide epitopes in dissolved and particulate organic matter during a series of diatom blooms in the North Sea, and discover a fucose-containing sulphated polysaccharide (FCSP) that resists enzymatic degradation, accumulates and aggregates. Previously only known as a macroalgal polysaccharide, we find FCSP to be secreted by several globally abundant diatom species including the genera Chaetoceros and Thalassiosira. These findings provide evidence for a novel polysaccharide candidate to contribute to carbon sequestration in the ocean.
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Affiliation(s)
- Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - Andreas Sichert
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - T Ben Francis
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Jutta Niggemann
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, 26129, Oldenburg, Germany
| | - Antje Wichels
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, 27498, Helgoland, Germany
| | - William G T Willats
- Newcastle University, School of Natural and Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany.
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28
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Zueva A, Silchenko A, Rasin A, Kusaykin M, Usoltseva R, Kalinovsky A, Kurilenko V, Zvyagintseva T, Thinh P, Ermakova S. Expression and biochemical characterization of two recombinant fucoidanases from the marine bacterium Wenyingzhuangia fucanilytica CZ1127T. Int J Biol Macromol 2020; 164:3025-3037. [DOI: 10.1016/j.ijbiomac.2020.08.131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/30/2020] [Accepted: 08/16/2020] [Indexed: 12/16/2022]
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29
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Vuillemin M, Silchenko AS, Cao HTT, Kokoulin MS, Trang VTD, Holck J, Ermakova SP, Meyer AS, Mikkelsen MD. Functional Characterization of a New GH107 Endo-α-(1,4)-Fucoidanase from the Marine Bacterium Formosa haliotis. Mar Drugs 2020; 18:E562. [PMID: 33213084 PMCID: PMC7698502 DOI: 10.3390/md18110562] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 12/27/2022] Open
Abstract
Fucoidans from brown macroalgae are sulfated fucose-rich polysaccharides, that have several beneficial biological activities, including anti-inflammatory and anti-tumor effects. Controlled enzymatic depolymerization of the fucoidan backbone can help produce homogeneous, defined fucoidan products for structure-function research and pharmaceutical uses. However, only a few endo-fucoidanases have been described. This article reports the genome-based discovery, recombinant expression in Escherichia coli, stabilization, and functional characterization of a new bacterial endo-α-(1,4)-fucoidanase, Fhf1, from Formosa haliotis. Fhf1 catalyzes the cleavage of α-(1,4)-glycosidic linkages in fucoidans built of alternating α-(1,3)-/α-(1,4)-linked l-fucopyranosyl sulfated at C2. The native Fhf1 is 1120 amino acids long and belongs to glycoside hydrolase (GH) family 107. Deletion of the signal peptide and a 470 amino acid long C-terminal stretch led to the recombinant expression of a robust, minimized enzyme, Fhf1Δ470 (71 kDa). Fhf1Δ470 has optimal activity at pH 8, 37-40 °C, can tolerate up to 500 mM NaCl, and requires the presence of divalent cations, either Ca2+, Mn2+, Zn2+ or Ni2+, for maximal activity. This new enzyme has the potential to serve the need for controlled enzymatic fucoidan depolymerization to produce bioactive sulfated fucoidan oligomers.
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Affiliation(s)
- Marlene Vuillemin
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Artem S. Silchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Hang Thi Thuy Cao
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam;
| | - Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Vo Thi Dieu Trang
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
- NhaTrang Institute of Technology Research and Application, Vietnam Academy of Science and Technology, 02 Hung Vuong Street, Nhatrang 650000, Vietnam;
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Svetlana P. Ermakova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, 159, Prospect 100-let Vladivostoku, 690022 Vladivostok, Russia; (A.S.S.); (M.S.K); (S.P.E.)
| | - Anne S. Meyer
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
| | - Maria Dalgaard Mikkelsen
- Protein Chemistry and Enzyme Technology Section, DTU Bioengineering, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs Lyngby, Denmark; (M.V.); (V.T.D.T.); (J.H.); (A.S.M.)
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30
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Dobbs JM, Jenkins ML, Burke JE. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2202-2209. [PMID: 32869988 DOI: 10.1021/jasms.0c00283] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filtering of nonspecifically binding contaminant proteins from affinity purification mass spectrometry (AP-MS) data is a well-established strategy to improve statistical confidence in identified proteins. The CRAPome (contaminant repository for affinity purification) describes the contaminating background content present in many purification strategies. However, full contaminant lists for nickel-nitrilotriacetic acid (NiNTA) and glutathione S-transferase (GST) affinity matrices are lacking. Similarly, no Spodoptera frugiperda (Sf9) contaminants are available, and only the FLAG-purified contaminants are described for Escherichia coli. For MS experiments that use recombinant protein, such as structural mass spectrometry experiments (hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking, and radical foot-printing), failing to include these contaminants in the search database during the initial tandem MS (MS/MS) identification stage can result in complications in peptide identification. We have created contaminant FASTA databases for Sf9 and E. coli NiNTA or GST purification strategies and show that the use of these databases can effectively improve HDX-MS protein coverage, fragment count, and confidence in peptide identification. This approach provides a robust strategy toward the design of contaminant databases for any purification approach that will expand the complexity of systems able to be interrogated by HDX-MS.
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Affiliation(s)
- Joseph M Dobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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31
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Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026-1039. [PMID: 32451471 DOI: 10.1038/s41564-020-0720-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany.
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32
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Shen J, Chang Y, Zhang Y, Mei X, Xue C. Discovery and Characterization of an Endo-1,3-Fucanase From Marine Bacterium Wenyingzhuangia fucanilytica: A Novel Glycoside Hydrolase Family. Front Microbiol 2020; 11:1674. [PMID: 32849348 PMCID: PMC7401878 DOI: 10.3389/fmicb.2020.01674] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/26/2020] [Indexed: 01/05/2023] Open
Abstract
Sulfated fucans are important marine polysaccharides widely distributed in brown algae and echinoderms, which gained increasing research interest for their various biological and biomedical activities. Fucanases could serve as tools in the bioconversion and structural investigation of sulfated fucans. A few gene-defined endo-1,4-fucanases have been characterized, while the sequence of endo-1,3-fucanase remain unstudied. Here, an endo-1,3-fucanase gene funA was screened from the genome of marine bacterium Wenyingzhuangia fucanilytica CZ1127T using transcriptomics. None of the previously reported glycoside hydrolase domains were predicted in the enzyme FunA, which hydrolyzed sulfated fucans in a random endo-acting manner. Ultrahigh performance size exclusion chromatography-mass spectrometry and nuclear magnetic resonance analyses revealed that FunA specifically cleaves α-1,3 glycosidic linkage between 2-O-sulfated and non-sulfated fucose residues. FunA exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. D206 and E264 were critical for the functioning of FunA as identified by the site-directed mutagenesis. Another five homologs of FunA were confirmed to possess endo-1,3-fucanase activities. This is the first report on the sequence of endo-1,3-fucanase. The novelty of FunA and its homologs in sequences and activity shed light on a novel glycoside hydrolase family, GH168.
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Affiliation(s)
- Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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33
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Alejandre-Colomo C, Harder J, Fuchs BM, Rosselló-Móra R, Amann R. High-throughput cultivation of heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2020; 43:126066. [PMID: 32019686 DOI: 10.1016/j.syapm.2020.126066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/11/2019] [Accepted: 01/09/2020] [Indexed: 01/22/2023]
Abstract
On-going studies of phytoplankton-bacterioplankton interactions at the long-term ecological research site Helgoland Roads have indicated that many of the heterotrophic bacterial taxa have not yet been cultivated. A high-throughput approach combining whole cell matrix-assisted laser desorption ionization - time of flight mass spectroscopy with 16S rRNA gene sequencing was applied to the spring bloom of 2016. Aiming at an assessment of cultivability during a spring bloom, cultivation on solid marine media had to be used since dilution to extinction would not have been feasible for a high-throughput approach, as performed in this study. A total of 5023 isolates were obtained from nine weekly samples on eight different solid media between the early-bloom and post-bloom periods. Most of the 4136 strains identified affiliated with Bacteroidetes (13.3%), Gammaproteobacteria (26.9%), Alphaproteobacteria (40.6%) and Actinobacteria (6.7%). Of the 271 operational phylogenetic units (OPUs) identified, 13 are likely to represent novel genera and 143 novel species. A comparison with 16S rRNA gene tag data indicated that most of the isolates were rather rare in surface waters, with the exception of five OPUs affiliating with Rhodobacteraceae, Polaribacter, Psychromonas and Pseudoalteromonas. The effort yielded many novel isolates, yet most of the abundant heterotrophic bacteria still remained elusive. The large strain collection obtained will not only provide insights into the succession of the cultivable fraction of the bacterioplankton, but also enable fine-tuned taxonomic and physiological follow-up studies for improving our knowledge on heterotrophic bacteria in North Sea waters.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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34
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Buijs Y, Bech PK, Vazquez-Albacete D, Bentzon-Tilia M, Sonnenschein EC, Gram L, Zhang SD. Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies. Nat Prod Rep 2019; 36:1333-1350. [DOI: 10.1039/c9np00020h] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review covers the recent advances in molecular tools and strategies for studies and use of natural products from marine Proteobacteria.
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Affiliation(s)
- Yannick Buijs
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Pernille Kjersgaard Bech
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Dario Vazquez-Albacete
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
| | - Sheng-Da Zhang
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- DK-2800 Kgs Lyngby
- Denmark
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35
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Kim IJ, Kim DH, Nam KH, Kim KH. Enzymatic synthesis of l-fucose from l-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:282. [PMID: 31827610 PMCID: PMC6894278 DOI: 10.1186/s13068-019-1619-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/24/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND l-Fucose is a rare sugar with potential uses in the pharmaceutical, cosmetic, and food industries. The enzymatic approach using l-fucose isomerase, which interconverts l-fucose and l-fuculose, can be an efficient way of producing l-fucose for industrial applications. Here, we performed biochemical and structural analyses of l-fucose isomerase identified from a novel species of Raoultella (RdFucI). RESULTS RdFucI exhibited higher enzymatic activity for l-fuculose than for l-fucose, and the rate for the reverse reaction of converting l-fuculose to l-fucose was higher than that for the forward reaction of converting l-fucose to l-fuculose. In the equilibrium mixture, a much higher proportion of l-fucose (~ ninefold) was achieved at 30 °C and pH 7, indicating that the enzyme-catalyzed reaction favors the formation of l-fucose from l-fuculose. When biochemical analysis was conducted using l-fuculose as the substrate, the optimal conditions for RdFucI activity were determined to be 40 °C and pH 10. However, the equilibrium composition was not affected by reaction temperature in the range of 30 to 50 °C. Furthermore, RdFucI was found to be a metalloenzyme requiring Mn2+ as a cofactor. The comparative crystal structural analysis of RdFucI revealed the distinct conformation of α7-α8 loop of RdFucI. The loop is present at the entry of the substrate binding pocket and may affect the catalytic activity. CONCLUSIONS RdFucI-catalyzed isomerization favored the reaction from l-fuculose to l-fucose. The biochemical and structural data of RdFucI will be helpful for the better understanding of the molecular mechanism of l-FucIs and the industrial production of l-fucose.
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Affiliation(s)
- In Jung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 02841 South Korea
| | - Do Hyoung Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 02841 South Korea
| | - Ki Hyun Nam
- Department of Biotechnology, Korea University Graduate School, Seoul, 02841 South Korea
- Institute of Life Science and Natural Resources, Korea University, Seoul, 02841 South Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University Graduate School, Seoul, 02841 South Korea
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