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Sparviero S, Dicke MD, Rosch TM, Castillo T, Salgado-Lugo H, Galindo E, Peña C, Büchs J. Yeast extracts from different manufacturers and supplementation of amino acids and micro elements reveal a remarkable impact on alginate production by A. vinelandii ATCC9046. Microb Cell Fact 2023; 22:99. [PMID: 37170263 PMCID: PMC10176783 DOI: 10.1186/s12934-023-02112-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND In research and production, reproducibility is a key factor, to meet high quality and safety standards and maintain productivity. For microbial fermentations, complex substrates and media components are often used. The complex media components can vary in composition, depending on the lot and manufacturing process. These variations can have an immense impact on the results of biological cultivations. The aim of this work was to investigate and characterize the influence of the complex media component yeast extract on cultivations of Azotobacter vinelandii under microaerobic conditions. Under these conditions, the organism produces the biopolymer alginate. The focus of the investigation was on the respiration activity, cell growth and alginate production. RESULTS Yeast extracts from 6 different manufacturers and 2 different lots from one manufacturer were evaluated. Significant differences on respiratory activity, growth and production were observed. Concentration variations of three different yeast extracts showed that the performance of poorly performing yeast extracts can be improved by simply increasing their concentration. On the other hand, the results with well-performing yeast extracts seem to reach a saturation, when their concentration is increased. Cultivations with poorly performing yeast extract were supplemented with grouped amino acids, single amino acids and micro elements. Beneficial results were obtained with the supplementation of copper sulphate, cysteine or a combination of both. Furthermore, a correlation between the accumulated oxygen transfer and the final viscosity (as a key performance indicator), was established. CONCLUSION The choice of yeast extract is crucial for A. vinelandii cultivations, to maintain reproducibility and comparability between cultivations. The proper use of specific yeast extracts allows the cultivation results to be specifically optimised. In addition, supplements can be applied to modify and improve the properties of the alginate. The results only scratch the surface of the underlying mechanisms, as they are not providing explanations on a molecular level. However, the findings show the potential of optimising media containing yeast extract for alginate production with A. vinelandii, as well as the potential of targeted supplementation of the media.
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Affiliation(s)
- Sarah Sparviero
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Max Daniel Dicke
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Tobias M Rosch
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany
| | - Tania Castillo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Holjes Salgado-Lugo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
- Programa Investigadoras e Investigadores por México del CONACyT, Consejo Nacional de Ciencia y Tecnología, 03940, Mexico City, México
| | - Enrique Galindo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Carlos Peña
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Universidad Nacional Autónoma de México, Ave. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Jochen Büchs
- Aachener Verfahrenstechnik - Chair of Biochemical Engineering, RWTH Aachen University, Bldg. NGP², Forckenbeckstr. 51, 52074, Aachen, Germany.
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2
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Mazéas L, Yonamine R, Barbeyron T, Henrissat B, Drula E, Terrapon N, Nagasato C, Hervé C. Assembly and synthesis of the extracellular matrix in brown algae. Semin Cell Dev Biol 2023; 134:112-124. [PMID: 35307283 DOI: 10.1016/j.semcdb.2022.03.005] [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: 11/15/2021] [Revised: 02/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022]
Abstract
In brown algae, the extracellular matrix (ECM) and its constitutive polymers play crucial roles in specialized functions, including algal growth and development. In this review we offer an integrative view of ECM construction in brown algae. We briefly report the chemical composition of its main constituents, and how these are interlinked in a structural model. We examine the ECM assembly at the tissue and cell level, with consideration on its structure in vivo and on the putative subcellular sites for the synthesis of its main constituents. We further discuss the biosynthetic pathways of two major polysaccharides, alginates and sulfated fucans, and the progress made beyond the candidate genes with the biochemical validation of encoded proteins. Key enzymes involved in the elongation of the glycan chains are still unknown and predictions have been made at the gene level. Here, we offer a re-examination of some glycosyltransferases and sulfotransferases from published genomes. Overall, our analysis suggests novel investigations to be performed at both the cellular and biochemical levels. First, to depict the location of polysaccharide structures in tissues. Secondly, to identify putative actors in the ECM synthesis to be functionally studied in the future.
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Affiliation(s)
- Lisa Mazéas
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Rina Yonamine
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Tristan Barbeyron
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Bernard Henrissat
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Technical University of Denmark, DTU Bioengineering, DK-2800 Kgs., Lyngby, Denmark
| | - Elodie Drula
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Nicolas Terrapon
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Cécile Hervé
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
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3
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Wang S, Zhang J, Wei F, Li W, Wen L. Facile Synthesis of Sugar Nucleotides from Common Sugars by the Cascade Conversion Strategy. J Am Chem Soc 2022; 144:9980-9989. [PMID: 35583341 DOI: 10.1021/jacs.2c03138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sugar nucleotides are essential glycosylation donors in the carbohydrate metabolism. Naturally, most sugar nucleotides are derived from a limited number of common sugar nucleotides by de novo biosynthetic pathways, undergoing single or multiple reactions such as dehydration, epimerization, isomerization, oxidation, reduction, amination, and acetylation reactions. However, it is widely believed that such complex bioconversions are not practical for synthetic use due to the high preparation cost and great difficulties in product isolation. Therefore, most of the discovered sugar nucleotides are not readily available. Here, based on de novo biosynthesis mainly, 13 difficult-to-access sugar nucleotides were successfully prepared from two common sugars D-Man and sucrose in high yields, at a multigram scale, and without the need for tedious purification manipulations. This work demonstrated that de novo biosynthesis, although undergoing complex reactions, is also practical and cost-effective for synthetic use by employing a cascade conversion strategy.
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Affiliation(s)
- Shasha Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiang Su 210023, China
| | - Jiabin Zhang
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai 201203, China.,Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China
| | - Fangyu Wei
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanjin Li
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai 201203, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Media, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiang Su 210023, China
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Shao Z, Duan D. The Cell Wall Polysaccharides Biosynthesis in Seaweeds: A Molecular Perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:902823. [PMID: 35620682 PMCID: PMC9127767 DOI: 10.3389/fpls.2022.902823] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 05/16/2023]
Abstract
Cell wall polysaccharides (CWPS) of seaweeds play crucial roles in mechanical shear resistance, cell-cell adhesion and the interactions with changeable marine environments. They have diverse applications in food, cosmetics, agriculture, pharmaceuticals and therapeutics. The recent boost of multi-omics sequence analysis has rapidly progressed the mining of presumed genes encoding enzymes involved in CWPS biosynthesis pathways. In this review, we summarize the biosynthetic pathways of alginate, fucoidan, agar, carrageenan and ulvan in seaweeds referred to the literatures on published genomes and biochemical characterization of encoded enzymes. Some transcriptomic data were briefly reported to discuss the correlation between gene expression levels and CWPS contents. Mannuronan C-5 epimerase (MC5E) and carbohydrate sulfotransferase (CST) are crucial enzymes for alginate and sulfated CWPS, respectively. Nonetheless, most CWPS-relevant genes were merely investigated by gene mining and phylogenetic analysis. We offer an integrative view of CWPS biosynthesis from a molecular perspective and discuss about the underlying regulation mechanism. However, a clear understanding of the relationship between chemical structure and bioactivities of CWPS is limited, and reverse genetic manipulation and effective gene editing tools need to be developed in future.
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Affiliation(s)
- Zhanru Shao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co., Ltd., Qingdao, China
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5
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Pengyan Z, Chang L, Zhanru S, Fuli L, Jianting Y, Delin D. Genome-wide transcriptome profiling and characterization of mannuronan C5-epimerases in Saccharina japonica. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Gerdol M, Visintin A, Kaleb S, Spazzali F, Pallavicini A, Falace A. Gene expression response of the alga Fucus virsoides (Fucales, Ochrophyta) to glyphosate solution exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115483. [PMID: 32889518 DOI: 10.1016/j.envpol.2020.115483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Fucus virsoides is an ecologically important canopy-forming brown algae endemic to the Adriatic Sea. Once widespread in marine coastal areas, this species underwent a rapid population decline and is now confined to small residual areas. Although the reasons behind this progressive disappearance are still a matter of debate, F. virsoides may suffer, like other macroalgae, from the potential toxic effects of glyphosate-based herbicides. Here, through a transcriptomic approach, we investigate the molecular basis of the high susceptibility of this species to glyphosate solution, previously observed at the morphological and eco-physiological levels. By simulating runoff event in a factorial experiment, we exposed F. virsoides to glyphosate (Roundup® 2.0), either alone or in association with nutrient enrichment, highlighting significant alterations of gene expression profiles that were already visible after three days of exposure. In particular, glyphosate exposure determined the near-complete expression shutdown of several genes involved in photosynthesis, protein synthesis and stress response molecular pathways. Curiously, these detrimental effects were partially mitigated by nutrient supplementation, which may explain the survival of relict population in confined areas with high nutrient inputs.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Andrea Visintin
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Kaleb
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Annalisa Falace
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
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7
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Pengyan Z, Fuli L, Siqing C, Zhourui L, Wenjun W, Xiutao S. Comparative Ubiquitome Analysis under Heat Stress Reveals Diverse Functions of Ubiquitination in Saccharina japonica. Int J Mol Sci 2020; 21:E8210. [PMID: 33153009 PMCID: PMC7663155 DOI: 10.3390/ijms21218210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 01/25/2023] Open
Abstract
Ubiquitination is a major post-translational modification involved in nearly all aspects of eukaryotic biology. Previous RNA-Seq studies showed that ubiquitination plays essential roles in the heat tolerance of Saccharina japonica, but to date, large-scale profiling of the ubiquitome in S. japonica has not been reported. To better understand the regulatory roles of ubiquitination in heat responses of S. japonica, we investigated its ubiquitome under normal and heat stress by the combination of affinity enrichment and high-resolution liquid chromatography-tandem mass spectroscopy analysis. Altogether, 3305 lysine ubiquitination sites in 1562 protein groups were identified. After normalization, 152 lysine ubiquitination sites in 106 proteins were significantly upregulated and 208 lysine ubiquitination sites in 131 proteins were significantly downregulated in response to heat stress. Protein annotation and functional analysis suggested that ubiquitination modulates a variety of essential cellular and physiological processes, including but not limited to the ubiquitin-26S proteasome system, ribosome, carbohydrate metabolism, and oxidative phosphorylation. Our results provide a global view of the heat response ubiquitome in S. japonica, and could facilitate future studies on the physiological roles of these ubiquitination-related proteins.
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Affiliation(s)
- Zhang Pengyan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Liu Fuli
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Chen Siqing
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Liang Zhourui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Wang Wenjun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Sun Xiutao
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Z.P.); (C.S.); (L.Z.); (W.W.); (S.X.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Shao Z, Zhang P, Lu C, Li S, Chen Z, Wang X, Duan D. Transcriptome sequencing of Saccharina japonica sporophytes during whole developmental periods reveals regulatory networks underlying alginate and mannitol biosynthesis. BMC Genomics 2019; 20:975. [PMID: 31830918 PMCID: PMC6909449 DOI: 10.1186/s12864-019-6366-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Alginate is an important cell wall component and mannitol is a soluble storage carbon substance in the brown seaweed Saccharina japonica. Their contents vary with kelp developmental periods and harvesting time. Alginate and mannitol regulatory networks and molecular mechanisms are largely unknown. RESULTS With WGCNA and trend analysis of 20,940 known genes and 4264 new genes produced from transcriptome sequencing of 30 kelp samples from different stages and tissues, we deduced that ribosomal proteins, light harvesting complex proteins and "imm upregulated 3" gene family are closely associated with the meristematic growth and kelp maturity. Moreover, 134 and 6 genes directly involved in the alginate and mannitol metabolism were identified, respectively. Mannose-6-phosphate isomerase (MPI2), phosphomannomutase (PMM1), GDP-mannose 6-dehydrogenase (GMD3) and mannuronate C5-epimerase (MC5E70 and MC5E122) are closely related with the high content of alginate in the distal blade. Mannitol accumulation in the basal blade might be ascribed to high expression of mannitol-1-phosphate dehydrogenase (M1PDH1) and mannitol-1-phosphatase (M1Pase) (in biosynthesis direction) and low expression of mannitol-2-dehydrogenase (M2DH) and Fructokinase (FK) (in degradation direction). Oxidative phosphorylation and photosynthesis provide ATP and NADH for mannitol metabolism whereas glycosylated cycle and tricarboxylic acid (TCA) cycle produce GTP for alginate biosynthesis. RNA/protein synthesis and transportation might affect alginate complex polymerization and secretion processes. Cryptochrome (CRY-DASH), xanthophyll cycle, photosynthesis and carbon fixation influence the production of intermediate metabolite of fructose-6-phosphate, contributing to high content of mannitol in the basal blade. CONCLUSIONS The network of co-responsive DNA synthesis, repair and proteolysis are presumed to be involved in alginate polymerization and secretion, while upstream light-responsive reactions are important for mannitol accumulation in meristem of kelp. Our transcriptome analysis provides new insights into the transcriptional regulatory networks underlying the biosynthesis of alginate and mannitol during S. japonica developments.
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Affiliation(s)
- Zhanru Shao
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
| | - Pengyan Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071 People’s Republic of China
| | - Chang Lu
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100093 People’s Republic of China
| | - Shaoxuan Li
- Qingdao Academy of Agricultural Sciences, Qingdao, 266100 People’s Republic of China
| | - Zhihang Chen
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100093 People’s Republic of China
| | - Xiuliang Wang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
| | - Delin Duan
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071 People’s Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Jimo, Qingdao, 266237 People’s Republic of China
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Brightmoon Seaweed Group Co Ltd, Qingdao, 266400 People’s Republic of China
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Nègre D, Aite M, Belcour A, Frioux C, Brillet-Guéguen L, Liu X, Bordron P, Godfroy O, Lipinska AP, Leblanc C, Siegel A, Dittami SM, Corre E, Markov GV. Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. Antioxidants (Basel) 2019; 8:E564. [PMID: 31744163 PMCID: PMC6912245 DOI: 10.3390/antiox8110564] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022] Open
Abstract
Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of Saccharina japonica and Cladosiphon okamuranus has provided the necessary data for the reconstruction of Genome-Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of Ectocarpus siliculosus to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by Saccharina japonica, its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches.
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Affiliation(s)
- Delphine Nègre
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, 29680 Roscoff, France
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, 9, Rue Bias, 44035 Nantes, France
| | - Méziane Aite
- Université de Rennes 1, Institute for Research in IT and Random Systems (IRISA), Equipe Dyliss, 35052 Rennes, France
| | - Arnaud Belcour
- Université de Rennes 1, Institute for Research in IT and Random Systems (IRISA), Equipe Dyliss, 35052 Rennes, France
| | - Clémence Frioux
- Université de Rennes 1, Institute for Research in IT and Random Systems (IRISA), Equipe Dyliss, 35052 Rennes, France
- Quadram Institute, Colney Lane, Norwich NR4 7UQ, UK
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Xi Liu
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Philippe Bordron
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Olivier Godfroy
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anne Siegel
- Université de Rennes 1, Institute for Research in IT and Random Systems (IRISA), Equipe Dyliss, 35052 Rennes, France
| | - Simon M. Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, 29680 Roscoff, France
| | - Gabriel V. Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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Sakuta R, Nakamura N. Production of Hexaric Acids from Biomass. Int J Mol Sci 2019; 20:E3660. [PMID: 31357431 PMCID: PMC6695620 DOI: 10.3390/ijms20153660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/15/2022] Open
Abstract
Sugar acids obtained by aldohexose oxidation of both the terminal aldehyde group and the hydroxy group at the other end to carboxyl groups are called hexaric acids (i.e., six-carbon aldaric acids). Because hexaric acids have four secondary hydroxy groups that are stereochemically diverse and two carboxyl groups, various applications of these acids have been studied. Conventionally, hexaric acids have been produced mainly by nitric acid oxidation of aldohexose, but full-scale commercialization has not been realized; there are many problems regarding yield, safety, environmental burden, etc. In recent years, therefore, improvements in hexaric acid production by nitric acid oxidation have been made, while new production methods, including biocatalytic methods, are actively being studied. In this paper, we summarize these production methods in addition to research on the application of hexaric acids.
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Affiliation(s)
- Riku Sakuta
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan
| | - Nobuhumi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakacho, Koganei, Tokyo 184-8588, Japan.
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11
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Luan H, Yao J, Chen Z, Duan D. The 40S Ribosomal Protein S6 Response to Blue Light by Interaction with SjAUREO in Saccharina japonica. Int J Mol Sci 2019; 20:E2414. [PMID: 31096691 PMCID: PMC6566693 DOI: 10.3390/ijms20102414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023] Open
Abstract
Blue light (BL) plays an important role in regulation of the growth and development of aquatic plants and land plants. Aureochrome (AUREO), the recent BL photoreceptor identified in photosynthetic stramenopile algae, is involved in the photomorphogenesis and early development of Saccharina japonica porophytes (kelp). However the factors that interact with the SjAUREO under BL conditions specifically are not clear. Here in our study, three high quality cDNA libraries with CFU over 5 × 106 and a recombination rate of 100% were constructed respectively through white light (WL), BL and darkness (DK) treatments to the juvenile sporophytes. Based on the constructed cDNA libraries, the interactors of SjAUREO were screened and analyzed. There are eighty-four genes encoding the sixteen predicted proteins from the BL cDNA library, sixty-eight genes encoding eighteen predicted proteins from the DK cDNA library, and seventy-four genes encoding nineteen proteins from the WL cDNA library. All the predicted proteins are presumed to interact with SjAUREO when co-expressed with SjAUREO seperately. The 40S ribosomal protein S6 (RPS6), which only exists in the BL treated cDNA library except for two other libraries, and which is essential for cell proliferation and is involved in cell cycle progression, was selected for detailed analysis. We showed that its transcription was up-regulated by BL, and was highly transcribed in the basal blade (meristem region) of juvenile sporophytes but less in the distal part. Taken together, our results indicated that RPS6 was highly involved in BL-mediated kelp cellular division and photomorphogenesis by interacting with SjAUREO.
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Affiliation(s)
- Hexiang Luan
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jianting Yao
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Zhihang Chen
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- University of the Chinese Academy of Sciences, Beijing 100093, China.
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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