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Liu GL, Wu SL, Sun Z, Xing MD, Chi ZM, Liu YJ. ι-Carrageenan catabolism is initiated by key sulfatases in the marine bacterium Pseudoalteromonas haloplanktis LL1. Appl Environ Microbiol 2024; 90:e0025524. [PMID: 38874338 PMCID: PMC11267874 DOI: 10.1128/aem.00255-24] [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: 02/13/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024] Open
Abstract
Marine bacteria contribute substantially to cycle macroalgae polysaccharides in marine environments. Carrageenans are the primary cell wall polysaccharides of red macroalgae. The carrageenan catabolism mechanism and pathways are still largely unclear. Pseudoalteromonas is a representative bacterial genus that can utilize carrageenan. We previously isolated the strain Pseudoalteromonas haloplanktis LL1 that could grow on ι-carrageenan but produce no ι-carrageenase. Here, through a combination of bioinformatic, biochemical, and genetic analyses, we determined that P. haloplanktis LL1 processed a desulfurization-depolymerization sequential pathway for ι-carrageenan utilization, which was initiated by key sulfatases PhSulf1 and PhSulf2. PhSulf2 acted as an endo/exo-G4S (4-O-sulfation-β-D-galactopyranose) sulfatase, while PhSulf1 was identified as a novel endo-DA2S sulfatase that could function extracellularly. Because of the unique activity of PhSulf1 toward ι-carrageenan rather than oligosaccharides, P. haloplanktis LL1 was considered to have a distinct ι-carrageenan catabolic pathway compared to other known ι-carrageenan-degrading bacteria, which mainly employ multifunctional G4S sulfatases and exo-DA2S (2-O-sulfation-3,6-anhydro-α-D-galactopyranose) sulfatase for sulfate removal. Furthermore, we detected widespread occurrence of PhSulf1-encoding gene homologs in the global ocean, indicating the prevalence of such endo-acting DA2S sulfatases as well as the related ι-carrageenan catabolism pathway. This research provides valuable insights into the enzymatic processes involved in carrageenan catabolism within marine ecological systems.IMPORTANCECarrageenan is a type of linear sulfated polysaccharide that plays a significant role in forming cell walls of marine algae and is found extensively distributed throughout the world's oceans. To the best of our current knowledge, the ι-carrageenan catabolism in marine bacteria either follows the depolymerization-desulfurization sequential process initiated by ι-carrageenase or starts from the desulfurization step catalyzed by exo-acting sulfatases. In this study, we found that the marine bacterium Pseudoalteromonas haloplanktis LL1 processes a distinct pathway for ι-carrageenan catabolism employing a specific endo-acting DA2S-sulfatase PhSulf1 and a multifunctional G4S sulfatase PhSulf2. The unique PhSulf1 homologs appear to be widely present on a global scale, indicating the indispensable contribution of the marine bacteria containing the distinct ι-carrageenan catabolism pathway. Therefore, this study would significantly enrich our understanding of the molecular mechanisms underlying carrageenan utilization, providing valuable insights into the intricate roles of marine bacteria in polysaccharide cycling in marine environments.
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Affiliation(s)
- Guang-Lei Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Sheng-Lei Wu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Zhe Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Meng-Dan Xing
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Zhen-Ming Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- MOE Key Laboratory of Evolution and Marine Biodiversity, Qingdao, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Wang H, Zhu B. Directed preparation of algal oligosaccharides with specific structures by algal polysaccharide degrading enzymes. Int J Biol Macromol 2024; 277:134093. [PMID: 39053825 DOI: 10.1016/j.ijbiomac.2024.134093] [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: 04/07/2024] [Revised: 07/15/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Seaweed polysaccharides have a wide range of sources and rich content, with various biological activities such as anti-inflammatory, anti-tumor, anticoagulant, and blood pressure lowering. They can be applied in fields such as food, agriculture, and medicine. However, the poor solubility of macromolecular seaweed polysaccharides limits their further application. Reports have shown that some biological activities of seaweed oligosaccharides are more extensive and superior to that of seaweed polysaccharides. Therefore, reducing the degree of polymerization of polysaccharides will be the key to the high value utilization of seaweed polysaccharide resources. There are three main methods for degrading algal polysaccharides into algal oligosaccharides, physical, chemical and enzymatic degradation. Among them, enzymatic degradation has been a hot research topic in recent years. Various types of algal polysaccharide hydrolases and related glycosidases are powerful tools for the preparation of algal oligosaccharides, including α-agarases, β-agaroses, α-neoagarose hydrolases and β-galactosidases that are related to agar, κ-carrageenases, ι-carrageenases and λ-carrageenases that are related to carrageenan, β-porphyranases that are related to porphyran, funoran hydrolases that are related to funoran, alginate lyases that are related to alginate and ulvan lyases related to ulvan. This paper describes the bioactivities of agar oligosaccharide, carrageenan oligosaccharide, porphyran oligosaccharide, funoran oligosaccharide, alginate oligosaccharide and ulvan oligosaccharide and provides a detailed review of the progress of research on the enzymatic preparation of these six oligosaccharides. At the same time, the problems and challenges faced are presented to guide and improve the preparation and application of algal oligosaccharides in the future.
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Affiliation(s)
- Hui Wang
- College of Food Science and Light Industry, Nanjing Tech University, 211086, China
| | - Benwei Zhu
- College of Food Science and Light Industry, Nanjing Tech University, 211086, China.
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3
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Jiang C, Ma Y, Wang W, Sun J, Hao J, Mao X. Systematic review on carrageenolytic enzymes: From metabolic pathways to applications in biotechnology. Biotechnol Adv 2024; 73:108351. [PMID: 38582331 DOI: 10.1016/j.biotechadv.2024.108351] [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: 10/31/2023] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Carrageenan, the major carbohydrate component of some red algae, is an important renewable bioresource with very large annual outputs. Different types of carrageenolytic enzymes in the carrageenan metabolic pathway are potentially valuable for the production of carrageenan oligosaccharides, biofuel, and other chemicals obtained from carrageenan. However, these enzymes are not well-developed for oligosaccharide or biofuel production. For further application, comprehensive knowledge of carrageenolytic enzymes is essential. Therefore, in this review, we first summarize various carrageenolytic enzymes, including the recently discovered β-carrageenase, carrageenan-specific sulfatase, exo-α-3,6-anhydro-D-galactosidase (D-ADAGase), and exo-β-galactosidase (BGase), and describe their enzymatic characteristics. Subsequently, the carrageenan metabolic pathways are systematically presented and applications of carrageenases and carrageenan oligosaccharides are illustrated with examples. Finally, this paper discusses critical aspects that can aid researchers in constructing cascade catalytic systems and engineered microorganisms to efficiently produce carrageenan oligosaccharides or other value-added chemicals through the degradation of carrageenan. Overall, this paper offers a comprehensive overview of carrageenolytic enzymes, providing valuable insights for further exploration and application of these enzymes.
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Affiliation(s)
- Chengcheng Jiang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts, National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yuqi Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts, National Laboratory for Marine Science and Technology, Qingdao 266071, China; College of Fisheries and Life Science, Dalian Ocean University, Dalian 116000, China
| | - Wei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts, National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jingjing Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts, National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jianhua Hao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Laboratory for Marine Drugs and Byproducts, National Laboratory for Marine Science and Technology, Qingdao 266071, China; Jiangsu Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resource, Lianyungang 222005, China.
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
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4
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Fuchs A, Hupfeld E, Sieber V. To gel or not to gel - Tuning the sulfation pattern of carrageenans to expand their field of application. Carbohydr Polym 2024; 333:121930. [PMID: 38494212 DOI: 10.1016/j.carbpol.2024.121930] [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: 11/23/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024]
Abstract
Carrageenans represent a major cell wall component of red macro algae and, as established gelling and thickening agents, they contribute significantly to a broad variety of commercial applications in the food and cosmetic industry. As a highly sulfated class of linear polysaccharides, their functional properties are strongly related to the sulfation pattern of their carrabiose repeating units. Therefore, the biocatalytic fine-tuning of these polymers by generating tailored sulfation architectures harnessing the hydrolytic activity of sulfatases could be a powerful tool to produce novel polymer structures with tuned properties to expand applications of carrageenans beyond their current use. To contribute to this vision, we sought to identify novel carrageenan sulfatases by studying several putative carrageenolytic clusters in marine heterotrophic bacteria. This approach revealed two novel formylglycine-dependent sulfatases from Cellulophaga algicola DSM 14237 and Cellulophaga baltica DSM 24729 with promiscuous hydrolytic activity towards the sulfated galactose in the industrially established ι- and κ-carrageenan, converting them into α- and β-carrageenan, respectively, and enabling the production of a variety of novel pure and hybrid carrageenans. The rheological analysis of these enzymatically generated structures revealed significantly altered physicochemical properties that may open the gate to a variety of novel carrageenan-based applications.
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Affiliation(s)
- Alexander Fuchs
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Enrico Hupfeld
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Schulgasse 16, 94315 Straubing, Germany; SynBioFoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany; TUM Catalysis Research Center, Ernst-Otto-Fischer-Straße1, 85748 Garching, Germany; School of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia.
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5
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Fuchs A, Romeis D, Hupfeld E, Sieber V. Biocatalytic Conversion of Carrageenans for the Production of 3,6-Anhydro-D-galactose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5816-5827. [PMID: 38442258 PMCID: PMC10958521 DOI: 10.1021/acs.jafc.3c08613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
Marine biomass stands out as a sustainable resource for generating value-added chemicals. In particular, anhydrosugars derived from carrageenans exhibit a variety of biological functions, rendering them highly promising for utilization and cascading in food, cosmetic, and biotechnological applications. However, the limitation of available sulfatases to break down the complex sulfation patterns of carrageenans poses a significant limitation for the sustainable production of valuable bioproducts from red algae. In this study, we screened several carrageenolytic polysaccharide utilization loci for novel sulfatase activities to assist the efficient conversion of a variety of sulfated galactans into the target product 3,6-anhydro-D-galactose. Inspired by the carrageenolytic pathways in marine heterotrophic bacteria, we systematically combined these novel sulfatases with other carrageenolytic enzymes, facilitating the development of the first enzymatic one-pot biotransformation of ι- and κ-carrageenan to 3,6-anhdyro-D-galactose. We further showed the applicability of this enzymatic bioconversion to a broad series of hybrid carrageenans, rendering this process a promising and sustainable approach for the production of value-added biomolecules from red-algal feedstocks.
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Affiliation(s)
- Alexander Fuchs
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Dennis Romeis
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Enrico Hupfeld
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair
of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology
and Sustainability, Technical University
of Munich, Schulgasse 16, 94315 Straubing, Germany
- SynBioFoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Catalytic
Research Center, Ernst-Otto-Fischer-Straße1, 85748 Garching, Germany
- School
of Chemistry and Molecular Biosciences, The University of Queensland, 68 Copper Road, St. Lucia 4072, Australia
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6
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Elmarhoum S, Ako K, Munialo CD, Rharbi Y. Helicity degree of carrageenan conformation determines the polysaccharide and water interactions. Carbohydr Polym 2023; 314:120952. [PMID: 37173054 DOI: 10.1016/j.carbpol.2023.120952] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/31/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
The polysaccharide in solution at critical concentration, Cc (g/L), is assimilated to a nano hydrogel (nHG) made of a single polysaccharide chain. Taking as reference the characteristic temperature of 20 ± 2 °C at which kappa-carrageenan (κ-Car) nHG swelling is greater with a Cc = 0.55 ± 0.05 g/L, the temperature of the minimum deswelling in the presence of KCl was found at 30 ± 2 °C for 5 mM with a Cc = 1.15 ± 0.05 g/L but not measurable above 100 °C for 10 mM of which Cc = 1.3 ± 0.05 g/L. Lowering the temperature to 5 °C, contraction of the nHG and further coil-helix transition with self-assembly increases the sample's viscosity, which steadily evolves with time in a logarithmic scale. Accordingly, the relative increment of the viscosity per unit of concentration, Rv (L/g), should increase in agreement with increasing polysaccharide concentration. But the Rv decreases for κ-Car samples above 3.5 ± 0.5 g/L in the presence of 10 mM KCl under steady shear 15 s-1. This reflects a decrease of κ-Car helicity degree knowing that the polysaccharide is rather hydrophilic when its helicity degree is the lowest.
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Affiliation(s)
- Said Elmarhoum
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
| | - Komla Ako
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France.
| | - Claire D Munialo
- Food Land and Agribusiness Management Department Harper Adams University Newport, Shropshire TF10 8NB, UK
| | - Yahya Rharbi
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
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7
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Podell S, Oliver A, Kelly LW, Sparagon WJ, Plominsky AM, Nelson RS, Laurens LML, Augyte S, Sims NA, Nelson CE, Allen EE. Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides. Appl Environ Microbiol 2023; 89:e0215422. [PMID: 37133385 DOI: 10.1128/aem.02154-22] [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] [Indexed: 05/04/2023] Open
Abstract
Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.
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Affiliation(s)
- Sheila Podell
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Aaron Oliver
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Linda Wegley Kelly
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Wesley J Sparagon
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Alvaro M Plominsky
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | | | | | | | | | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Eric E Allen
- Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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8
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Poulet L, Mathieu S, Drouillard S, Buon L, Touvrey M, Helbert W. α-Carrageenan: An alternative route for the heterogenous phase degradation of hybrid ι-/κ-carrageenan. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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9
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Elmarhoum S, Mathieu S, Ako K, Helbert W. Sulfate groups position determines the ionic selectivity and syneresis properties of carrageenan systems. Carbohydr Polym 2023; 299:120166. [PMID: 36876782 DOI: 10.1016/j.carbpol.2022.120166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/28/2022] [Accepted: 09/23/2022] [Indexed: 10/14/2022]
Abstract
The salt sensitivity and selectivity feature of α-carrageenan (α-Car) were investigated and compared with κ-carrageenan (κ-Car) and iota-carrageenan (ι-Car). These carrageenans are identified by one sulfate group on the 3,6-anhydro-D-galactose (DA) for α-Car, D-galactose (G) for κ-Car and on both carrabiose moieties (G and DA) for ι-Car. The viscosity and temperature, where order-disorder transition have been observed, were greater in presence of CaCl2 for α-Car and ι-Car compared with KCl and NaCl. Conversely, the reactivity of κ-Car systems were greater in presence of KCl than CaCl2. Unlike κ-Car systems, the gelation of α-Car in presence of KCl was observed without syneresis. Thus, the position of sulfate group on the carrabiose determines the importance of counterion valency too. The α-Car could be a good alternative to κ-Car to reduce the syneresis effects.
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Affiliation(s)
- Said Elmarhoum
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France
| | - Sophie Mathieu
- Univ. Grenoble Alpes, CNRS, CERMAV, F-38000 Grenoble, France
| | - Komla Ako
- Univ. Grenoble Alpes, CNRS, Grenoble INP, LRP, 38000 Grenoble, France.
| | - William Helbert
- Univ. Grenoble Alpes, CNRS, CERMAV, F-38000 Grenoble, France
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Rheological study of α- and κ-carrageenan expansion in solution as effects of the position of the sulfate group. Int J Biol Macromol 2022; 223:1138-1144. [PMID: 36395929 DOI: 10.1016/j.ijbiomac.2022.11.128] [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: 07/16/2022] [Revised: 11/08/2022] [Accepted: 11/13/2022] [Indexed: 11/16/2022]
Abstract
The viscosity of carrageenan solutions in the coil state was greater for α-carrageenan (α-Car) compared with that for κ-carrageenan (κ-Car); thus, the impact of one sulfate group on 3,6-anhydro-D-galactose was compared with the impact of one sulfate group on D-galactose units of the carrabiose residues. The thermal expansion coefficient of the solutions, B2 × Tc, characterizes the way the viscosity decreases because of extension of the physical bonds of the systems to their rupture point (Tc) under increasing temperature. The Tc and B2 × Tc of water were equal to (100 ± 5) °C and (1.57 ± 0.05) × 10-2/°C, respectively. The Tc of the α-Car and κ-Car systems increased after the addition of CaCl2 and KCl, respectively, and with increasing polysaccharide concentration. However, the B2 × Tc of the α-Car and κ-Car systems were rather sensitive to CaCl2 and KCl, respectively. In the overall solutions examined, the expansion of α-Car systems was found to be between 1.5 × 10-2/°C and 1.61 × 10-2/°C, greater than the expansion of κ-Car systems, which was between 1.5 × 10-2/°C and 1.2 × 10-2/°C. Thus, α-Car is a good alternative to κ-Car for reducing syneresis phenomena, and its sensitivity as ι-Car to divalent cations would be due to the anhydro cycle.
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11
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Stam M, Lelièvre P, Hoebeke M, Corre E, Barbeyron T, Michel G. SulfAtlas, the sulfatase database: state of the art and new developments. Nucleic Acids Res 2022; 51:D647-D653. [PMID: 36318251 PMCID: PMC9825549 DOI: 10.1093/nar/gkac977] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1-S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.
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Affiliation(s)
| | | | - Mark Hoebeke
- Sorbonne Université, CNRS, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, Bretagne, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, Bretagne, France
| | - Tristan Barbeyron
- Correspondence may also be addressed to Tristan Barbeyron. Tel: +33 298 29 23 30; Fax: +33 298 29 23 24;
| | - Gurvan Michel
- To whom correspondence should be addressed. Tel: +33 298 29 23 30; Fax: +33 298 29 23 24;
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12
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Hettle AG, Vickers CJ, Boraston AB. Sulfatases: Critical Enzymes for Algal Polysaccharide Processing. FRONTIERS IN PLANT SCIENCE 2022; 13:837636. [PMID: 35574087 PMCID: PMC9096561 DOI: 10.3389/fpls.2022.837636] [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: 12/16/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Microbial sulfatases are important biocatalysts in the marine environment where they play a key role in the catabolic biotransformation of abundant sulphated algal polysaccharides. The sulphate esters decorating algal polysaccharides, such as carrageenan, fucoidan and ulvan, can constitute up to 40% of the biopolymer dry weight. The use of this plentiful carbon and energy source by heterotrophic microbes is enabled in part by the sulfatases encoded in their genomes. Sulfatase catalysed hydrolytic removal of sulphate esters is a key reaction at various stages of the enzymatic cascade that depolymerises sulphated polysaccharides into monosaccharides that can enter energy yielding metabolic pathways. As the critical roles of sulfatases in the metabolism of sulphated polysaccharides from marine algae is increasingly revealed, the structural and functional analysis of these enzymes becomes an important component of understanding these metabolic pathways. The S1 family of formylglycine-dependent sulfatases is the largest and most functionally diverse sulfatase family that is frequently active on polysaccharides. Here, we review this important sulfatase family with emphasis on recent developments in studying the structural and functional relationship between sulfatases and their sulphated algal polysaccharide substrates. This analysis utilises the recently proposed active site nomenclature for sulfatases. We will highlight the key role of sulfatases, not only in marine carbon cycling, but also as potential biocatalysts for the production of a variety of novel tailor made sulphated oligomers, which are useful products in, for example, pharmaceutical or cosmetic applications.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Chelsea J. Vickers
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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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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14
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Xu X, Deng X, Lin J, Yang J. Characterization and substrate-accelerated thermal inactivation kinetics of a new serine-type arylsulfatase. Enzyme Microb Technol 2021; 154:109961. [PMID: 34952364 DOI: 10.1016/j.enzmictec.2021.109961] [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: 10/05/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 11/03/2022]
Abstract
Arylsulfatase is useful in industrial agar processing by removing sulfate groups. A full-length arylsulfatase gene, designated ArySMA1, was obtained from marine bacteria Serratia sp. SM1. The ArySMA1 gene encoded a novel serine-type arylsulfatase and the enzymatic properties were characterized. The enzyme presented notable capacity of removing sulfate groups from natural algae substrates. Kinetic study suggested that the microscopic thermal inactivation rate of ArySMA1 in free form was smaller than that of the enzyme-substrate complex. The presence of substrate could unexpectedly accelerate ArySMA1 to deactivate at high temperature. Such phenomenon was opposite to many findings that substrate could stabilize enzymes against heat. Molecular dynamics simulation and ANS fluorescent assay indicated the substrate led the hydrophobic regions of the active site more flexible and the sulfate group of the substrate could retard the processivity of ArySMA1 catalysis. This study provides guidance for agar desulfation and down-stream processing industry.
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Affiliation(s)
- Xinqi Xu
- College of Biological Science and Engineering, Fuzhou University, 350116, China
| | - Xiangzhen Deng
- College of Biological Science and Engineering, Fuzhou University, 350116, China
| | - Juan Lin
- College of Biological Science and Engineering, Fuzhou University, 350116, China
| | - Jie Yang
- College of Biological Science and Engineering, Fuzhou University, 350116, China.
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15
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de Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Jackson SA, Dobson ADW, Laport MS. Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11. Int J Biol Macromol 2021; 191:973-995. [PMID: 34555402 DOI: 10.1016/j.ijbiomac.2021.09.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/01/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Active heterotrophic metabolism is a critical metabolic role performed by sponge-associated microorganisms, but little is known about their capacity to metabolize marine polysaccharides (MPs). Here, we investigated the genome of the sponge-derived Pseudoalteromonas sp. strain PA2MD11 focusing on its macroalgal carbohydrate-degrading potential. Carbohydrate-active enzymes (CAZymes) for the depolymerization of agar and alginate were found in PA2MD11's genome, including glycoside hydrolases (GHs) and polysaccharide lyases (PLs) belonging to families GH16, GH50 and GH117, and PL6 and PL17, respectively. A gene potentially encoding a sulfatase was also identified, which may play a role in the strain's ability to consume carrageenans. The complete metabolism of agar and alginate by PA2MD11 could also be predicted and was consistent with the results obtained in physiological assays. The polysaccharide utilization locus (PUL) potentially involved in the metabolism of agarose contained mobile genetic elements from other marine Gammaproteobacteria and its unusual larger size might be due to gene duplication events. Homology modelling and structural protein analyses of the agarases, alginate lyases and sulfatase depicted clear conservation of catalytic machinery and protein folding together with suitable industrially-relevant features. Pseudoalteromonas sp. PA2MD11 is therefore a source of potential MP-degrading biocatalysts for biorefinery applications and in the preparation of pharmacologically-active oligosaccharides.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil; School of Microbiology, University College Cork, T12 Y960 Cork, Ireland
| | - Isabelle Rodrigues Lopes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil
| | - Anna Luiza Bauer Canellas
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil
| | - Guilherme Muricy
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n°, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Stephen Anthony Jackson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland; Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland; Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil.
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A novel thermostable prokaryotic fucoidan active sulfatase PsFucS1 with an unusual quaternary hexameric structure. Sci Rep 2021; 11:19523. [PMID: 34593864 PMCID: PMC8484680 DOI: 10.1038/s41598-021-98588-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/06/2021] [Indexed: 12/20/2022] Open
Abstract
Fucoidans are sulfated, fucose-rich marine polysaccharides primarily found in cell walls of brown seaweeds (macroalgae). Fucoidans are known to possess beneficial bioactivities depending on their structure and sulfation degree. Here, we report the first functional characterization and the first crystal structure of a prokaryotic sulfatase, PsFucS1, belonging to sulfatase subfamily S1_13, able to release sulfate from fucoidan oligosaccharides. PsFucS1 was identified in the genome of a Pseudoalteromonas sp. isolated from sea cucumber gut. PsFucS1 (57 kDa) is Ca2+ dependent and has an unusually high optimal temperature (68 °C) and thermostability. Further, the PsFucS1 displays a unique quaternary hexameric structure comprising a tight trimeric dimer complex. The structural data imply that this hexamer formation results from an uncommon interaction of each PsFucS1 monomer that is oriented perpendicular to the common dimer interface (~ 1500 Å2) that can be found in analogous sulfatases. The uncommon interaction involves interfacing (1246 Å2) through a bundle of α-helices in the N-terminal domain to form a trimeric ring structure. The high thermostability may be related to this unusual quaternary hexameric structure formation that is suggested to represent a novel protein thermostabilization mechanism.
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17
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Rhein-Knudsen N, Meyer AS. Chemistry, gelation, and enzymatic modification of seaweed food hydrocolloids. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.01.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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Simon F, Kiss E, Szabó M, Fábián I. The Chlorination of N-Methyl Amino Acids with Hypochlorous Acid: Kinetics and Mechanisms. Chem Res Toxicol 2020; 33:2189-2196. [PMID: 32633499 DOI: 10.1021/acs.chemrestox.0c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation and decomposition kinetics of N-chloro-N-methyl amino acids were studied to predict the fate and impact of these compounds in water treatment technologies and biological systems. These compounds form in fast second-order reactions between N-methyl amino acids and hypochlorous acid. The comparison of the activation parameters for the reactions of N-methyl substituted and nonsubstituted branched-chain amino acids reveals the transition-state features less organized structure and stronger bonds between the reactants in the reactions with the N-methyl derivatives. This is due to a combined positive inductive effect of the N-methyl group and the alkyl side chain as well as to the steric effects of the substituents. N-Methyl-N-chloro amino acids decompose much faster than the nonsubstituted compounds. The reaction rates do not depend on the pH, and the same final product is formed in the entire pH range. N-Chlorosarcosine is an exception, as it decomposes via competing paths, kdobs = kd + kdOH[OH-], yielding different final products. This feature is most likely due to the lack of an alkyl substituent on the α-carbon atom. Under physiological pH, aldehydes and methylamine form in these reactions, which are not particularly toxic.
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Affiliation(s)
- Fruzsina Simon
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Eszter Kiss
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Mária Szabó
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary.,MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
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19
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Lipinska AP, Collén J, Krueger-Hadfield SA, Mora T, Ficko-Blean E. To gel or not to gel: differential expression of carrageenan-related genes between the gametophyte and tetasporophyte life cycle stages of the red alga Chondrus crispus. Sci Rep 2020; 10:11498. [PMID: 32661246 PMCID: PMC7359372 DOI: 10.1038/s41598-020-67728-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/28/2020] [Indexed: 01/22/2023] Open
Abstract
Chondrus crispus is a marine red alga with sulfated galactans, called carrageenans, in its extracellular matrix. Chondrus has a complex haplodiplontic life cycle, alternating between male and female gametophytes (n) and tetrasporophytes (2n). The Chondrus life cycle stages are isomorphic; however, a major phenotypic difference is that carrageenan composition varies significantly between the tetrasporophytes (mainly lambda-carrageenan) and the gametophytes (mainly kappa/iota-carrageenans). The disparity in carrageenan structures, which confer different chemical properties, strongly suggests differential regulation of carrageenan-active genes between the phases of the Chondrus life cycles. We used a combination of taxonomy, biochemistry and molecular biology to characterize the tetrasporophytes and male and female gametophytes from Chondrus individuals isolated from the rocky seashore off the northern coast of France. Transcriptomic analyses reveal differential gene expression of genes encoding several galactose-sulfurylases, carbohydrate-sulfotransferases, glycosyltransferases, and one family 16 glycoside hydrolase. Differential expression of carrageenan-related genes was found primarily between gametophytes and tetrasporophytes, but also between the male and female gametophytes. The differential expression of these multigenic genes provides a rare glimpse into cell wall biosynthesis in algae. Furthermore, it strongly supports that carrageenan metabolism holds an important role in the physiological differentiation between the isomorphic life cycle stages of Chondrus.
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Affiliation(s)
- Agnieszka P Lipinska
- Station Biologique de Roscoff, UMR8227, Laboratory of Integrative Biology of Marine Models, CNRS and Sorbonne University, Place Georges Teissier, 29688, Roscoff, France.
| | - Jonas Collén
- Station Biologique de Roscoff, UMR8227, Laboratory of Integrative Biology of Marine Models, CNRS and Sorbonne University, Place Georges Teissier, 29688, Roscoff, France
| | - Stacy A Krueger-Hadfield
- Department of Biology, The University of Alabama At Birmingham, Campbell Hall 464, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Theo Mora
- Station Biologique de Roscoff, UMR8227, Laboratory of Integrative Biology of Marine Models, CNRS and Sorbonne University, Place Georges Teissier, 29688, Roscoff, France
| | - Elizabeth Ficko-Blean
- Station Biologique de Roscoff, UMR8227, Laboratory of Integrative Biology of Marine Models, CNRS and Sorbonne University, Place Georges Teissier, 29688, Roscoff, France.
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20
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Szabó M, Bíró V, Simon F, Fábián I. The decomposition of N-chloro amino acids of essential branched-chain amino acids: Kinetics and mechanism. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:120988. [PMID: 31484104 DOI: 10.1016/j.jhazmat.2019.120988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 06/10/2023]
Abstract
The formation of N-chloro-amino acids is of outmost importance in water treatment technologies and also in vivo processes. These compounds are considered as secondary disinfectants and play important role in the defense mechanism against invading pathogens in biological systems. Adversary effects, such as apoptosis or necrosis are also associated with these compounds and the intermediates and final products formed during their decomposition. In the present study, the decomposition kinetics of the N-chloro derivatives of branched chain amino acids (BCAAs) - leucine, isoleucine, valine - were studied. On the basis of spectrophotometric measurements, it was confirmed that the decomposition proceeds via a spontaneous and an OH- assisted path in each case: kobs = k + kOH[OH-]. 1H, 13C NMR and MS experiments were also performed to identify the products and to monitor the progress of the reactions. It was established that the pH independent and the [OH-] dependent paths lead to the formation of the same aldehyde in each system (isovaleraldehyde, 2-methyl-butyraldehyde, and isobutyraldehyde) as a primary product. Under alkaline conditions, a portion of the aldehydes are converted into the corresponding Schiff-bases by the excess amino acid in a reversible process. A common mechanism was proposed for these reactions which postulates the formation of imines and hemiaminals as reactive intermediates.
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Affiliation(s)
- Mária Szabó
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary
| | - Vivien Bíró
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Simon
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Debrecen, Hungary; MTA-DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group, University of Debrecen, Debrecen, Hungary.
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21
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Hettle AG, Hobbs JK, Pluvinage B, Vickers C, Abe KT, Salama-Alber O, McGuire BE, Hehemann JH, Hui JPM, Berrue F, Banskota A, Zhang J, Bottos EM, Van Hamme J, Boraston AB. Insights into the κ/ι-carrageenan metabolism pathway of some marine Pseudoalteromonas species. Commun Biol 2019; 2:474. [PMID: 31886414 PMCID: PMC6923384 DOI: 10.1038/s42003-019-0721-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023] Open
Abstract
Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-carrageenan specific polysaccharide utilization locus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.
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Affiliation(s)
- Andrew G. Hettle
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Chelsea Vickers
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: School of Biological Sciences, Victoria University, PO Box 600, Wellington, 6012 New Zealand
| | - Kento T. Abe
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Ave, Rm 992, Toronto, ON M5G1X5 Canada
| | - Orly Salama-Alber
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Bailey E. McGuire
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
| | - Jan-Hendrik Hehemann
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
- Present Address: Marum and Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Joseph P. M. Hui
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Fabrice Berrue
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Arjun Banskota
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, 1411 Oxford Street, Halifax, NS B3H 3Z1 Canada
| | - Eric M. Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Jonathan Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, British Columbia V2C 0C8 Canada
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada
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Khan BM, Qiu HM, Xu SY, Liu Y, Cheong KL. Physicochemical characterization and antioxidant activity of sulphated polysaccharides derived from Porphyra haitanensis. Int J Biol Macromol 2019; 145:1155-1161. [PMID: 31730957 DOI: 10.1016/j.ijbiomac.2019.10.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/28/2019] [Accepted: 10/03/2019] [Indexed: 01/05/2023]
Abstract
This study was designed to fully characterize Porphyra haitanensis polysaccharides, and to evaluate their antioxidant activity. The polysaccharides primarily contained galactose and 3,6-anhydrogalactose in a molar ratio of 1.2:1.0, respectively and sulfate content about 3.8%. The molecular weight of polysaccharides is 2.5 × 105 Da. Scanning electron microscopy and atomic force microscopy of the polysaccharides pointed towards an irregular network with more or less hexagonal and a few rectangular pores. The chemical structure was confirmed through Fourier transform infrared spectroscopy, and 1D and 2D nuclear magnetic resonance structural characterization wherein → 4-3,6-anhydro-α-L-galactopyranose-(1 → 3)-β-D-galactopyranose segments. The extracted polysaccharides revealed relatively high 2, 2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical scavenging activity (53.16% at 2 mg/mL), moderate 2,2-diphenyl-1-picrylhydrazyl radical scavenging efficacy (34.63% at 2 mg/mL), and low hydroxyl radical scavenging potential (23.80% at 2 mg/mL). Further purification of these polysaccharides, hence, is advised for their potential role as antioxidants in the food, pharmaceutical and cosmeceutical industry.
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Affiliation(s)
- Bilal Muhammad Khan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, PR China; University Institute of Biochemistry and Biotechnology, PMAS - Arid Agriculture University, Rawalpindi, Punjab 46300, Pakistan.
| | - Hua-Mai Qiu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, PR China.
| | - Shu-Ying Xu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, PR China.
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, PR China.
| | - Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, PR China.
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23
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van Vliet DM, Palakawong Na Ayudthaya S, Diop S, Villanueva L, Stams AJM, Sánchez-Andrea I. Anaerobic Degradation of Sulfated Polysaccharides by Two Novel Kiritimatiellales Strains Isolated From Black Sea Sediment. Front Microbiol 2019; 10:253. [PMID: 30833937 PMCID: PMC6388578 DOI: 10.3389/fmicb.2019.00253] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/30/2019] [Indexed: 12/04/2022] Open
Abstract
The marine environment contains a large diversity of sulfated polysaccharides and other glycopolymers. Saccharolytic microorganisms degrade these compounds through hydrolysis, which includes the hydrolysis of sulfate groups from sugars by sulfatases. Various marine bacteria of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum have exceptionally high numbers of sulfatase genes associated with the degradation of sulfated polysaccharides. However, thus far no sulfatase-rich marine anaerobes are known. In this study, we aimed to isolate marine anaerobes using sulfated polysaccharides as substrate. Anoxic enrichment cultures were set up with a mineral brackish marine medium, inoculated with anoxic Black Sea sediment sampled at 2,100 m water depth water and incubated at 15°C (in situ T = 8°C) for several weeks. Community analysis by 16S rRNA gene amplicon sequencing revealed the enrichment of Kiritimatiellaeota clade R76-B128 bacteria in the enrichments with the sulfated polysaccharides fucoidan and iota-carrageenan as substrate. We isolated two strains, F1 and F21, which represent a novel family within the order of the Kiritimatiellales. They were capable of growth on various mono-, di-, and polysaccharides, including fucoidan. The desulfation of iota-carrageenan by strain F21 was confirmed quantitatively by an increase in free sulfate concentration. Strains F1 and F21 represent the first marine sulfatase-rich anaerobes, encoding more sulfatases (521 and 480, 8.0 and 8.4% of all coding sequences, respectively) than any other microorganism currently known. Specific encoded sulfatase subfamilies could be involved in desulfating fucoidan (S1_15, S1_17 and S1_25) and iota-carrageenan (S1_19). Strains F1 and F21 had a sulfatase gene classification profile more similar to aerobic than anaerobic sulfatase-rich PVC bacteria, including Kiritimatiella glycovorans, the only other cultured representative within the Kiritimatiellaeota. Both strains encoded a single anaerobic sulfatase-maturating enzyme which could be responsible for post-translational modification of formylglycine-dependent sulfatases. Strains F1 and F21 are potential anaerobic platforms for future studies on sulfatases and their maturation enzymes.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Susakul Palakawong Na Ayudthaya
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand
| | - Sally Diop
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Den Burg, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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Schultz-Johansen M, Bech PK, Hennessy RC, Glaring MA, Barbeyron T, Czjzek M, Stougaard P. A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66 T Encoded in a Sizeable Polysaccharide Utilization Locus. Front Microbiol 2018; 9:839. [PMID: 29774012 PMCID: PMC5943477 DOI: 10.3389/fmicb.2018.00839] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66T is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases. Based on a first functional characterization combined with a comparative sequence analysis, we confirmed the enzymatic activities of several enzymes required for red algal polysaccharide degradation by the bacterium. In particular, we report for the first time, the discovery of novel enzyme activities targeting furcellaran, a hybrid carrageenan containing both β-carrageenan and κ/β-carrageenan motifs. Some of these enzymes represent a new subfamily within the CAZy classification. From the combined analyses, we propose models for the complete degradation of agar and κ/β-type carrageenan by P. hydrolytica S66T. The novel enzymes described here may find value in new bio-based industries and advance our understanding of the mechanisms responsible for recycling of red algal polysaccharides in marine ecosystems.
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Affiliation(s)
- Mikkel Schultz-Johansen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Pernille K Bech
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rosanna C Hennessy
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mikkel A Glaring
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Peter Stougaard
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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25
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The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme. Structure 2018; 26:747-758.e4. [PMID: 29681469 DOI: 10.1016/j.str.2018.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/26/2018] [Accepted: 03/20/2018] [Indexed: 12/11/2022]
Abstract
Sulfatases play a biologically important role by cleaving sulfate groups from molecules. They can be identified on the basis of signature sequences within their primary structures, and the largest family, S1, has predictable features that contribute specifically to the recognition and catalytic removal of sulfate groups. However, despite advances in the prediction and understanding of S1 sulfatases, a major question regards the molecular determinants that drive substrate recognition beyond the targeted sulfate group. Here, through analysis of an endo-4S-ι-carrageenan sulfatase (PsS1_19A) from Pseudoalteromonas sp. PS47, particularly X-ray crystal structures in complex with intact substrates, we show that specific recognition of the substrate leaving group components, in this case carbohydrate, provides the enzyme with specificity for its substrate. On the basis of these results we propose a catalytic subsite nomenclature that we anticipate will form a general foundation for understanding and describing the molecular basis of substrate recognition by sulfatases.
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26
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Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales). Genomics 2018; 110:124-133. [DOI: 10.1016/j.ygeno.2017.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/23/2022]
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27
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Ortiz-Tena JG, Rühmann B, Sieber V. Colorimetric Determination of Sulfate via an Enzyme Cascade for High-Throughput Detection of Sulfatase Activity. Anal Chem 2018; 90:2526-2533. [PMID: 29307190 DOI: 10.1021/acs.analchem.7b03719] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput screening (HTS) methods have become decisive for the discovery and development of new biocatalysts and their application in numerous fields. Sulfatases, a broad class of biocatalysts that hydrolyze sulfate esters, are involved in diverse relevant cellular functions (e.g., signaling and hormonal regulation) and are therefore gaining importance, particularly in the medical field. Additionally, various technical applications have been recently devised. One of the major challenges in the field of enzyme development is the sensitive and high-throughput detection of the actual product of the biocatalyst of interest without the need for chromophore analogues. Addressing this issue, a colorimetric assay for sulfatases was developed and validated for detecting sulfate through a two-step enzymatic cascade, with a linear detection range of 3.3 (limit of detection) up to 250 μM. The procedure is compatible with relevant compounds employed in sulfatase reactions, including cosolvents, cations, and buffers. The assay was optimized and performed as part of a 96-well screening workflow that included bacterial growth, heterologous sulfatase expression, cell lysis, sulfate ester hydrolysis, inactivation of cell lysate, and colorimetric sulfate determination. With this procedure, the activity of an aryl and an alkyl sulfatase could be confirmed and validated. Overall, this assay provides a simple and fast alternative for screening and engineering sulfatases from DNA libraries (e.g., using metagenomics) with medical or synthetic relevance.
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Affiliation(s)
- Jose G Ortiz-Tena
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany.,Fraunhofer IGB , Straubing Branch BioCat, 94315 Straubing, Germany.,TUM Catalysis Research Center , Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany.,The University of Queensland , School of Chemistry and Molecular Biosciences, 68 Copper Road, St. Lucia 4072, Australia
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28
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Ficko-Blean E, Préchoux A, Thomas F, Rochat T, Larocque R, Zhu Y, Stam M, Génicot S, Jam M, Calteau A, Viart B, Ropartz D, Pérez-Pascual D, Correc G, Matard-Mann M, Stubbs KA, Rogniaux H, Jeudy A, Barbeyron T, Médigue C, Czjzek M, Vallenet D, McBride MJ, Duchaud E, Michel G. Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nat Commun 2017; 8:1685. [PMID: 29162826 PMCID: PMC5698469 DOI: 10.1038/s41467-017-01832-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 10/17/2017] [Indexed: 12/01/2022] Open
Abstract
Macroalgae contribute substantially to primary production in coastal ecosystems. Their biomass, mainly consisting of polysaccharides, is cycled into the environment by marine heterotrophic bacteria using largely uncharacterized mechanisms. Here we describe the complete catabolic pathway for carrageenans, major cell wall polysaccharides of red macroalgae, in the marine heterotrophic bacterium Zobellia galactanivorans. Carrageenan catabolism relies on a multifaceted carrageenan-induced regulon, including a non-canonical polysaccharide utilization locus (PUL) and genes distal to the PUL, including a susCD-like pair. The carrageenan utilization system is well conserved in marine Bacteroidetes but modified in other phyla of marine heterotrophic bacteria. The core system is completed by additional functions that might be assumed by non-orthologous genes in different species. This complex genetic structure may be the result of multiple evolutionary events including gene duplications and horizontal gene transfers. These results allow for an extension on the definition of bacterial PUL-mediated polysaccharide digestion. Carrageenans, major cell wall polysaccharides of red macroalgae, are metabolised by marine heterotrophic bacteria through unclear mechanisms. Here, the authors identify an unusual polysaccharide-utilization locus encoding carrageenan catabolism in a marine bacterium, and characterise the complete pathway.
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Affiliation(s)
- Elizabeth Ficko-Blean
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Aurélie Préchoux
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - François Thomas
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Tatiana Rochat
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert Larocque
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Yongtao Zhu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, Milwaukee, WI, USA
| | - Mark Stam
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Sabine Génicot
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Murielle Jam
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Alexandra Calteau
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Benjamin Viart
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - David Ropartz
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316, Nantes, France
| | | | - Gaëlle Correc
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Maria Matard-Mann
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies, F-44316, Nantes, France
| | - Alexandra Jeudy
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - Claudine Médigue
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France
| | - David Vallenet
- UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000, Évry, France
| | - Mark J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, 53201, Milwaukee, WI, USA
| | - Eric Duchaud
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, Bretagne, France.
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Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity. PLoS One 2016; 11:e0164846. [PMID: 27749924 PMCID: PMC5066984 DOI: 10.1371/journal.pone.0164846] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/30/2016] [Indexed: 12/18/2022] Open
Abstract
Sulfatases cleave sulfate groups from various molecules and constitute a biologically and industrially important group of enzymes. However, the number of sulfatases whose substrate has been characterized is limited in comparison to the huge diversity of sulfated compounds, yielding functional annotations of sulfatases particularly prone to flaws and misinterpretations. In the context of the explosion of genomic data, a classification system allowing a better prediction of substrate specificity and for setting the limit of functional annotations is urgently needed for sulfatases. Here, after an overview on the diversity of sulfated compounds and on the known sulfatases, we propose a classification database, SulfAtlas (http://abims.sb-roscoff.fr/sulfatlas/), based on sequence homology and composed of four families of sulfatases. The formylglycine-dependent sulfatases, which constitute the largest family, are also divided by phylogenetic approach into 73 subfamilies, each subfamily corresponding to either a known specificity or to an uncharacterized substrate. SulfAtlas summarizes information about the different families of sulfatases. Within a family a web page displays the list of its subfamilies (when they exist) and the list of EC numbers. The family or subfamily page shows some descriptors and a table with all the UniProt accession numbers linked to the databases UniProt, ExplorEnz, and PDB.
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30
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Préchoux A, Genicot S, Rogniaux H, Helbert W. Enzyme-Assisted Preparation of Furcellaran-Like κ-/β-Carrageenan. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:133-143. [PMID: 26585588 DOI: 10.1007/s10126-015-9675-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/19/2015] [Indexed: 06/05/2023]
Abstract
Carrageenans are sulfated galactans that are widely used in industrial applications for their thickening and gelling properties, which vary according to the amount and distribution of ester sulfate groups along the galactan backbone. To determine and direct the sulfation of κ-carrageenan moieties, we purified an endo-κ-carrageenan sulfatase (Q15XH1 accession in UniprotKB) from Pseudoalteromonas atlantica T6c extracts. Based on sequence analyses and exploration of the genomic environment of Q15XH1, we discovered and characterized a second endo-κ-carrageenan sulfatase (Q15XG7 accession in UniprotKB). Both enzymes convert κ-carrageenan into a hybrid, furcellaran-like κ-/β-carrageenan. We compared the protein sequences of these two new κ-carrageenan sulfatases and that of a previously reported ι-carrageenan sulfatase with other predicted sulfatases in the P. atlantica genome, revealing the existence of additional new carrageenan sulfatases.
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Affiliation(s)
- Aurélie Préchoux
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Sabine Genicot
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Hélène Rogniaux
- INRA, Biopolymers Interactions Assemblies, 44316, Nantes, France
| | - William Helbert
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France.
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, 29680, Roscoff, France.
- Centre de Recherches sur les Macromolécules Végétales (CERMAV, UPR-CNRS 5301), Affiliated with the Université Joseph Fourier (UJF), BP53, 38041, Grenoble Cedex 9, France.
- Institut de Chimie Moléculaire de Grenoble (ICMG, FR-CNRS 2607), Grenoble Cedex 9, France.
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Rhein-Knudsen N, Ale MT, Meyer AS. Seaweed hydrocolloid production: an update on enzyme assisted extraction and modification technologies. Mar Drugs 2015; 13:3340-59. [PMID: 26023840 PMCID: PMC4483632 DOI: 10.3390/md13063340] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/13/2015] [Indexed: 11/16/2022] Open
Abstract
Agar, alginate, and carrageenans are high-value seaweed hydrocolloids, which are used as gelation and thickening agents in different food, pharmaceutical, and biotechnological applications. The annual global production of these hydrocolloids has recently reached 100,000 tons with a gross market value just above US$ 1.1 billion. The techno-functional properties of the seaweed polysaccharides depend strictly on their unique structural make-up, notably degree and position of sulfation and presence of anhydro-bridges. Classical extraction techniques include hot alkali treatments, but recent research has shown promising results with enzymes. Current methods mainly involve use of commercially available enzyme mixtures developed for terrestrial plant material processing. Application of seaweed polysaccharide targeted enzymes allows for selective extraction at mild conditions as well as tailor-made modifications of the hydrocolloids to obtain specific functionalities. This review provides an update of the detailed structural features of κ-, ι-, λ-carrageenans, agars, and alginate, and a thorough discussion of enzyme assisted extraction and processing techniques for these hydrocolloids.
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Affiliation(s)
- Nanna Rhein-Knudsen
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Søltofts Plads, Building 229, DK-2800 Lyngby, Denmark.
| | - Marcel Tutor Ale
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Søltofts Plads, Building 229, DK-2800 Lyngby, Denmark.
| | - Anne S Meyer
- Center for Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Søltofts Plads, Building 229, DK-2800 Lyngby, Denmark.
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Szabó M, Baranyai Z, Somsák L, Fábián I. Decomposition of N-Chloroglycine in Alkaline Aqueous Solution: Kinetics and Mechanism. Chem Res Toxicol 2015; 28:1282-91. [PMID: 25849302 DOI: 10.1021/acs.chemrestox.5b00084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mária Szabó
- Department of Inorganic and Analytical Chemistry, and ‡Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
| | - Zsolt Baranyai
- Department of Inorganic and Analytical Chemistry, and ‡Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
| | - László Somsák
- Department of Inorganic and Analytical Chemistry, and ‡Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
| | - István Fábián
- Department of Inorganic and Analytical Chemistry, and ‡Department of Organic Chemistry, University of Debrecen, Debrecen, Hungary
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33
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Genicot SM, Groisillier A, Rogniaux H, Meslet-Cladière L, Barbeyron T, Helbert W. Discovery of a novel iota carrageenan sulfatase isolated from the marine bacterium Pseudoalteromonas carrageenovora. Front Chem 2014; 2:67. [PMID: 25207269 PMCID: PMC4144425 DOI: 10.3389/fchem.2014.00067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/03/2014] [Indexed: 11/15/2022] Open
Abstract
Carrageenans are sulfated polysaccharides extracted from the cell wall of some marine red algae. These polysaccharides are widely used as gelling, stabilizing, and viscosifying agents in the food and pharmaceutical industries. Since the rheological properties of these polysaccharides depend on their sulfate content, we screened several isolated marine bacteria for carrageenan specific sulfatase activity, in the aim of developing enzymatic bioconversion of carrageenans. As a result of the screening, an iota-carrageenan sulfatase was detected in the cell-free lysate of the marine bacterium Pseudoalteromonas carrageenovora strain PscT. It was purified through Phenyl Sepharose and Diethylaminoethyl Sepharose chromatography. The pure enzyme, Psc ι-CgsA, was characterized. It had a molecular weight of 115.9 kDaltons and exhibited an optimal activity/stability at pH ~8.3 and at 40 ± 5°C. It was inactivated by phenylmethylsulfonyl fluoride but not by ethylene diamine tetraacetic acid. Psc ι-CgsA specifically catalyzes the hydrolysis of the 4-S sulfate of iota-carrageenan. The purified enzyme could transform iota-carrageenan into hybrid iota-/alpha- or pure alpha-carrageenan under controlled conditions. The gene encoding Psc ι-CgsA, a protein of 1038 amino acids, was cloned into Escherichia coli, and the sequence analysis revealed that Psc ι-CgsA has more than 90% sequence identity with a putative uncharacterized protein Q3IKL4 from the marine strain Pseudoalteromonas haloplanktis TAC 125, but besides this did not share any homology to characterized sulfatases. Phylogenetic studies show that P. carrageenovora sulfatase thus represents the first characterized member of a new sulfatase family, with a C-terminal domain having strong similarity with the superfamily of amidohydrolases, highlighting the still unexplored diversity of marine polysaccharide modifying enzymes.
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Affiliation(s)
- Sabine M Genicot
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Université Paris 06 Roscoff, France ; UMR 8227, Centre National de la Recherche Scientifique, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Agnès Groisillier
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Université Paris 06 Roscoff, France ; UMR 8227, Centre National de la Recherche Scientifique, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Hélène Rogniaux
- INRA, UR1268 Biopolymers Interactions Assemblies Nantes, France
| | - Laurence Meslet-Cladière
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Université Paris 06 Roscoff, France ; UMR 8227, Centre National de la Recherche Scientifique, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; EA3882, LUBEM, Technopôle Brest-Iroise, Université de Bretagne Occidentale Plouzané, France
| | - Tristan Barbeyron
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Université Paris 06 Roscoff, France ; UMR 8227, Centre National de la Recherche Scientifique, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - William Helbert
- UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, UPMC Université Paris 06 Roscoff, France ; UMR 8227, Centre National de la Recherche Scientifique, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; Centre de Recherches sur les Macromolécules Végétales (CERMAV, UPR-CNRS 5301), Université Joseph Fourier, and Member of the Institut de Chimie Moléculaire de Grenoble (ICMG, FR-CNRS 2607) Grenoble, France
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Préchoux A, Helbert W. Preparation and detailed NMR analyses of a series of oligo-α-carrageenans. Carbohydr Polym 2013; 101:864-70. [PMID: 24299849 DOI: 10.1016/j.carbpol.2013.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
Abstract
Standard oligo-ι-carrageenans were produced with ι-carrageenases isolated from the marine bacteria Alteromonas fortis and Pseudolalteromonas atlantica. The carrageenans were then desulfated using a 4S-carrageenan-sulfatase purified from P. atlantica. Using chromatography and NMR analyses, we characterized a series of new standard neo-α-carrageenan oligosaccharides.
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Affiliation(s)
- Aurélie Préchoux
- Centre National de la Recherche Scientifique, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules", Station Biologique, F-29682 Roscoff Cedex, France
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