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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 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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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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3
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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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4
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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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5
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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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6
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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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7
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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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8
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Qu L, Cai R, Hu Z, Wang H. Metagenomic assemblage genomes analyses reveal the polysaccharides hydrolyzing potential of marine group II euryarchaea. ENVIRONMENTAL RESEARCH 2022; 209:112865. [PMID: 35120891 DOI: 10.1016/j.envres.2022.112865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/02/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Marine group II euryarchaea (MGII) dominates the planktonic archaeal community in global surface seawater and is associated to particulate organic matters mainly composed of polysaccharides. However, the polysaccharides metabolism of MGII euryarchaea is unclear. In this study, the distribution and polysaccharides metabolism potential of MGII euryarchaea in the estuary were investigated. High-throughput sequencing of 16S rRNA genes showed that MGII euryarchaea was the predominant archaeal group in the Pearl River Estuary (PRE), and the relative abundance of MGII euryarchaea in particle-attached fraction was higher than that in free-living fractions. A total of 19 metagenome-assembled genomes (MAGs) were successfully reconstructed from metagenomic data, of which 10 MAGs were grouped as MGII euryarchaea according to phylogenomic analysis. Genes encoding a variety of carbohydrate-active enzymes (CAZymes) were found in MAGs/genomes of MGII euryarchaea. These CAZymes annotated in MAGs were capable of hydrolyzing many polysaccharides, including α-glucans, β-glucans, xylans, nitrogen-containing polysaccharides, and some insoluble galactans. The results also indicated that MGII euryarchaea has some unique enzymes that can hydrolyze starch, β-1,3-glucans, complex xylans, carrageenan, and agarose. Collectively, our results demonstrated that MGII euryarchaea has great polysaccharides hydrolysis potential and could play an important role in the carbon cycle of marine ecosystem.
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Affiliation(s)
- Liping Qu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Runlin Cai
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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9
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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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10
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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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11
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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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12
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Saluri M, Kaljuvee KL, Paalme T, Reile I, Tuvikene R. Structural variability and rheological properties of furcellaran. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Dittami SM, Peters AF, West JA, Cariou T, KleinJan H, Burgunter-Delamare B, Prechoux A, Egan S, Boyen C. Revisiting Australian Ectocarpus subulatus (Phaeophyceae) From the Hopkins River: Distribution, Abiotic Environment, and Associated Microbiota. JOURNAL OF PHYCOLOGY 2020; 56:719-729. [PMID: 31965565 DOI: 10.1111/jpy.12970] [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: 10/30/2019] [Accepted: 01/07/2020] [Indexed: 05/24/2023]
Abstract
In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to the genus Ectocarpus. It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. To provide more background information on this model, we assessed if Ectocarpus was still present in the Hopkins river 22 years after the original finding, estimated its present distribution, described its abiotic environment, and determined its in situ microbial composition. We sampled for Ectocarpus at 15 sites along the Hopkins River as well as 10 neighboring sites and found individuals with ITS and cox1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls. The salinity of the water at these sites ranged from 3.1 to 6.9, and it was rich in sulfate (1-5 mM). The diversity of bacteria associated with the algae in situ (1312 operational taxonomic units) was one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from algal filaments on site. In particular, species of Planctomycetes were abundant in situ but rare in laboratory cultures. Our results confirmed that Ectocarpus was still present in the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.
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Affiliation(s)
- Simon M Dittami
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Akira F Peters
- Bezhin Rosko, 40 Rue des Pêcheurs, 29250, Santec, France
| | - John A West
- Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thierry Cariou
- CNRS, FR2424, Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Hetty KleinJan
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Bertille Burgunter-Delamare
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Aurélie Prechoux
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Catherine Boyen
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
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14
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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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15
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Béhar G, Renodon‐Cornière A, Kambarev S, Vukojicic P, Caroff N, Corvec S, Mouratou B, Pecorari F. Whole‐bacterium ribosome display selection for isolation of highly specific anti‐
Staphyloccocus aureus
Affitins for detection‐ and capture‐based biomedical applications. Biotechnol Bioeng 2019; 116:1844-1855. [DOI: 10.1002/bit.26989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/27/2019] [Accepted: 04/11/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ghislaine Béhar
- CRCINA, INSERM, CNRSUniversité d'Angers, Université de NantesNantes France
| | | | - Stanimir Kambarev
- CRCINA, INSERM, CNRSUniversité d'Angers, Université de NantesNantes France
| | - Petar Vukojicic
- CRCINA, INSERM, CNRSUniversité d'Angers, Université de NantesNantes France
| | - Nathalie Caroff
- EA3826 Thérapeutiques cliniques et expérimentales des infections, UFR de MédecineUniversité de NantesNantes France
| | - Stéphane Corvec
- CRCINA, INSERMUniversité d'Angers, Université de NantesNantes France
- Service de Bactériologie – Hygiène hospitalièreCHU de NantesNantes France
| | - Barbara Mouratou
- CRCINA, INSERM, CNRSUniversité d'Angers, Université de NantesNantes France
| | - Frédéric Pecorari
- CRCINA, INSERM, CNRSUniversité d'Angers, Université de NantesNantes France
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16
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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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17
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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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18
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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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19
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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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20
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He C, Muramatsu H, Kato SI, Ohnishi K. Characterization of an Alteromonas long-type ulvan lyase involved in the degradation of ulvan extracted from Ulva ohnoi. Biosci Biotechnol Biochem 2017; 81:2145-2151. [PMID: 28958183 DOI: 10.1080/09168451.2017.1379352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ulvan is a sulfated polysaccharide found in the cell wall of the green algae Ulva. We first isolated several ulvan-utilizing Alteromonas sp. from the feces of small marine animals. The strain with the highest ulvan-degrading activity, KUL17, was analyzed further. We identified a 55-kDa ulvan-degrading protein secreted by this strain and cloned the gene encoding for it. The deduced amino acid sequence indicated that the enzyme belongs to polysaccharide lyase family 24 and thus the protein was named ulvan lyase. The predicted molecular mass of this enzyme is 110 kDa, which is different from that of the identified protein. By deletion analysis, the catalytic domain was proven to be located on the N-terminal half of the protein. KUL17 contains two ulvan lyases, one long and one short, but the secreted and cleaved long ulvan lyase was demonstrated to be the major enzyme for ulvan degradation.
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Affiliation(s)
- Chuan He
- a The United Graduate School of Agricultural Sciences , Ehime University , Ehime , Japan
| | - Hisashi Muramatsu
- b Faculty of Agriculture and Marine Sciences , Kochi University , Kochi , Japan
| | - Shin-Ichiro Kato
- c Research Institute of Molecular Genetics , Kochi University , Kochi , Japan
| | - Kouhei Ohnishi
- c Research Institute of Molecular Genetics , Kochi University , Kochi , Japan
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21
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Thomas F, Bordron P, Eveillard D, Michel G. Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses. Front Microbiol 2017; 8:1808. [PMID: 28983288 PMCID: PMC5613140 DOI: 10.3389/fmicb.2017.01808] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/05/2017] [Indexed: 11/13/2022] Open
Abstract
Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans DsijT, originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.
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Affiliation(s)
- François Thomas
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffRoscoff, France
| | - Philippe Bordron
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, FR2424, Analysis and Bioinformatics for Marine Science, Station Biologique de RoscoffRoscoff, France.,Mathomics, Center for Mathematical Modeling, Universidad de ChileSantiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de ChileSantiago, Chile
| | - Damien Eveillard
- Université de Nantes, Laboratoire des Sciences du Numérique de Nantes, Centre National de la Recherche Scientifique, ECN, IMTANantes, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffRoscoff, 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: 101] [Impact Index Per Article: 12.6] [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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