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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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2
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A Novel Carrageenan Metabolic Pathway in Flavobacterium algicola. Appl Environ Microbiol 2022; 88:e0110022. [PMID: 36036580 PMCID: PMC9499021 DOI: 10.1128/aem.01100-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbohydrate-active enzymes are important components of the polysaccharide metabolism system in marine bacteria. Carrageenase is indispensable for forming carrageenan catalytic pathways. Here, two GH16_13 carrageenases showed likely hydrolysis activities toward different types of carrageenans (e.g., κ-, hybrid β/κ, hybrid α/ι, and hybrid λ), which indicates that a novel pathway is present in the marine bacterium Flavobacterium algicola to use κ-carrageenan (KC), ι-carrageenan (IC), and λ-carrageenan (LC). A comparative study described the different features with another reported pathway based on the specific carrageenans (κ, ι, and λ) and expanded the carrageenan metabolic versatility in F. algicola. A further comparative genomic analysis of carrageenan-degrading bacteria indicated different distributions of carrageenan metabolism-related genes in marine bacteria. The crucial core genes encoding the GH127 α-3,6-anhydro-d-galactosidase (ADAG) and 3,6-anhydro-d-galactose (d-AHG)-utilized cluster have been conserved during evolution. This analysis further revealed the horizontal gene transfer (HGT) phenomenon of the carrageenan polysaccharide utilization loci (CarPUL) from Bacteroidetes to other bacterial phyla, as well as the versatility of carrageenan catalytic activities in marine bacteria through different metabolic pathways. IMPORTANCE Based on the premise that the specific carrageenan-based pathway involved in carrageenan use by Flavobacterium algicola has been identified, another pathway was further analyzed, and it involved two GH16_13 carrageenases. Among all the characterized carrageenases, the members of GH16_13 accounted for only a small portion. Here, the functional analysis of two GH16_13 carrageenases suggested their hydrolysis effects on different types of carrageenans (e.g., κ, hybrid β/κ, hybrid α/ι-, and hybrid λ-), which led to the identification of another pathway. Further exploration enabled us to elucidate the novel pathway that metabolizes KC and IC in F. algicola successfully. The coexistence of these two pathways may provide improved survivability by F. algicola in the marine environment.
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3
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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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Enzymatic Verification and Comparative Analysis of Carrageenan Metabolism Pathways in Marine Bacterium Flavobacterium algicola. Appl Environ Microbiol 2022; 88:e0025622. [PMID: 35293779 DOI: 10.1128/aem.00256-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine bacteria usually contain polysaccharide utilization loci (PUL) for metabolizing red algae polysaccharides. They are of great significance in the carbon cycle of the marine ecosystem, as well as in supporting marine heterotrophic bacterial growth. Here, we described the whole κ-carrageenan (KC), ι-carrageenan (IC), and partial λ-carrageenan (LC) catabolic pathways in a marine Gram-negative bacterium, Flavobacterium algicola, which is involved carrageenan polysaccharide hydrolases, oligosaccharide sulfatases, oligosaccharide glycosidases, and the 3,6-anhydro-d-galactose (d-AHG) utilization-related enzymes harbored in the carrageenan-specific PUL. In the pathways, the KC and IC were hydrolyzed into 4-sugar-unit oligomers by specific glycoside hydrolases. Then, the multifunctional G4S sulfatases would remove their nonreducing ends' G4S sulfate groups, while the ι-neocarratetrose (Nι4) product would further lose the nonreducing end of its DA2S group. Furthermore, the neocarrageenan oligosaccharides (NCOSs) with no G4S and DA2S groups in their nonreducing ends would completely be decomposed into d-Gal and d-AHG. Finally, the released d-AHG would enter the cytoplasmic four-step enzymatic process, and an l-rhamnose-H+ transporter (RhaT) was preliminarily verified for the function for transportation of d-AHG. Moreover, comparative analysis with the reported carrageenan metabolism pathways further implied the diversity of microbial systems for utilizing the red algae carrageenan. IMPORTANCE Carrageenan is the main polysaccharide of red macroalgae and is composed of d-AHG and d-Gal. The carrageenan PUL (CarPUL)-encoded enzymes exist in many marine bacteria for decomposing carrageenan to provide self-growth. Here, the related enzymes in Flavobacterium algicola for metabolizing carrageenan were characterized for describing the catabolic pathways, notably, although the specific polysaccharide hydrolases existed that were like previous studies. A multifunctional G4S sulfatase also existed, which was devoted to the removal of G4S or G2S sulfate groups from three kinds of NCOSs. Additionally, the transformation of three types of carrageenans into two monomers, d-Gal and d-AHG, occurred outside the cell with no periplasmic reactions that existed in previously reported pathways. These results help to clarify the diversity of marine bacteria using macroalgae polysaccharides.
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5
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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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6
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Optimization of Fermentation Conditions for Carrageenase Production by Cellulophaga Species: A Comparative Study. BIOLOGY 2021; 10:biology10100971. [PMID: 34681070 PMCID: PMC8533080 DOI: 10.3390/biology10100971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022]
Abstract
Simple Summary Cellulophaga species are rarely studied marine bacteria with the potential for carrageenase production. We examined the carrageenase secretion ability of six bacterial species from the Cellulophaga genus. Among them, C. algicola produced the maximum amount of ι-carrageenase. Most of the bacteria produced their highest quantity of enzymes at 25 °C after 48 h of incubation time. The maximum enzyme production was achieved with the fermentation medium composition of 30 g/L sea salt, 1.4 g/L furcellaran and 3 g/L yeast extract. In addition, the properties of the ultrafiltered ι-carrageenase extracted from C. algicola were studied. Abstract Carrageenases appear in various species of marine bacteria and are widely used for the degradation of carrageenans, the commercially significant sulphated polysaccharides. The carrageenase production ability of six different Cellulophaga species was identified, with ι-carrageenase being the most abundant carrageenolytic enzyme. C. algicola was the most potent strain, followed by C. fucicola and C. geojensis, whereas C. pacifica was the least effective carrageenase producer among the studied strains. The enzyme production was maximized using the one-factor-at-a-time optimization method. The optimal incubation temperature was identified as 25 °C and the incubation time was set as 48 h for all tested species. The optimal medium composition for Cellulophaga strains was determined as 30 g/L sea salt, 1.4 g/L furcellaran, and 3 g/L yeast extract. An ultrafiltered enzyme extracted from C. algicola had the highest activity at around 40 °C. The optimal pH for enzymatic degradation was determined as 7.8, and the enzyme was fairly stable at temperatures up to 40 °C.
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Chernysheva N, Bystritskaya E, Likhatskaya G, Nedashkovskaya O, Isaeva M. Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia. Molecules 2021; 26:2387. [PMID: 33924031 PMCID: PMC8073546 DOI: 10.3390/molecules26082387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 12/04/2022] Open
Abstract
We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus-specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs.
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Affiliation(s)
| | | | | | | | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia; (N.C.); (E.B.); (G.L.); (O.N.)
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8
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Fermentation optimization, purification and biochemical characterization of ι-carrageenase from marine bacterium Cellulophaga baltica. Int J Biol Macromol 2020; 166:789-797. [PMID: 33157133 DOI: 10.1016/j.ijbiomac.2020.10.236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/11/2020] [Accepted: 10/30/2020] [Indexed: 01/19/2023]
Abstract
The ι-carrageenan degrading marine bacterium, Cellulophaga baltica, was isolated from the surface of a filamentous red alga Vertebrata fucoides. Maximum ι-carrageenase production was optimized by single-factor experiments. Optimal fermentation conditions were 1.6 g/L furcellaran, 4 g/L yeast extract as carbon sources, 5 g/L sea salt, and 48 h of incubation time at 20 °C. Extracellular ι-carrageenase from the culture supernatant was purified by ultrafiltration, ammonium sulfate precipitation, and finally by anion-exchange chromatography, showed a 26-fold increase in specific activity as compared to that in the crude enzyme. According to the results from SDS-PAGE and HPLC-SEC, the molecular weight of the purified enzyme was estimated to be 31 kDa. The purified enzyme showed the maximum specific activity of 571 U/mg at 40 °C and pH 7.5-8.0. It maintained 73% of the total activity below 40 °C and 90% of its total activity at pH 7.2. Notably, the enzyme is a cold-adapted ι-carrageenase, which showed 33.4% of the maximum activity at 10 °C. The enzyme was stimulated by Na+, K+, and NH4+, whereas Ca2+, Mg2+, Fe3+, sea salt, and EDTA acted as enzyme inhibitors.
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9
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Sun H, Gao L, Xue C, Mao X. Marine-polysaccharide degrading enzymes: Status and prospects. Compr Rev Food Sci Food Saf 2020; 19:2767-2796. [PMID: 33337030 DOI: 10.1111/1541-4337.12630] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
Marine-polysaccharide degrading enzymes have recently been studied extensively. They are particularly interesting as they catalyze the cleavage of glycosidic bonds in polysaccharide macromolecules and produce oligosaccharides with low degrees of polymerization. Numerous findings have demonstrated that marine polysaccharides and their biotransformed products possess beneficial properties including antitumor, antiviral, anticoagulant, and anti-inflammatory activities, and they have great value in healthcare, cosmetics, the food industry, and agriculture. Exploitation of enzymes that can degrade marine polysaccharides is in the ascendant, and is important for high-value use of marine biomass resources. In this review, we describe research and prospects regarding the classification, biochemical properties, and catalytic mechanisms of the main types of marine-polysaccharide degrading enzymes, focusing on chitinase, chitosanase, alginate lyase, agarase, and carrageenase, and their product oligosaccharides. The state-of-the-art discussion of marine-polysaccharide degrading enzymes and their properties offers information that might enable more efficient production of marine oligosaccharides. We also highlight current problems in the field of marine-polysaccharide degrading enzymes and trends in their development. Understanding the properties, catalytic mechanisms, and modification of known enzymes will aid the identification of novel enzymes to degrade marine polysaccharides and facilitation of their use in various biotechnological processes.
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Affiliation(s)
- Huihui Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Li Gao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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10
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Itoh T, Intuy R, Suyotha W, Hayashi J, Yano S, Makabe K, Wakayama M, Hibi T. Structural insights into substrate recognition and catalysis by glycoside hydrolase family 87 α‐1,3‐glucanase from
Paenibacillus glycanilyticus
FH11. FEBS J 2019; 287:2524-2543. [DOI: 10.1111/febs.15161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/02/2019] [Accepted: 11/28/2019] [Indexed: 01/20/2023]
Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology Fukui Prefectural University Eiheiji‐cho Japan
| | - Rattanaporn Intuy
- Department of Biotechnology College of Life Sciences Ritsumeikan University Kusatsu Japan
| | - Wasana Suyotha
- Department of Industrial Biotechnology Faculty of Agro‐industry Prince of Songkla University Hat Yai Thailand
| | - Junji Hayashi
- Department of Biotechnology College of Life Sciences Ritsumeikan University Kusatsu Japan
| | - Shigekazu Yano
- Department of Biochemical Engineering Graduate School of Science and Engineering Yamagata University Yonezawa Japan
| | - Koki Makabe
- Department of Biochemical Engineering Graduate School of Science and Engineering Yamagata University Yonezawa Japan
| | - Mamoru Wakayama
- Department of Biotechnology College of Life Sciences Ritsumeikan University Kusatsu Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology Fukui Prefectural University Eiheiji‐cho Japan
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11
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Barbeyron T, Zonta E, Le Panse S, Duchaud E, Michel G. Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas. Int J Syst Evol Microbiol 2019; 69:2514-2521. [DOI: 10.1099/ijsem.0.003533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tristan Barbeyron
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Erwann Zonta
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Sophie Le Panse
- 2CNRS / Sorbonne Université, FR 2424 Research and training in marine biology, Merimage platform, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Eric Duchaud
- 3INRA VIM-UR0892 Molecular Immunology and Virology, research group of Infection and Immunity of Fish, Research Center of Jouy-en-Josas, F-78352 Jouy-en-Josas, Ile-de-France, France
| | - Gurvan Michel
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
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12
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Naretto A, Fanuel M, Ropartz D, Rogniaux H, Larocque R, Czjzek M, Tellier C, Michel G. The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily. J Biol Chem 2019; 294:6923-6939. [PMID: 30846563 DOI: 10.1074/jbc.ra118.006609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 02/28/2019] [Indexed: 01/09/2023] Open
Abstract
Agars are sulfated galactans from red macroalgae and are composed of a d-galactose (G unit) and l-galactose (L unit) alternatively linked by α-1,3 and β-1,4 glycosidic bonds. These polysaccharides display high complexity, with numerous modifications of their backbone (e.g. presence of a 3,6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (β-agarases and β-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium Zobellia galactanivorans (ZgAgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family β-agarases and β-porphyranases. Using a large red algae collection, we demonstrate that ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of ZgAgaC on agar extracted from Osmundea pinnatifida By resolving the crystal structure of ZgAgaC at high resolution (1.3 Å) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC recognizes agarose via a mechanism different from that of classical β-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that ZgAgaC homologs define a new GH16 subfamily distinct from β-porphyranases and classical β-agarases.
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Affiliation(s)
- Anaïs Naretto
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Mathieu Fanuel
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - David Ropartz
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - Hélène Rogniaux
- the Institut National de la Recherche Agronomique (INRA), Unité de Recherche Biopolymères Interactions Assemblages (BIA), 44000 Nantes, France, and
| | - Robert Larocque
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Mirjam Czjzek
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France
| | - Charles Tellier
- the Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR 6286 CNRS, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, France
| | - Gurvan Michel
- From Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne, France,
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13
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Xu Y, Mao W, Gao W, Chi Z, Chi Z, Liu G. Efficient production of a recombinant ι-carrageenase in Brevibacillus choshinensis using a new integrative vector for the preparation of ι-carrageenan oligosaccharides. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Xiao Q, Zhu Y, Li J, Wu C, Ni H, Xiao A. Fermentation optimization and enzyme characterization of a new ι-Carrageenase from Pseudoalteromonas carrageenovora ASY5. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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15
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Matard-Mann M, Bernard T, Leroux C, Barbeyron T, Larocque R, Préchoux A, Jeudy A, Jam M, Nyvall Collén P, Michel G, Czjzek M. Structural insights into marine carbohydrate degradation by family GH16 κ-carrageenases. J Biol Chem 2017; 292:19919-19934. [PMID: 29030427 PMCID: PMC5712629 DOI: 10.1074/jbc.m117.808279] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Indexed: 11/06/2022] Open
Abstract
Carrageenans are sulfated α-1,3-β-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on κ-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the β-1,4 linkage of κ-carrageenan. We have solved the crystal structure of the catalytic module of ZgCgkA from Zobellia galactanivorans at 1.66 Å resolution and compared it with the only other structure available, that of PcCgkA from Pseudoalteromonas carrageenovora 9T (ATCC 43555T). We also describe the first substrate complex in the inactivated mutant form of PcCgkA at 1.7 Å resolution. The structural and biochemical comparison of these enzymes suggests key determinants that underlie the functional properties of this subfamily. In particular, we identified several arginine residues that interact with the polyanionic substrate, and confirmed the functional relevance of these amino acids using a targeted mutagenesis strategy. These results give new insight into the diversity of the κ-carrageenase subfamily. The phylogenetic analyses show the presence of several distinct clades of enzymes that relate to differences in modes of action or subtle differences within the same substrate specificity, matching the hybrid character of the κ-carrageenan polymer.
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Affiliation(s)
- Maria Matard-Mann
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
- Amadéite SAS, "Pôle Biotechnologique" du Haut du Bois, 56580 Bréhan, France
| | - Thomas Bernard
- the Architecture et Fonction des Macromolécules Biologiques, Unité Mixed de Recherche 6098, CNRS, Universités Aix-Marseille I and II, Case 932, 163 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Cédric Leroux
- the Sorbonne Universités, UPMC Université Paris 06, CNRS, FR 2424, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France, and
| | - Tristan Barbeyron
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Robert Larocque
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Aurélie Préchoux
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Alexandra Jeudy
- the Sorbonne Universités, UPMC Université Paris 06, CNRS, FR 2424, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France, and
| | - Murielle Jam
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Pi Nyvall Collén
- Amadéite SAS, "Pôle Biotechnologique" du Haut du Bois, 56580 Bréhan, France
| | - Gurvan Michel
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France
| | - Mirjam Czjzek
- From the Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 Roscoff, Bretagne, France,
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16
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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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17
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Shen J, Chang Y, Dong S, Chen F. Cloning, expression and characterization of a ι-carrageenase from marine bacterium Wenyingzhuangia fucanilytica : A biocatalyst for producing ι-carrageenan oligosaccharides. J Biotechnol 2017; 259:103-109. [DOI: 10.1016/j.jbiotec.2017.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/27/2017] [Accepted: 07/27/2017] [Indexed: 01/24/2023]
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18
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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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19
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Chauhan PS, Saxena A. Bacterial carrageenases: an overview of production and biotechnological applications. 3 Biotech 2016; 6:146. [PMID: 28330218 PMCID: PMC4919138 DOI: 10.1007/s13205-016-0461-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/19/2022] Open
Abstract
Carrageenan, one of the phycocolloids is a sulfated galactan made up of linear chains of galactose and 3,6-anhydrogalactose with alternating α-(1 → 3) and β-(1 → 4) linkages and further classified based on the number and the position of sulfated ester(s); κ-, ι- and λ-carrageenan. Enzymes which degrade carrageenans are called k-, ι-, and λ-carrageenases. They all are endohydrolases that cleave the internal β-(1-4) linkages of carrageenans yielding products of the oligo-carrageenans. These enzymes are produced only by bacteria specifically gram negative bacteria. Majority of the marine bacteria produce these enzymes extracellularly and their activity is in wide range of temperature. They have found potential applications in biomedical field, bioethanol production, textile industry, as a detergent additive and for isolation of protoplast of algae etc. A comprehensive information shall be helpful for the effective understanding and application of these enzymes. In this review exhaustive information of bacterial carrageenases reported till date has been done. All the aspects like sources, production conditions, characterization, cloning and- biotechnological applications are summarized.
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Affiliation(s)
- Prakram Singh Chauhan
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University Parkville Campus, 381, Royal Parade, Melbourne, VIC, 3052, Australia.
| | - Arunika Saxena
- Department of Chemistry, Samrat Prithviraj Chauhan Government College, Beawar Road, Ajmer, Rajasthan, India
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20
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Martin M, Vandermies M, Joyeux C, Martin R, Barbeyron T, Michel G, Vandenbol M. Discovering novel enzymes by functional screening of plurigenomic libraries from alga-associated Flavobacteriia and Gammaproteobacteria. Microbiol Res 2016; 186-187:52-61. [PMID: 27242143 DOI: 10.1016/j.micres.2016.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/17/2016] [Accepted: 03/22/2016] [Indexed: 11/22/2022]
Abstract
Alga-associated microorganisms, in the context of their numerous interactions with the host and the complexity of the marine environment, are known to produce diverse hydrolytic enzymes with original biochemistry. We recently isolated several macroalgal-polysaccharide-degrading bacteria from the surface of the brown alga Ascophyllum nodosum. These active isolates belong to two classes: the Flavobacteriia and the Gammaproteobacteria. In the present study, we constructed two "plurigenomic" (with multiple bacterial genomes) libraries with the 5 most interesting isolates (regarding their phylogeny and their enzymatic activities) of each class (Fv and Gm libraries). Both libraries were screened for diverse hydrolytic activities. Five activities, out of the 48 previously identified in the natural polysaccharolytic isolates, were recovered by functional screening: a xylanase (GmXyl7), a beta-glucosidase (GmBg1), an esterase (GmEst7) and two iota-carrageenases (Fvi2.5 and Gmi1.3). We discuss here the potential role of the used host-cell, the average DNA insert-sizes and the used restriction enzymes on the divergent screening yields obtained for both libraries and get deeper inside the "great screen anomaly". Interestingly, the discovered esterase probably stands for a novel family of homoserine o-acetyltransferase-like-esterases, while the two iota-carrageenases represent new members of the poorly known GH82 family (containing only 19 proteins since its description in 2000). These original results demonstrate the efficiency of our uncommon "plurigenomic" library approach and the underexplored potential of alga-associated cultivable microbiota for the identification of novel and algal-specific enzymes.
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Affiliation(s)
- Marjolaine Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium.
| | - Marie Vandermies
- Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Coline Joyeux
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Renée Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Tristan Barbeyron
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, Bretagne, France
| | - Gurvan Michel
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, Bretagne, France
| | - Micheline Vandenbol
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
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21
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Masuda Y, Okuyama M, Iizuka T, Nakai H, Saburi W, Fukukawa T, Maneesan J, Tagami T, Naraoka T, Mori H, Kimura A. Purification and characterization of a chloride ion-dependent α-glucosidase from the midgut gland of Japanese scallop (Patinopecten yessoensis). Biosci Biotechnol Biochem 2015; 80:479-85. [PMID: 26645800 DOI: 10.1080/09168451.2015.1116926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Marine glycoside hydrolases hold enormous potential due to their habitat-related characteristics such as salt tolerance, barophilicity, and cold tolerance. We purified an α-glucosidase (PYG) from the midgut gland of the Japanese scallop (Patinopecten yessoensis) and found that this enzyme has unique characteristics. The use of acarbose affinity chromatography during the purification was particularly effective, increasing the specific activity 570-fold. PYG is an interesting chloride ion-dependent enzyme. Chloride ion causes distinctive changes in its enzymatic properties, increasing its hydrolysis rate, changing the pH profile of its enzyme activity, shifting the range of its pH stability to the alkaline region, and raising its optimal temperature from 37 to 55 °C. Furthermore, chloride ion altered PYG's substrate specificity. PYG exhibited the highest Vmax/Km value toward maltooctaose in the absence of chloride ion and toward maltotriose in the presence of chloride ion.
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Affiliation(s)
- Yasushi Masuda
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Masayuki Okuyama
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Takahisa Iizuka
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Hiroyuki Nakai
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Wataru Saburi
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Taro Fukukawa
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Janjira Maneesan
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Takayoshi Tagami
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | | | - Haruhide Mori
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Atsuo Kimura
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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22
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Ficko-Blean E, Duffieux D, Rebuffet É, Larocque R, Groisillier A, Michel G, Czjzek M. Biochemical and structural investigation of two paralogous glycoside hydrolases fromZobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family. ACTA ACUST UNITED AC 2015; 71:209-23. [DOI: 10.1107/s1399004714025024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/14/2014] [Indexed: 01/25/2023]
Abstract
The family 117 glycoside hydrolase (GH117) enzymes have exo-α-1,3-(3,6-anhydro)-L-galactosidase activity, removing terminal nonreducing α-1,3-linked 3,6-anhydro-L-galactose residues from their red algal neoagarose substrate. These enzymes have previously been phylogenetically divided into clades, and only the clade A enzymes have been experimentally studied to date. The investigation of two GH117 enzymes, Zg3615 and Zg3597, produced by the marine bacteriumZobellia galactanivoransreveals structural, biochemical and further phylogenetic diversity between clades. A product complex with the unusual β-3,6-anhydro-L-galactose residue sheds light on the inverting catalytic mechanism of the GH117 enzymes as well as the structure of this unique sugar produced by hydrolysis of the agarophyte red algal cell wall.
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23
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The mannitol utilization system of the marine bacterium Zobellia galactanivorans. Appl Environ Microbiol 2014; 81:1799-812. [PMID: 25548051 DOI: 10.1128/aem.02808-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. In particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. Zobellia galactanivorans (Flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. Annotation of its genome revealed the presence of genes potentially involved in mannitol catabolism, and we describe here the biochemical characterization of a recombinant mannitol-2-dehydrogenase (M2DH) and a fructokinase (FK). Among the observations, the M2DH of Z. galactanivorans was active as a monomer, did not require metal ions for catalysis, and featured a narrow substrate specificity. The FK characterized was active on fructose and mannose in the presence of a monocation, preferentially K(+). Furthermore, the genes coding for these two proteins were adjacent in the genome and were located directly downstream of three loci likely to encode an ATP binding cassette (ABC) transporter complex, suggesting organization into an operon. Gene expression analysis supported this hypothesis and showed the induction of these five genes after culture of Z. galactanivorans in the presence of mannitol as the sole source of carbon. This operon for mannitol catabolism was identified in only 6 genomes of Flavobacteriaceae among the 76 publicly available at the time of the analysis. It is not conserved in all Bacteroidetes; some species contain a predicted mannitol permease instead of a putative ABC transporter complex upstream of M2DH and FK ortholog genes.
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24
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Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications. Appl Microbiol Biotechnol 2014; 98:2917-35. [PMID: 24562178 DOI: 10.1007/s00253-014-5557-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/17/2014] [Accepted: 01/20/2014] [Indexed: 01/02/2023]
Abstract
Marine microorganisms play key roles in every marine ecological process, hence the growing interest in studying their populations and functions. Microbial communities on algae remain underexplored, however, despite their huge biodiversity and the fact that they differ markedly from those living freely in seawater. The study of this microbiota and of its relationships with algal hosts should provide crucial information for ecological investigations on algae and aquatic ecosystems. Furthermore, because these microorganisms interact with algae in multiple, complex ways, they constitute an interesting source of novel bioactive compounds with biotechnological potential, such as dehalogenases, antimicrobials, and alga-specific polysaccharidases (e.g., agarases, carrageenases, and alginate lyases). Here, to demonstrate the huge potential of alga-associated organisms and their metabolites in developing future biotechnological applications, we first describe the immense diversity and density of these microbial biofilms. We further describe their complex interactions with algae, leading to the production of specific bioactive compounds and hydrolytic enzymes of biotechnological interest. We end with a glance at their potential use in medical and industrial applications.
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25
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Labourel A, Jam M, Jeudy A, Hehemann JH, Czjzek M, Michel G. The β-glucanase ZgLamA from Zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin. J Biol Chem 2013; 289:2027-42. [PMID: 24337571 DOI: 10.1074/jbc.m113.538843] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Laminarinase is commonly used to describe β-1,3-glucanases widespread throughout Archaea, bacteria, and several eukaryotic lineages. Some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. Here we report the heterologous expression and subsequent biochemical and structural characterization of ZgLamAGH16 from Zobellia galactanivorans, the first GH16 laminarinase from a marine bacterium associated with seaweeds. ZgLamAGH16 contains a unique additional loop, compared with other GH16 laminarinases, which is composed of 17 amino acids and gives a bent shape to the active site cleft of the enzyme. This particular topology is perfectly adapted to the U-shaped conformation of laminarin chains in solution and thus explains the predominant specificity of ZgLamAGH16 for this substrate. The three-dimensional structure of the enzyme and two enzyme-substrate complexes, one with laminaritetraose and the other with a trisaccharide of 1,3-1,4-β-d-glucan, have been determined at 1.5, 1.35, and 1.13 Å resolution, respectively. The structural comparison of substrate recognition pattern between these complexes allows the proposition that ZgLamAGH16 likely diverged from an ancestral broad specificity GH16 β-glucanase and evolved toward a bent active site topology adapted to efficient degradation of algal laminarin.
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Affiliation(s)
- Aurore Labourel
- From Sorbonne Universités, UPMC Université Paris 06, UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France and
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26
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Ma S, Duan G, Chai W, Geng C, Tan Y, Wang L, Le Sourd F, Michel G, Yu W, Han F. Purification, cloning, characterization and essential amino acid residues analysis of a new ι-carrageenase from Cellulophaga sp. QY3. PLoS One 2013; 8:e64666. [PMID: 23741363 PMCID: PMC3669377 DOI: 10.1371/journal.pone.0064666] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/16/2013] [Indexed: 11/27/2022] Open
Abstract
ι-Carrageenases belong to family 82 of glycoside hydrolases that degrade sulfated galactans in the red algae known as ι-carrageenans. The catalytic mechanism and some substrate-binding residues of family GH82 have been studied but the substrate recognition and binding mechanism of this family have not been fully elucidated. We report here the purification, cloning and characterization of a new ι-carrageenase CgiA_Ce from the marine bacterium Cellulophaga sp. QY3. CgiA_Ce was the most thermostable carrageenase described so far. It was most active at 50°C and pH 7.0 and retained more than 70% of the original activity after incubation at 50°C for 1 h at pH 7.0 or at pH 5.0–10.6 for 24 h. CgiA_Ce was an endo-type ι-carrageenase; it cleaved ι-carrageenan yielding neo-ι-carrabiose and neo-ι-carratetraose as the main end products, and neo-ι-carrahexaose was the minimum substrate. Sequence analysis and structure modeling showed that CgiA_Ce is indeed a new member of family GH82. Moreover, sequence analysis of ι-carrageenases revealed that the amino acid residues at subsites −1 and +1 were more conserved than those at other subsites. Site-directed mutagenesis followed by kinetic analysis identified three strictly conserved residues at subsites −1 and +1 of ι-carrageenases, G228, Y229 and R254 in CgiA_Ce, which played important roles for substrate binding. Furthermore, our results suggested that Y229 and R254 in CgiA_Ce interacted specifically with the sulfate groups of the sugar moieties located at subsites −1 and +1, shedding light on the mechanism of ι-carrageenan recognition in the family GH82.
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Affiliation(s)
- Su Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, China
- Laboratory of Glycobiology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Gaofei Duan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, China
- Laboratory of Glycobiology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Wengang Chai
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Glycosciences Laboratory, Department of Medicine, Imperial College, London, United Kingdom
| | - Cunliang Geng
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Yulong Tan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, China
- Laboratory of Glycobiology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Lushan Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Frédéric Le Sourd
- UPMC University Paris 6, Paris, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, Brittany, France
| | - Gurvan Michel
- UPMC University Paris 6, Paris, France
- CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, Brittany, France
| | - Wengong Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, China
- Laboratory of Glycobiology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Feng Han
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, Ocean University of China, Qingdao, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, Qingdao, China
- Laboratory of Glycobiology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- * E-mail:
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Chi WJ, Chang YK, Hong SK. Agar degradation by microorganisms and agar-degrading enzymes. Appl Microbiol Biotechnol 2012; 94:917-30. [PMID: 22526785 DOI: 10.1007/s00253-012-4023-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 11/30/2022]
Abstract
Agar is a mixture of heterogeneous galactans, mainly composed of 3,6-anhydro-L-galactoses (or L-galactose-6-sulfates) D-galactoses and L-galactoses (routinely in the forms of 3,6-anhydro-L-galactoses or L-galactose-6-sulfates) alternately linked by β-(1,4) and α-(1,3) linkages. It is a major component of the cell walls of red algae and has been used in a variety of laboratory and industrial applications, owing to its jellifying properties. Many microorganisms that can hydrolyze and metabolize agar as a carbon and energy source have been identified in seawater and marine sediments. Agarolytic microorganisms commonly produce agarases, which catalyze the hydrolysis of agar. Numerous agarases have been identified in microorganisms of various genera. They are classified according to their cleavage pattern into three types-α-agarase, β-agarase, and β-porphyranase. Although, in a broad sense, many other agarases are involved in complete hydrolysis of agar, most of those identified are β-agarases. In this article we review agarolytic microorganisms and their agar-hydrolyzing systems, covering β-agarases as well as α-agarases, α-neoagarobiose hydrolases, and β-porphyranases, with emphasis on the recent discoveries. We also present an overview of the biochemical and structural characteristics of the various types of agarases. Further, we summarize and compare the agar-hydrolyzing systems of two specific microorganisms: Gram-negative Saccharophagus degradans 2-40 and Gram-positive Streptomyces coelicolor A3(2). We conclude with a brief discussion of the importance of agarases and their possible future application in producing oligosaccharides with various nutraceutical activities and in sustainably generating stock chemicals for biorefinement and bioenergy.
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Affiliation(s)
- Won-Jae Chi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, Korea
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Rebuffet E, Groisillier A, Thompson A, Jeudy A, Barbeyron T, Czjzek M, Michel G. Discovery and structural characterization of a novel glycosidase family of marine origin. Environ Microbiol 2011; 13:1253-70. [PMID: 21332624 DOI: 10.1111/j.1462-2920.2011.02426.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genomic data on heterotrophic marine bacteria suggest the crucial role that microbes play in the global carbon cycle. However, the massive presence of hypothetical proteins hampers our understanding of the mechanisms by which this carbon cycle is carried out. Moreover, genomic data from marine microorganisms are essentially annotated in the light of the biochemical knowledge accumulated on bacteria and fungi which decompose terrestrial plants. However marine algal polysaccharides clearly differ from their terrestrial counterparts, and their associated enzymes usually constitute novel protein families. In this study, we have applied a combination of bioinformatics, targeted activity screening and structural biology to characterize a hypothetical protein from the marine bacterium Zobellia galactanivorans, which is distantly related to GH43 family. This protein is in fact a 1,3-α-3,6-anhydro-l-galactosidase (AhgA) which catalyses the last step in the degradation pathway of agars, a family of polysaccharides unique to red macroalgae. AhgA adopts a β-propeller fold and displays a zinc-dependent catalytic machinery. This enzyme is the first representative of a new family of glycoside hydrolases, especially abundant in coastal waters. Such genes of marine origin have been transferred to symbiotic microbes associated with marine fishes, but also with some specific human populations.
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Affiliation(s)
- Etienne Rebuffet
- UPMC University Paris 6 CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, Roscoff, Bretagne, France
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Thomas F, Barbeyron T, Michel G. Evaluation of reference genes for real-time quantitative PCR in the marine flavobacterium Zobellia galactanivorans. J Microbiol Methods 2011; 84:61-6. [DOI: 10.1016/j.mimet.2010.10.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 01/22/2023]
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