1
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Miksch S, Orellana LH, Oggerin de Orube M, Vidal-Melgosa S, Solanki V, Hehemann JH, Amann R, Knittel K. Taxonomic and functional stability overrules seasonality in polar benthic microbiomes. ISME J 2024; 18:wrad005. [PMID: 38365229 PMCID: PMC10811738 DOI: 10.1093/ismejo/wrad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 02/18/2024]
Abstract
Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.
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Affiliation(s)
- Sebastian Miksch
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Monike Oggerin de Orube
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Vipul Solanki
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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2
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Yu XA, McLean C, Hehemann JH, Angeles-Albores D, Wu F, Muszyński A, Corzett CH, Azadi P, Kujawinski EB, Alm EJ, Polz MF. Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics. ISME J 2024; 18:wrad013. [PMID: 38365244 PMCID: PMC10811730 DOI: 10.1093/ismejo/wrad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.
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Affiliation(s)
- Xiaoqian Annie Yu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Craig McLean
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
- MIT/WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Jan-Hendrik Hehemann
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David Angeles-Albores
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Fuqing Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, United States
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Eric J Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Martin F Polz
- Division of Microbial Ecology, Department of Microbiology and Ecosystems Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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3
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Priest T, Vidal-Melgosa S, Hehemann JH, Amann R, Fuchs BM. Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic. ISME Commun 2023; 3:130. [PMID: 38071398 PMCID: PMC10710508 DOI: 10.1038/s43705-023-00324-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 02/13/2024]
Abstract
Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through 'omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.
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Affiliation(s)
- Taylor Priest
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Clerc EE, Raina JB, Keegstra JM, Landry Z, Pontrelli S, Alcolombri U, Lambert BS, Anelli V, Vincent F, Masdeu-Navarro M, Sichert A, De Schaetzen F, Sauer U, Simó R, Hehemann JH, Vardi A, Seymour JR, Stocker R. Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP. Nat Commun 2023; 14:8080. [PMID: 38057294 DOI: 10.1038/s41467-023-43143-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of these large molecules is largely unknown. Using in situ and laboratory-based chemotaxis assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharides laminarin and alginate. Unexpectedly, these polysaccharides elicited stronger chemoattraction than their oligo- and monosaccharide constituents. Furthermore, chemotaxis towards laminarin was strongly enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. We demonstrate that marine bacteria are capable of strong chemotaxis towards large soluble polysaccharides and uncover a new ecological role for DMSP in enhancing this attraction. These navigation behaviours may contribute to the rapid turnover of polymers in the ocean, with important consequences for marine carbon cycling.
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Affiliation(s)
- Estelle E Clerc
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Johannes M Keegstra
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Zachary Landry
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Uria Alcolombri
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
- Institute for Life Sciences, Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bennett S Lambert
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Valerio Anelli
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Developmental Biology Unit, European Molecular Biological Laboratory, Heidelberg, 69117, Germany
| | | | - Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frédéric De Schaetzen
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, Barcelona, Catalonia, Spain
| | | | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
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5
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Dutschei T, Beidler I, Bartosik D, Seeßelberg JM, Teune M, Bäumgen M, Ferreira SQ, Heldmann J, Nagel F, Krull J, Berndt L, Methling K, Hein M, Becher D, Langer P, Delcea M, Lalk M, Lammers M, Höhne M, Hehemann JH, Schweder T, Bornscheuer UT. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ Microbiol 2023; 25:1713-1727. [PMID: 37121608 DOI: 10.1111/1462-2920.16390] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
Marine Bacteroidetes that degrade polysaccharides contribute to carbon cycling in the ocean. Organic matter, including glycans from terrestrial plants, might enter the oceans through rivers. Whether marine bacteria degrade structurally related glycans from diverse sources including terrestrial plants and marine algae was previously unknown. We show that the marine bacterium Flavimarina sp. Hel_I_48 encodes two polysaccharide utilization loci (PULs) which degrade xylans from terrestrial plants and marine algae. Biochemical experiments revealed activity and specificity of the encoded xylanases and associated enzymes of these PULs. Proteomics indicated that these genomic regions respond to glucuronoxylans and arabinoxylans. Substrate specificities of key enzymes suggest dedicated metabolic pathways for xylan utilization. Some of the xylanases were active on different xylans with the conserved β-1,4-linked xylose main chain. Enzyme activity was consistent with growth curves showing Flavimarina sp. Hel_I_48 uses structurally different xylans. The observed abundance of related xylan-degrading enzyme repertoires in genomes of other marine Bacteroidetes indicates similar activities are common in the ocean. The here presented data show that certain marine bacteria are genetically and biochemically variable enough to access parts of structurally diverse xylans from terrestrial plants as well as from marine algal sources.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Irena Beidler
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Julia-Maria Seeßelberg
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michelle Teune
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Soraia Querido Ferreira
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Julia Heldmann
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Felix Nagel
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Martin Hein
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Peter Langer
- Department of Organic Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lalk
- Department of Cellular Biochemistry and Metabolomics, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Matthias Höhne
- Department of Protein Biochemistry, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., Greifswald, Germany
- Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
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6
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Sidhu C, Kirstein IV, Meunier CL, Rick J, Fofonova V, Wiltshire KH, Steinke N, Vidal-Melgosa S, Hehemann JH, Huettel B, Schweder T, Fuchs BM, Amann RI, Teeling H. Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom. Microbiome 2023; 11:77. [PMID: 37069671 PMCID: PMC10108472 DOI: 10.1186/s40168-023-01517-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/15/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biomass on a global scale. This biomass is largely composed of distinct polysaccharides, and the microbial decomposition of these polysaccharides is therefore a process of prime importance. RESULTS In 2020, we sampled a complete biphasic spring bloom in the German Bight over a 90-day period. Bacterioplankton metagenomes from 30 time points allowed reconstruction of 251 metagenome-assembled genomes (MAGs). Corresponding metatranscriptomes highlighted 50 particularly active MAGs of the most abundant clades, including many polysaccharide degraders. Saccharide measurements together with bacterial polysaccharide utilization loci (PUL) expression data identified β-glucans (diatom laminarin) and α-glucans as the most prominent and actively metabolized dissolved polysaccharide substrates. Both substrates were consumed throughout the bloom, with α-glucan PUL expression peaking at the beginning of the second bloom phase shortly after a peak in flagellate and the nadir in bacterial total cell counts. CONCLUSIONS We show that the amounts and composition of dissolved polysaccharides, in particular abundant storage polysaccharides, have a pronounced influence on the composition of abundant bacterioplankton members during phytoplankton blooms, some of which compete for similar polysaccharide niches. We hypothesize that besides the release of algal glycans, also recycling of bacterial glycans as a result of increased bacterial cell mortality can have a significant influence on bacterioplankton composition during phytoplankton blooms. Video Abstract.
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Affiliation(s)
- Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Inga V. Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Cédric L. Meunier
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Hafenstraße 43, 25992 List/Sylt, Germany
| | - Vera Fofonova
- Alfred Wegener Institute for Polar and Marine Research, Klußmannstraße 3, 27570 Bremerhaven, Germany
| | - Karen H. Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, P.O. Box 180, 27483 Helgoland, Germany
| | - Nicola Steinke
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Leobener Straße 8, 28359 Bremen, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl Von Linné-Weg 10, 50829 Cologne, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489 Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489 Greifswald, Germany
| | - Bernhard M. Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Rudolf I. Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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7
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Vincent F, Gralka M, Schleyer G, Schatz D, Cabrera-Brufau M, Kuhlisch C, Sichert A, Vidal-Melgosa S, Mayers K, Barak-Gavish N, Flores JM, Masdeu-Navarro M, Egge JK, Larsen A, Hehemann JH, Marrasé C, Simó R, Cordero OX, Vardi A. Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms. Nat Commun 2023; 14:510. [PMID: 36720878 PMCID: PMC9889395 DOI: 10.1038/s41467-023-36049-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Algal blooms are hotspots of marine primary production and play central roles in microbial ecology and global elemental cycling. Upon demise of the bloom, organic carbon is partly respired and partly transferred to either higher trophic levels, bacterial biomass production or sinking. Viral infection can lead to bloom termination, but its impact on the fate of carbon remains largely unquantified. Here, we characterize the interplay between viral infection and the composition of a bloom-associated microbiome and consequently the evolving biogeochemical landscape, by conducting a large-scale mesocosm experiment where we monitor seven induced coccolithophore blooms. The blooms show different degrees of viral infection and reveal that only high levels of viral infection are followed by significant shifts in the composition of free-living bacterial and eukaryotic assemblages. Intriguingly, upon viral infection the biomass of eukaryotic heterotrophs (thraustochytrids) rivals that of bacteria as potential recyclers of organic matter. By combining modeling and quantification of active viral infection at a single-cell resolution, we estimate that viral infection causes a 2-4 fold increase in per-cell rates of extracellular carbon release in the form of acidic polysaccharides and particulate inorganic carbon, two major contributors to carbon sinking into the deep ocean. These results reveal the impact of viral infection on the fate of carbon through microbial recyclers of organic matter in large-scale coccolithophore blooms.
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Affiliation(s)
- Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.,Developmental Biology Unit, European Molecular Biological Laboratory, 69117, Heidelberg, Germany
| | - Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Systems Biology Lab, Amsterdam Institute for Life and Environment (A-Life)/Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081, Amsterdam, The Netherlands
| | - Guy Schleyer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Andreas Sichert
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA.,Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Kyle Mayers
- NORCE Norwegian Research Centre, 5008, Bergen, Norway
| | - Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - J Michel Flores
- Department of Earth and Planetary Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | | | - Jorun Karin Egge
- Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Aud Larsen
- NORCE Norwegian Research Centre, 5008, Bergen, Norway.,Department of Biological Sciences (BIO), University of Bergen, 5020, Bergen, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Celia Marrasé
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Rafel Simó
- Institut de Ciències del Mar, CSIC, 08003, Barcelona, Spain
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, 02145, MA, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel.
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8
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Buck-Wiese H, Andskog MA, Nguyen NP, Bligh M, Asmala E, Vidal-Melgosa S, Liebeke M, Gustafsson C, Hehemann JH. Fucoid brown algae inject fucoidan carbon into the ocean. Proc Natl Acad Sci U S A 2023; 120:e2210561119. [PMID: 36584294 PMCID: PMC9910443 DOI: 10.1073/pnas.2210561119] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 01/01/2023] Open
Abstract
Brown algae annually convert gigatons of carbon dioxide into carbohydrates, including the complex extracellular matrix polysaccharide fucoidan. Due to its persistence in the environment, fucoidan is potentially a pathway for marine carbon sequestration. Rates of fucoidan secretion by brown algae remain unknown due to the challenge of identifying and quantifying complex polysaccharides in seawater. We adapted the techniques of anion exchange chromatography, enzyme-linked immunosorbent assay, and biocatalytic enzyme-based assay for detection and quantification of fucoidan. We found the brown alga Fucus vesiculosus at the Baltic Sea coast of south-west Finland to secrete 0.3% of their biomass as fucoidan per day. Dissolved fucoidan concentrations in seawater adjacent to algae reached up to 0.48 mg L-1. Fucoidan accumulated during incubations of F. vesiculosus, significantly more in light than in darkness. Maximum estimation by acid hydrolysis indicated fucoidan secretion at a rate of 28 to 40 mg C kg-1 h-1, accounting for 44 to 50% of all exuded dissolved organic carbon. Composed only of carbon, oxygen, hydrogen, and sulfur, fucoidan secretion does not consume nutrients enabling carbon sequestration independent of algal growth. Extrapolated over a year, the algae sequester more carbon into secreted fucoidan than their biomass. The global utility of fucoidan secretion is an alternative pathway for carbon dioxide removal by brown algae without the need to harvest or bury algal biomass.
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Affiliation(s)
- Hagen Buck-Wiese
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359Bremen, Germany
| | - Mona A. Andskog
- Centre for Coastal Biogeochemistry, Southern Cross University, 2480Lismore, Australia
| | - Nguyen P. Nguyen
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359Bremen, Germany
| | - Margot Bligh
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359Bremen, Germany
| | - Eero Asmala
- Geological Survey of Finland, Environmental Solutions, 02151Espoo, Finland
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359Bremen, Germany
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
| | - Camilla Gustafsson
- University of Helsinki, Tvärminne Zoological Station, 10900Hanko, Finland
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359Bremen, Germany
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9
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Bligh M, Nguyen N, Buck-Wiese H, Vidal-Melgosa S, Hehemann JH. Structures and functions of algal glycans shape their capacity to sequester carbon in the ocean. Curr Opin Chem Biol 2022; 71:102204. [PMID: 36155346 DOI: 10.1016/j.cbpa.2022.102204] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 01/27/2023]
Abstract
Algae synthesise structurally complex glycans to build a protective barrier, the extracellular matrix. One function of matrix glycans is to slow down microorganisms that try to enzymatically enter living algae and degrade and convert their organic carbon back to carbon dioxide. We propose that matrix glycans lock up carbon in the ocean by controlling degradation of organic carbon by bacteria and other microbes not only while algae are alive, but also after death. Data revised in this review shows accumulation of algal glycans in the ocean underscoring the challenge bacteria and other microbes face to breach the glycan barrier with carbohydrate active enzymes. Briefly we also update on methods required to certify the uncertain magnitude and unknown molecular causes of glycan-controlled carbon sequestration in a changing ocean.
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Affiliation(s)
- Margot Bligh
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Nguyen Nguyen
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Hagen Buck-Wiese
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany; University of Bremen, MARUM Centre for Marine Environmental Sciences Bremen, Germany.
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10
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Dutschei T, Zühlke MK, Welsch N, Eisenack T, Hilkmann M, Krull J, Stühle C, Brott S, Dürwald A, Reisky L, Hehemann JH, Becher D, Schweder T, Bornscheuer UT. Metabolic engineering enables Bacillus licheniformis to grow on the marine polysaccharide ulvan. Microb Cell Fact 2022; 21:207. [PMID: 36217189 PMCID: PMC9549685 DOI: 10.1186/s12934-022-01931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Marine algae are responsible for half of the global primary production, converting carbon dioxide into organic compounds like carbohydrates. Particularly in eutrophic waters, they can grow into massive algal blooms. This polysaccharide rich biomass represents a cheap and abundant renewable carbon source. In nature, the diverse group of polysaccharides is decomposed by highly specialized microbial catabolic systems. We elucidated the complete degradation pathway of the green algae-specific polysaccharide ulvan in previous studies using a toolbox of enzymes discovered in the marine flavobacterium Formosa agariphila and recombinantly expressed in Escherichia coli. Results In this study we show that ulvan from algal biomass can be used as feedstock for a biotechnological production strain using recombinantly expressed carbohydrate-active enzymes. We demonstrate that Bacillus licheniformis is able to grow on ulvan-derived xylose-containing oligosaccharides. Comparative growth experiments with different ulvan hydrolysates and physiological proteogenomic analyses indicated that analogues of the F. agariphila ulvan lyase and an unsaturated β-glucuronylhydrolase are missing in B. licheniformis. We reveal that the heterologous expression of these two marine enzymes in B. licheniformis enables an efficient conversion of the algal polysaccharide ulvan as carbon and energy source. Conclusion Our data demonstrate the physiological capability of the industrially relevant bacterium B. licheniformis to grow on ulvan. We present a metabolic engineering strategy to enable ulvan-based biorefinery processes using this bacterial cell factory. With this study, we provide a stepping stone for the development of future bioprocesses with Bacillus using the abundant marine renewable carbon source ulvan. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01931-0.
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Affiliation(s)
- Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Marie-Katherin Zühlke
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Norma Welsch
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Tom Eisenack
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Maximilian Hilkmann
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany.,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany
| | - Joris Krull
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Carlo Stühle
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Stefan Brott
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Alexandra Dürwald
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany
| | - Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.,Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany.,Center for Marine Environmental Sciences (MARUM), University of Bremen, 28359, Bremen, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute for Microbiology, University of Greifswald, 17487, Greifswald, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany. .,Institute of Marine Biotechnology e.V., 17489, Greifswald, Germany.
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11
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Bäumgen M, Dutschei T, Bartosik D, Suster C, Reisky L, Gerlach N, Stanetty C, Mihovilovic MD, Schweder T, Hehemann JH, Bornscheuer UT. A new carbohydrate-active oligosaccharide dehydratase is involved in the degradation of ulvan. J Biol Chem 2021; 297:101210. [PMID: 34547290 PMCID: PMC8511951 DOI: 10.1016/j.jbc.2021.101210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/28/2022] Open
Abstract
Marine algae catalyze half of all global photosynthetic production of carbohydrates. Owing to their fast growth rates, Ulva spp. rapidly produce substantial amounts of carbohydrate-rich biomass and represent an emerging renewable energy and carbon resource. Their major cell wall polysaccharide is the anionic carbohydrate ulvan. Here, we describe a new enzymatic degradation pathway of the marine bacterium Formosa agariphila for ulvan oligosaccharides involving unsaturated uronic acid at the nonreducing end linked to rhamnose-3-sulfate and glucuronic or iduronic acid (Δ-Rha3S-GlcA/IdoA-Rha3S). Notably, we discovered a new dehydratase (P29_PDnc) acting on the nonreducing end of ulvan oligosaccharides, i.e., GlcA/IdoA-Rha3S, forming the aforementioned unsaturated uronic acid residue. This residue represents the substrate for GH105 glycoside hydrolases, which complements the enzymatic degradation pathway including one ulvan lyase, one multimodular sulfatase, three glycoside hydrolases, and the dehydratase P29_PDnc, the latter being described for the first time. Our research thus shows that the oligosaccharide dehydratase is involved in the degradation of carboxylated polysaccharides into monosaccharides.
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Affiliation(s)
- Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Theresa Dutschei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Daniel Bartosik
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Christoph Suster
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | - Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Nadine Gerlach
- Max Planck-Institute for Marine Microbiology, Bremen, Germany; Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | | | | | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, Bremen, Germany; Center for Marine Environmental Sciences (MARUM), University of Bremen, Bremen, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.
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12
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Sichert A, Le Gall S, Klau LJ, Laillet B, Rogniaux H, Aachmann FL, Hehemann JH. Ion-exchange purification and structural characterization of five sulfated fucoidans from brown algae. Glycobiology 2021; 31:352-357. [PMID: 32651947 PMCID: PMC8091464 DOI: 10.1093/glycob/cwaa064] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Fucoidans are a diverse class of sulfated polysaccharides integral to the cell wall of brown algae, and due to their various bioactivities, they are potential drugs. Standardized work with fucoidans is required for structure-function studies, but remains challenging since available fucoidan preparations are often contaminated with other algal compounds. Additionally, fucoidans are structurally diverse depending on species and season, urging the need for standardized purification protocols. Here, we use ion-exchange chromatography to purify different fucoidans and found a high structural diversity between fucoidans. Ion-exchange chromatography efficiently removes the polysaccharides alginate and laminarin and other contaminants such as proteins and phlorotannins across a broad range of fucoidans from major brown algal orders including Ectocarpales, Laminariales and Fucales. By monomer composition, linkage analysis and NMR characterization, we identified galacturonic acid, glucuronic acid and O-acetylation as new structural features of certain fucoidans and provided a novel structure of fucoidan from Durvillaea potatorum with α-1,3-linked fucose backbone and β-1,6 and β-1,3 galactose branches. This study emphasizes the use of standardized ion-exchange chromatography to obtain defined fucoidans for subsequent molecular studies.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359 Bremen, Germany
| | - Sophie Le Gall
- INRAE, UR BIA (Biopolymers Interactions Assemblies), F-44316 Nantes, France
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Leesa Jane Klau
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Brigitte Laillet
- INRAE, UR BIA (Biopolymers Interactions Assemblies), F-44316 Nantes, France
| | - Hélène Rogniaux
- INRAE, UR BIA (Biopolymers Interactions Assemblies), F-44316 Nantes, France
- INRAE, BIBS Facility, F-44316 Nantes, France
| | - Finn Lillelund Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359 Bremen, Germany
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13
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Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, Willats WGT, Fuchs BM, Teeling H, Becher D, Schweder T, Amann R, Hehemann JH. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun 2021; 12:1150. [PMID: 33608542 PMCID: PMC7896085 DOI: 10.1038/s41467-021-21009-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
The formation of sinking particles in the ocean, which promote carbon sequestration into deeper water and sediments, involves algal polysaccharides acting as an adhesive, binding together molecules, cells and minerals. These as yet unidentified adhesive polysaccharides must resist degradation by bacterial enzymes or else they dissolve and particles disassemble before exporting carbon. Here, using monoclonal antibodies as analytical tools, we trace the abundance of 27 polysaccharide epitopes in dissolved and particulate organic matter during a series of diatom blooms in the North Sea, and discover a fucose-containing sulphated polysaccharide (FCSP) that resists enzymatic degradation, accumulates and aggregates. Previously only known as a macroalgal polysaccharide, we find FCSP to be secreted by several globally abundant diatom species including the genera Chaetoceros and Thalassiosira. These findings provide evidence for a novel polysaccharide candidate to contribute to carbon sequestration in the ocean.
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Affiliation(s)
- Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - Andreas Sichert
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - T Ben Francis
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Jutta Niggemann
- University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, 26129, Oldenburg, Germany
| | - Antje Wichels
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Biologische Anstalt Helgoland, 27498, Helgoland, Germany
| | - William G T Willats
- Newcastle University, School of Natural and Environmental Sciences, Newcastle upon Tyne, NE1 7RU, UK
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany.
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14
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Klassen L, Reintjes G, Tingley JP, Jones DR, Hehemann JH, Smith AD, Schwinghamer TD, Arnosti C, Jin L, Alexander TW, Amundsen C, Thomas D, Amann R, McAllister TA, Abbott DW. Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria. Microbiome 2021; 9:23. [PMID: 33482928 PMCID: PMC7825182 DOI: 10.1186/s40168-020-00975-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/07/2020] [Indexed: 05/03/2023]
Abstract
Gut microbiomes, such as the microbial community that colonizes the rumen, have vast catabolic potential and play a vital role in host health and nutrition. By expanding our understanding of metabolic pathways in these ecosystems, we will garner foundational information for manipulating microbiome structure and function to influence host physiology. Currently, our knowledge of metabolic pathways relies heavily on inferences derived from metagenomics or culturing bacteria in vitro. However, novel approaches targeting specific cell physiologies can illuminate the functional potential encoded within microbial (meta)genomes to provide accurate assessments of metabolic abilities. Using fluorescently labeled polysaccharides, we visualized carbohydrate metabolism performed by single bacterial cells in a complex rumen sample, enabling a rapid assessment of their metabolic phenotype. Specifically, we identified bovine-adapted strains of Bacteroides thetaiotaomicron that metabolized yeast mannan in the rumen microbiome ex vivo and discerned the mechanistic differences between two distinct carbohydrate foraging behaviors, referred to as "medium grower" and "high grower." Using comparative whole-genome sequencing, RNA-seq, and carbohydrate-active enzyme fingerprinting, we could elucidate the strain-level variability in carbohydrate utilization systems of the two foraging behaviors to help predict individual strategies of nutrient acquisition. Here, we present a multi-faceted study using complimentary next-generation physiology and "omics" approaches to characterize microbial adaptation to a prebiotic in the rumen ecosystem. Video abstract.
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Affiliation(s)
- Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Greta Reintjes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Darryl R Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
- Center for Marine Environmental Sciences, University of Bremen (MARUM), 28359, Bremen, Germany
| | - Adam D Smith
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Timothy D Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, 27599-3300, NC, USA
| | - Long Jin
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Trevor W Alexander
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Carolyn Amundsen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Dallas Thomas
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, Alberta, T1J 4B1, Canada.
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada.
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15
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Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, Fernandez-Guerra A, Liebeke M, Schweder T, Polz MF, Hehemann JH. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol 2020; 5:1026-1039. [PMID: 32451471 DOI: 10.1038/s41564-020-0720-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/06/2020] [Indexed: 12/16/2022]
Abstract
Brown algae are important players in the global carbon cycle by fixing carbon dioxide into 1 Gt of biomass annually, yet the fate of fucoidan-their major cell wall polysaccharide-remains poorly understood. Microbial degradation of fucoidans is slower than that of other polysaccharides, suggesting that fucoidans are more recalcitrant and may sequester carbon in the ocean. This may be due to the complex, branched and highly sulfated structure of fucoidans, which also varies among species of brown algae. Here, we show that 'Lentimonas' sp. CC4, belonging to the Verrucomicrobia, acquired a remarkably complex machinery for the degradation of six different fucoidans. The strain accumulated 284 putative fucoidanases, including glycoside hydrolases, sulfatases and carbohydrate esterases, which are primarily located on a 0.89-megabase pair plasmid. Proteomics reveals that these enzymes assemble into substrate-specific pathways requiring about 100 enzymes per fucoidan from different species of brown algae. These enzymes depolymerize fucoidan into fucose, which is metabolized in a proteome-costly bacterial microcompartment that spatially constrains the metabolism of the toxic intermediate lactaldehyde. Marine metagenomes and microbial genomes show that Verrucomicrobia including 'Lentimonas' are abundant and highly specialized degraders of fucoidans and other complex polysaccharides. Overall, the complexity of the pathways underscores why fucoidans are probably recalcitrant and more slowly degraded, since only highly specialized organisms can effectively degrade them in the ocean.
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Affiliation(s)
- Andreas Sichert
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
| | - Christopher H Corzett
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Center for Marine Environmental Sciences, MARUM, University of Bremen, Bremen, Germany.
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16
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Buck-Wiese H, Fanuel M, Liebeke M, Le Mai Hoang K, Pardo-Vargas A, Seeberger PH, Hehemann JH, Rogniaux H, Jackson GP, Ropartz D. Discrimination of β-1,4- and β-1,3-Linkages in Native Oligosaccharides via Charge Transfer Dissociation Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:1249-1259. [PMID: 32309938 DOI: 10.1021/jasms.0c00087] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The connection between monosaccharides influences the structure, solubility, and biological function of carbohydrates. Although tandem mass spectrometry (MS/MS) often enables the compositional identification of carbohydrates, traditional MS/MS fragmentation methods fail to generate abundant cross-ring fragments of intrachain monosaccharides that could reveal carbohydrate connectivity. We examined the potential of helium-charge transfer dissociation (He-CTD) as a method of MS/MS to decipher the connectivity of β-1,4- and β-1,3-linked oligosaccharides. In contrast to collision-induced dissociation (CID), He-CTD of isolated oligosaccharide precursors produced both glycosidic and cross-ring cleavages of each monosaccharide. The radical-driven dissociation in He-CTD induced single cleavage events, without consecutive fragmentations, which facilitated structural interpretation. He-CTD of various standards up to a degree of polymerization of 7 showed that β-1,4- and β-1,3-linked carbohydrates can be distinguished based on diagnostic 3,5A fragment ions that are characteristic for β-1,4-linkages. Overall, fragment ion spectra from He-CTD contained sufficient information to infer the connectivity specifically for each glycosidic bond. When testing He-CTD to resolve the order of β-1,4- and β-1,3-linkages in mixed-linked oligosaccharide standards, He-CTD spectra sometimes provided less confident assignment of connectivity. Ion mobility spectrometry-mass spectrometry (IMS-MS) of the standards indicated that ambiguity in the He-CTD spectra was caused by isobaric impurities in the mixed-linked oligosaccharides. Radical-driven dissociation induced by He-CTD can thus expand MS/MS to carbohydrate linkage analysis, as demonstrated by the comprehensive fragment ion spectra on native oligosaccharides. The determination of connectivity in true unknowns would benefit from the separation of isobaric precursors, through UPLC or IMS, before linkage determination via He-CTD.
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Affiliation(s)
- Hagen Buck-Wiese
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
- Marine Glycobiology, Marum Center for Marine Environmental Sciences, Leobener Strasse 8, 28359 Bremen, Germany
| | - Mathieu Fanuel
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
| | - Manuel Liebeke
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
| | - Kim Le Mai Hoang
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Alonso Pardo-Vargas
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Free University Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Jan-Hendrik Hehemann
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
- Marine Glycobiology, Marum Center for Marine Environmental Sciences, Leobener Strasse 8, 28359 Bremen, Germany
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
| | - Glen P Jackson
- Department of Forensic and Investigative Science, West Virginia University, Morgantown, West Virginia 26506, United States
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France
- INRAE, BIBS facility, F-44316 Nantes, France
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17
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Wanke A, Rovenich H, Schwanke F, Velte S, Becker S, Hehemann JH, Wawra S, Zuccaro A. Plant species-specific recognition of long and short β-1,3-linked glucans is mediated by different receptor systems. Plant J 2020; 102:1142-1156. [PMID: 31925978 DOI: 10.1111/tpj.14688] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/26/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
Plants survey their environment for the presence of potentially harmful or beneficial microbes. During colonization, cell surface receptors perceive microbe-derived or modified-self ligands and initiate appropriate responses. The recognition of fungal chitin oligomers and the subsequent activation of plant immunity are well described. In contrast, the mechanisms underlying β-glucan recognition and signaling activation remain largely unexplored. Here, we systematically tested immune responses towards different β-glucan structures and show that responses vary between plant species. While leaves of the monocots Hordeum vulgare and Brachypodium distachyon can recognize longer (laminarin) and shorter (laminarihexaose) β-1,3-glucans with responses of varying intensity, duration and timing, leaves of the dicot Nicotiana benthamiana activate immunity in response to long β-1,3-glucans, whereas Arabidopsis thaliana and Capsella rubella perceive short β-1,3-glucans. Hydrolysis of the β-1,6 side-branches of laminarin demonstrated that not the glycosidic decoration but rather the degree of polymerization plays a pivotal role in the recognition of long-chain β-glucans. Moreover, in contrast to the recognition of short β-1,3-glucans in A. thaliana, perception of long β-1,3-glucans in N. benthamiana and rice is independent of CERK1, indicating that β-glucan recognition may be mediated by multiple β-glucan receptor systems.
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Affiliation(s)
- Alan Wanke
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hanna Rovenich
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
| | - Florian Schwanke
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
| | - Stefanie Velte
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
| | - Stefan Becker
- Center for Marine Environmental Sciences, University of Bremen, MARUM, 28359, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences, University of Bremen, MARUM, 28359, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Stephan Wawra
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
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18
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Becker S, Tebben J, Coffinet S, Wiltshire K, Iversen MH, Harder T, Hinrichs KU, Hehemann JH. Laminarin is a major molecule in the marine carbon cycle. Proc Natl Acad Sci U S A 2020; 117:6599-6607. [PMID: 32170018 PMCID: PMC7104365 DOI: 10.1073/pnas.1917001117] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Marine microalgae sequester as much CO2 into carbohydrates as terrestrial plants. Polymeric carbohydrates (i.e., glycans) provide carbon for heterotrophic organisms and constitute a carbon sink in the global oceans. The quantitative contributions of different algal glycans to cycling and sequestration of carbon remain unknown, partly because of the analytical challenge to quantify glycans in complex biological matrices. Here, we quantified a glycan structural type using a recently developed biocatalytic strategy, which involves laminarinase enzymes that specifically cleave the algal glycan laminarin into readily analyzable fragments. We measured laminarin along transects in the Arctic, Atlantic, and Pacific oceans and during three time series in the North Sea. These data revealed a median of 26 ± 17% laminarin within the particulate organic carbon pool. The observed correlation between chlorophyll and laminarin suggests an annual production of algal laminarin of 12 ± 8 gigatons: that is, approximately three times the annual atmospheric carbon dioxide increase by fossil fuel burning. Moreover, our data revealed that laminarin accounted for up to 50% of organic carbon in sinking diatom-containing particles, thus substantially contributing to carbon export from surface waters. Spatially and temporally variable laminarin concentrations in the sunlit ocean are driven by light availability. Collectively, these observations highlight the prominent ecological role and biogeochemical function of laminarin in oceanic carbon export and energy flow to higher trophic levels.
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Affiliation(s)
- Stefan Becker
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Jan Tebben
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Karen Wiltshire
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
| | - Morten Hvitfeldt Iversen
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Tilmann Harder
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany;
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Department of Geosciences, University of Bremen, 28359 Bremen, Germany
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Badur AH, Ammar EM, Yalamanchili G, Hehemann JH, Rao CV. Characterization of the GH16 and GH17 laminarinases from Vibrio breoganii 1C10. Appl Microbiol Biotechnol 2019; 104:161-171. [PMID: 31754764 DOI: 10.1007/s00253-019-10243-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
Laminarin is an abundant glucose polymer used as an energy reserve by micro- and macroalgae. Bacteria digest and consume laminarin with laminarinases. Their genomes frequently contain multiple homologs; however, the biological role for this replication remains unclear. We investigated the four laminarinases of glycoside hydrolase families GH16 and GH17 from the marine bacterium Vibrio breoganii 1C10, which can use laminarin as its sole carbon source. All four laminarinases employ an endolytic mechanism and specifically cleave the β-1,3-glycosidic bond. Two primarily produce low-molecular weight laminarin oligomers (DP 3-4) whereas the others primarily produce high-molecular weight oligomers (DP > 8), which suggests that these enzymes sequentially degrade laminarin. The results from this work provide an overview of the laminarinases from a single marine bacterium and also provide insights regarding how multiple laminarinases are used to degrade laminarin.
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Affiliation(s)
- Ahmet H Badur
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Ehab M Ammar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Genetic Engineering and Biotechnology Research Institute, University of Sadat City, El Sadat City, Egypt
| | - Geethika Yalamanchili
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Jan-Hendrik Hehemann
- MARUM MPG Bridge Group Marine Glycobiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
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21
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Reisky L, Préchoux A, Zühlke MK, Bäumgen M, Robb CS, Gerlach N, Roret T, Stanetty C, Larocque R, Michel G, Song T, Markert S, Unfried F, Mihovilovic MD, Trautwein-Schult A, Becher D, Schweder T, Bornscheuer UT, Hehemann JH. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol 2019; 15:803-812. [PMID: 31285597 DOI: 10.1038/s41589-019-0311-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022]
Abstract
Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.
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Affiliation(s)
- Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Aurélie Préchoux
- Sorbonne Université, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Marcus Bäumgen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany
| | - Craig S Robb
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Nadine Gerlach
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Thomas Roret
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France
| | | | - Robert Larocque
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Tao Song
- Max Planck-Institute for Marine Microbiology, Bremen, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | | | | | - Dörte Becher
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany. .,Institute of Marine Biotechnology, Greifswald, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.
| | - Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany.
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22
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Wawra S, Fesel P, Widmer H, Neumann U, Lahrmann U, Becker S, Hehemann JH, Langen G, Zuccaro A. FGB1 and WSC3 are in planta-induced β-glucan-binding fungal lectins with different functions. New Phytol 2019; 222:1493-1506. [PMID: 30688363 DOI: 10.1111/nph.15711] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
In the root endophyte Serendipita indica, several lectin-like members of the expanded multigene family of WSC proteins are transcriptionally induced in planta and are potentially involved in β-glucan remodeling at the fungal cell wall. Using biochemical and cytological approaches we show that one of these lectins, SiWSC3 with three WSC domains, is an integral fungal cell wall component that binds to long-chain β1-3-glucan but has no affinity for shorter β1-3- or β1-6-linked glucose oligomers. Comparative analysis with the previously identified β-glucan-binding lectin SiFGB1 demonstrated that whereas SiWSC3 does not require β1-6-linked glucose for efficient binding to branched β1-3-glucan, SiFGB1 does. In contrast to SiFGB1, the multivalent SiWSC3 lectin can efficiently agglutinate fungal cells and is additionally induced during fungus-fungus confrontation, suggesting different functions for these two β-glucan-binding lectins. Our results highlight the importance of the β-glucan cell wall component in plant-fungus interactions and the potential of β-glucan-binding lectins as specific detection tools for fungi in vivo.
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Affiliation(s)
- Stephan Wawra
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Philipp Fesel
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Heidi Widmer
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Ulla Neumann
- Central Microscopy (CeMic), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Urs Lahrmann
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Stefan Becker
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
- Center for Marine Environmental Sciences, University of Bremen, MARUM, Bremen, 28359, Germany
| | - Gregor Langen
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, University of Cologne, Cologne, 50674, Germany
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23
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Hehemann JH, Reintjes G, Klassen L, Smith AD, Ndeh D, Arnosti C, Amann R, Abbott DW. Single cell fluorescence imaging of glycan uptake by intestinal bacteria. ISME J 2019; 13:1883-1889. [PMID: 30936421 PMCID: PMC6776043 DOI: 10.1038/s41396-019-0406-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 12/03/2018] [Accepted: 02/27/2019] [Indexed: 01/15/2023]
Abstract
Microbes in the intestines of mammals degrade dietary glycans for energy and growth. The pathways required for polysaccharide utilization are functionally diverse; moreover, they are unequally dispersed between bacterial genomes. Hence, assigning metabolic phenotypes to genotypes remains a challenge in microbiome research. Here we demonstrate that glycan uptake in gut bacteria can be visualized with fluorescent glycan conjugates (FGCs) using epifluorescence microscopy. Yeast α-mannan and rhamnogalacturonan-II, two structurally distinct glycans from the cell walls of yeast and plants, respectively, were fluorescently labeled and fed to Bacteroides thetaiotaomicron VPI-5482. Wild-type cells rapidly consumed the FGCs and became fluorescent; whereas, strains that had deleted pathways for glycan degradation and transport were non-fluorescent. Uptake of FGCs, therefore, is direct evidence of genetic function and provides a direct method to assess specific glycan metabolism in intestinal bacteria at the single cell level.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany. .,Center for Marine Environmental Sciences, University of Bremen (MARUM), 28359, Bremen, Germany.
| | - Greta Reintjes
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Adam D Smith
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, The Medical School Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Rudolf Amann
- Max Planck-Institute for Marine Microbiology, 28359, Bremen, Germany
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
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24
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Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, Dittmar T, Freese HM, Becher D, Simon M, Wietz M. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J 2019; 13:92-103. [PMID: 30116038 PMCID: PMC6298977 DOI: 10.1038/s41396-018-0252-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/08/2022]
Abstract
Algal polysaccharides are an important bacterial nutrient source and central component of marine food webs. However, cellular and ecological aspects concerning the bacterial degradation of polysaccharide mixtures, as presumably abundant in natural habitats, are poorly understood. Here, we contextualize marine polysaccharide mixtures and their bacterial utilization in several ways using the model bacterium Alteromonas macleodii 83-1, which can degrade multiple algal polysaccharides and contributes to polysaccharide degradation in the oceans. Transcriptomic, proteomic and exometabolomic profiling revealed cellular adaptations of A. macleodii 83-1 when degrading a mix of laminarin, alginate and pectin. Strain 83-1 exhibited substrate prioritization driven by catabolite repression, with initial laminarin utilization followed by simultaneous alginate/pectin utilization. This biphasic phenotype coincided with pronounced shifts in gene expression, protein abundance and metabolite secretion, mainly involving CAZymes/polysaccharide utilization loci but also other functional traits. Distinct temporal changes in exometabolome composition, including the alginate/pectin-specific secretion of pyrroloquinoline quinone, suggest that substrate-dependent adaptations influence chemical interactions within the community. The ecological relevance of cellular adaptations was underlined by molecular evidence that common marine macroalgae, in particular Saccharina and Fucus, release mixtures of alginate and pectin-like rhamnogalacturonan. Moreover, CAZyme microdiversity and the genomic predisposition towards polysaccharide mixtures among Alteromonas spp. suggest polysaccharide-related traits as an ecophysiological factor, potentially relating to distinct 'carbohydrate utilization types' with different ecological strategies. Considering the substantial primary productivity of algae on global scales, these insights contribute to the understanding of bacteria-algae interactions and the remineralization of chemically diverse polysaccharide pools, a key step in marine carbon cycling.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alexandra Dürwald
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Silvia Vidal-Melgosa
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Jan-Hendrik Hehemann
- MARUM-MPI Bridge Group for Marine Glycobiology, University of Bremen, Bremen, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, Germany
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
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25
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Mystkowska AA, Robb C, Vidal-Melgosa S, Vanni C, Fernandez-Guerra A, Höhne M, Hehemann JH. Molecular recognition of the beta-glucans laminarin and pustulan by a SusD-like glycan-binding protein of a marine Bacteroidetes. FEBS J 2018; 285:4465-4481. [PMID: 30300505 DOI: 10.1111/febs.14674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 12/26/2022]
Abstract
Marine bacteria catabolize carbohydrate polymers of algae, which synthesize these structurally diverse molecules in ocean surface waters. Although algal glycans are an abundant carbon and energy source in the ocean, the molecular details that enable specific recognition between algal glycans and bacterial degraders remain largely unknown. Here we characterized a surface protein, GMSusD from the planktonic Bacteroidetes-Gramella sp. MAR_2010_102 that thrives during algal blooms. Our biochemical and structural analyses show that GMSusD binds glucose polysaccharides such as branched laminarin and linear pustulan. The 1.8 Å crystal structure of GMSusD indicates that three tryptophan residues form the putative glycan-binding site. Mutagenesis studies confirmed that these residues are crucial for laminarin recognition. We queried metagenomes of global surface water datasets for the occurrence of SusD-like proteins and found sequences with the three structurally conserved residues in different locations in the ocean. The molecular selectivity of GMSusD underscores that specific interactions are required for laminarin recognition. In conclusion, our findings provide insight into the molecular details of β-glucan binding by GMSusD and our bioinformatic analysis reveals that this molecular interaction may contribute to glucan cycling in the surface ocean.
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Affiliation(s)
- Agata Anna Mystkowska
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Craig Robb
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Silvia Vidal-Melgosa
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Chiara Vanni
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Jacobs University Bremen gGmbH, Bremen, Germany
| | - Matthias Höhne
- Institute of Biochemistry, Greifswald University, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences (MARUM), University of Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
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26
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Chen J, Robb CS, Unfried F, Kappelmann L, Markert S, Song T, Harder J, Avcı B, Becher D, Xie P, Amann RI, Hehemann JH, Schweder T, Teeling H. Alpha- and beta-mannan utilization by marine Bacteroidetes. Environ Microbiol 2018; 20:4127-4140. [PMID: 30246424 DOI: 10.1111/1462-2920.14414] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/12/2018] [Indexed: 11/28/2022]
Abstract
Marine microscopic algae carry out about half of the global carbon dioxide fixation into organic matter. They provide organic substrates for marine microbes such as members of the Bacteroidetes that degrade algal polysaccharides using carbohydrate-active enzymes (CAZymes). In Bacteroidetes genomes CAZyme encoding genes are mostly grouped in distinct regions termed polysaccharide utilization loci (PULs). While some studies have shown involvement of PULs in the degradation of algal polysaccharides, the specific substrates are for the most part still unknown. We investigated four marine Bacteroidetes isolated from the southern North Sea that harbour putative mannan-specific PULs. These PULs are similarly organized as PULs in human gut Bacteroides that digest α- and β-mannans from yeasts and plants respectively. Using proteomics and defined growth experiments with polysaccharides as sole carbon sources we could show that the investigated marine Bacteroidetes express the predicted functional proteins required for α- and β-mannan degradation. Our data suggest that algal mannans play an as yet unknown important role in the marine carbon cycle, and that biochemical principles established for gut or terrestrial microbes also apply to marine bacteria, even though their PULs are evolutionarily distant.
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Affiliation(s)
- Jing Chen
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Ocean, Hebei Agricultural University, Qinhuangdao, China
| | - Craig S Robb
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | | | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Tao Song
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Burak Avcı
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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27
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Kappelmann L, Krüger K, Hehemann JH, Harder J, Markert S, Unfried F, Becher D, Shapiro N, Schweder T, Amann RI, Teeling H. Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans. ISME J 2018; 13:76-91. [PMID: 30111868 PMCID: PMC6298971 DOI: 10.1038/s41396-018-0242-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/17/2018] [Accepted: 06/30/2018] [Indexed: 12/31/2022]
Abstract
Marine algae convert a substantial fraction of fixed carbon dioxide into various polysaccharides. Flavobacteriia that are specialized on algal polysaccharide degradation feature genomic clusters termed polysaccharide utilization loci (PULs). As knowledge on extant PUL diversity is sparse, we sequenced the genomes of 53 North Sea Flavobacteriia and obtained 400 PULs. Bioinformatic PUL annotations suggest usage of a large array of polysaccharides, including laminarin, α-glucans, and alginate as well as mannose-, fucose-, and xylose-rich substrates. Many of the PULs exhibit new genetic architectures and suggest substrates rarely described for marine environments. The isolates’ PUL repertoires often differed considerably within genera, corroborating ecological niche-associated glycan partitioning. Polysaccharide uptake in Flavobacteriia is mediated by SusCD-like transporter complexes. Respective protein trees revealed clustering according to polysaccharide specificities predicted by PUL annotations. Using the trees, we analyzed expression of SusC/D homologs in multiyear phytoplankton bloom-associated metaproteomes and found indications for profound changes in microbial utilization of laminarin, α-glucans, β-mannan, and sulfated xylan. We hence suggest the suitability of SusC/D-like transporter protein expression within heterotrophic bacteria as a proxy for the temporal utilization of discrete polysaccharides.
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Affiliation(s)
| | - Karen Krüger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Zentrum für Marine Umweltwissenschaften, Bremen, Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, University Greifswald, Greifswald, Germany
| | | | - Thomas Schweder
- Pharmaceutical Biotechnology, University Greifswald, Greifswald, Germany. .,Institute of Marine Biotechnology, Greifswald, Germany.
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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28
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Becker S, Hehemann JH. Laminarin Quantification in Microalgae with Enzymes from Marine Microbes. Bio Protoc 2018; 8:e2666. [PMID: 34286020 DOI: 10.21769/bioprotoc.2666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 11/02/2022] Open
Abstract
The marine beta-glucan laminarin is an abundant storage polysaccharide in microalgae. High production rates and rapid digestion by heterotrophic bacteria turn laminarin into an ideal carbon and energy source, and it is therefore a key player in the marine carbon cycle. As a main storage glucan laminarin also plays a central role in the energy metabolism of the microalgae (Percival and Ross, 1951; Myklestad, 1974; Painter, 1983). We take advantage of enzymes that digest laminarin selectively and can thereby quantify only this polysaccharide in environmental samples. These enzymes hydrolyze laminarin into glucose and oligosaccharides, which are measured with a standard reducing sugar assay to obtain the laminarin concentration. Prior to this assay, the three enzymes need to be produced via heterologous expression and purification. The assay can be used to monitor laminarin concentrations in environmental microalgae, which were concentrated from seawater by filtering, or in samples derived from algal lab cultures.
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Affiliation(s)
- Stefan Becker
- Center for Marine Environmental Sciences University of Bremen (MARUM), Marine Glycobiology, Bremen, Germany.,Max Planck-Institute for Marine Microbiology, Marine Glycobiology, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences University of Bremen (MARUM), Marine Glycobiology, Bremen, Germany.,Max Planck-Institute for Marine Microbiology, Marine Glycobiology, Bremen, Germany
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29
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Reisky L, Büchsenschütz HC, Engel J, Song T, Schweder T, Hehemann JH, Bornscheuer UT. Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases. Nat Chem Biol 2018; 14:342-344. [PMID: 29459682 DOI: 10.1038/s41589-018-0005-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/20/2017] [Indexed: 01/22/2023]
Abstract
Sugar O-methylation shields algal polysaccharides against microbial hydrolytic enzymes. Here, we describe cytochrome P450 monooxygenases from marine bacteria that, together with appropriate redox-partner proteins, catalyze the oxidative demethylation of 6-O-methyl-D-galactose, which is an abundant monosaccharide of the algal polysaccharides agarose and porphyran. This previously unknown biological function extends the group of carbohydrate-active enzymes to include the class of cytochrome P450 monooxygenases.
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Affiliation(s)
- Lukas Reisky
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Hanna C Büchsenschütz
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Jennifer Engel
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Tao Song
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,University of Bremen, Center for Marine Environmental Sciences (MARUM), Bremen, Germany.
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Greifswald, Germany.
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30
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Robb CS, Mystkowska AA, Hehemann JH. Crystal structure of a marine glycoside hydrolase family 99-related protein lacking catalytic machinery. Protein Sci 2017; 26:2445-2450. [PMID: 28884852 DOI: 10.1002/pro.3291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/05/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022]
Abstract
Algal polysaccharides of diverse structures are one of the most abundant carbon resources for heterotrophic, marine bacteria with coevolved digestive enzymes. A putative sulfo-mannan polysaccharide utilization locus, which is conserved in marine flavobacteria, contains an unusual GH99-like protein that lacks the conserved catalytic residues of glycoside hydrolase family 99. Using X-ray crystallography, we structurally characterized this protein from the marine flavobacterium Ochrovirga pacifica to help elucidate its molecular function. The structure reveals the absence of potential catalytic residues for polysaccharide hydrolysis, which-together with additional structural features-suggests this protein may be noncatalytic and involved in carbohydrate binding.
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Affiliation(s)
- Craig S Robb
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Agata Anna Mystkowska
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences, University of Bremen (MARUM), Bremen, 28359, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, 28359, Germany
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31
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Badur AH, Plutz MJ, Yalamanchili G, Jagtap SS, Schweder T, Unfried F, Markert S, Polz MF, Hehemann JH, Rao CV. Exploiting fine-scale genetic and physiological variation of closely related microbes to reveal unknown enzyme functions. J Biol Chem 2017; 292:13056-13067. [PMID: 28592491 DOI: 10.1074/jbc.m117.787192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/01/2017] [Indexed: 01/18/2023] Open
Abstract
Polysaccharide degradation by marine microbes represents one of the largest and most rapid heterotrophic transformations of organic matter in the environment. Microbes employ systems of complementary carbohydrate-specific enzymes to deconstruct algal or plant polysaccharides (glycans) into monosaccharides. Because of the high diversity of glycan substrates, the functions of these enzymes are often difficult to establish. One solution to this problem may lie within naturally occurring microdiversity; varying numbers of enzymes, due to gene loss, duplication, or transfer, among closely related environmental microbes create metabolic differences akin to those generated by knock-out strains engineered in the laboratory used to establish the functions of unknown genes. Inspired by this natural fine-scale microbial diversity, we show here that it can be used to develop hypotheses guiding biochemical experiments for establishing the role of these enzymes in nature. In this work, we investigated alginate degradation among closely related strains of the marine bacterium Vibrio splendidus One strain, V. splendidus 13B01, exhibited high extracellular alginate lyase activity compared with other V. splendidus strains. To identify the enzymes responsible for this high extracellular activity, we compared V. splendidus 13B01 with the previously characterized V. splendidus 12B01, which has low extracellular activity and lacks two alginate lyase genes present in V. splendidus 13B01. Using a combination of genomics, proteomics, biochemical, and functional screening, we identified a polysaccharide lyase family 7 enzyme that is unique to V. splendidus 13B01, secreted, and responsible for the rapid digestion of extracellular alginate. These results demonstrate the value of querying the enzymatic repertoires of closely related microbes to rapidly pinpoint key proteins with beneficial functions.
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Affiliation(s)
- Ahmet H Badur
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Matthew J Plutz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Geethika Yalamanchili
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst Moritz Arndt University of Greifswald, D-17489 Greifswald, Germany
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences University of Bremen (MARUM), Bremen 28359, Germany; Max Planck-Institute for Marine Microbiology, Celsiusstrasse 1, Bremen 28359, Germany.
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.
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32
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Hehemann JH, Truong LV, Unfried F, Welsch N, Kabisch J, Heiden SE, Junker S, Becher D, Thürmer A, Daniel R, Amann R, Schweder T. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 2017; 19:2320-2333. [PMID: 28276126 DOI: 10.1111/1462-2920.13726] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 01/09/2023]
Abstract
Mobile genomic islands distribute functional traits between microbes and habitats, yet it remains unclear how their proteins adapt to new environments. Here we used a comparative phylogenomic and proteomic approach to show that the marine bacterium Pseudoalteromonas haloplanktis ANT/505 acquired a genomic island with a functional pathway for pectin catabolism. Bioinformatics and biochemical experiments revealed that this pathway encodes a series of carbohydrate-active enzymes including two multi-modular pectate lyases, PelA and PelB. PelA is a large enzyme with a polysaccharide lyase family 1 (PL1) domain and a carbohydrate esterase family 8 domain, and PelB contains a PL1 domain and two carbohydrate-binding domains of family 13. Comparative phylogenomic analyses indicate that the pathway was most likely acquired from terrestrial microbes, yet we observed multi-modular orthologues only in marine bacteria. Proteomic experiments showed that P. haloplanktis ANT/505 secretes both pectate lyases into the environment in the presence of pectin. These multi-modular enzymes may therefore represent a marine innovation that enhances physical interaction with pectins to reduce loss of substrate and enzymes by diffusion. Our results revealed that marine bacteria can catabolize pectin, and highlight enzyme fusion as a potential adaptation that may facilitate microbial consumption of polymeric substrates in aquatic environments.
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Affiliation(s)
- Jan-Hendrik Hehemann
- MARUM, Center for Marine Environmental Sciences at the University of Bremen, Leobener Strasse, Bremen, D-28359, Germany.,Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Le Van Truong
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Institute of Biotechnology, Vietnamese Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Frank Unfried
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany.,Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Norma Welsch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Johannes Kabisch
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany.,Department of Biology, Computer-aided Synthetic Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt, D-64287, Germany
| | - Stefan E Heiden
- Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
| | - Sabryna Junker
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, D-17487, Germany
| | - Andrea Thürmer
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory (G2L), Institute of Microbiology and Genetics, University of Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, D-28359, Germany
| | - Thomas Schweder
- Institute of Marine Biotechnology, W.-Rathenau-Str. 49a, Greifswald, D-17489, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University, Felix-Hausdorff-Str. 3, Greifswald, D-17487, Germany
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33
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Labourel A, Jam M, Legentil L, Sylla B, Hehemann JH, Ferrières V, Czjzek M, Michel G. Structural and biochemical characterization of the laminarinaseZgLamCGH16fromZobellia galactanivoranssuggests preferred recognition of branched laminarin. ACTA ACUST UNITED AC 2015; 71:173-84. [DOI: 10.1107/s139900471402450x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/07/2014] [Indexed: 05/28/2023]
Abstract
Laminarin is a β-1,3-D-glucan displaying occasional β-1,6 branches. This storage polysaccharide of brown algae constitutes an abundant source of carbon for marine bacteria such asZobellia galactanivorans. This marine member of the Bacteroidetes possesses five putative β-1,3-glucanases [four belonging to glycosyl hydrolase family 16 (GH16) and one to GH64] with various modular architectures. Here, the characterization of the β-glucanaseZgLamC is reported. The catalytic GH16 module (ZgLamCGH16) was produced inEscherichia coliand purified. This recombinant enzyme has a preferential specificity for laminarin but also a significant activity on mixed-linked glucan (MLG). The structure of an inactive mutant ofZgLamCGH16in complex with a thio-β-1,3-hexaglucan substrate unravelled a straight active-site cleft with three additional pockets flanking subsites −1, −2 and −3. These lateral pockets are occupied by a glycerol, an acetate ion and a chloride ion, respectively. The presence of these molecules in the vicinity of the O6 hydroxyl group of each glucose moiety suggests thatZgLamCGH16accommodates branched laminarins as substrates. Altogether,ZgLamC is a secreted laminarinase that is likely to be involved in the initial step of degradation of branched laminarin, while the previously characterizedZgLamA efficiently degrades unbranched laminarin and oligo-laminarins.
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Hehemann JH, Boraston AB, Czjzek M. A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae. Curr Opin Struct Biol 2014; 28:77-86. [DOI: 10.1016/j.sbi.2014.07.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 10/24/2022]
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Hehemann JH, Law A, Redecke L, Boraston AB. The structure of RdDddP from Roseobacter denitrificans reveals that DMSP lyases in the DddP-family are metalloenzymes. PLoS One 2014; 9:e103128. [PMID: 25054772 PMCID: PMC4108388 DOI: 10.1371/journal.pone.0103128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Adrienne Law
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Lars Redecke
- Joint Laboratory for Structural Biology of Infection and Inflammation of the Universities of Hamburg and Lübeck, c/o DESY, Hamburg, Germany
| | - Alisdair B. Boraston
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
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Pagarete A, Kusonmano K, Petersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA. Dip in the gene pool: metagenomic survey of natural coccolithovirus communities. Virology 2014; 466-467:129-37. [PMID: 24947907 DOI: 10.1016/j.virol.2014.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
Abstract
Despite the global oceanic distribution and recognised biogeochemical impact of coccolithoviruses (EhV), their diversity remains poorly understood. Here we employed a metagenomic approach to study the occurrence and progression of natural EhV community genomic variability. Analysis of EhV metagenomes from the early and late stages of an induced bloom led to three main discoveries. First, we observed resilient and specific genomic signatures in the EhV community associated with the Norwegian coast, which reinforce the existence of limitations to the capacity of dispersal and genomic exchange among EhV populations. Second, we identified a hyper-variable region (approximately 21kbp long) in the coccolithovirus genome. Third, we observed a clear trend for EhV relative amino-acid diversity to reduce from early to late stages of the bloom. This study validated two new methodological combinations, and proved very useful in the discovery of new genomic features associated with coccolithovirus natural communities.
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Affiliation(s)
| | | | - Kjell Petersen
- Computational Biology Unit, University of Bergen, Norway
| | | | | | - William H Wilson
- Plymouth Marine Laboratory, Plymouth, UK; Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jan-Hendrik Hehemann
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pluvinage B, Hehemann JH, Boraston AB. Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans. J Biol Chem 2013; 288:28078-88. [PMID: 23921382 DOI: 10.1074/jbc.m113.491068] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The bacteria that metabolize agarose use multiple enzymes of complementary specificities to hydrolyze the glycosidic linkages in agarose, a linear polymer comprising the repeating disaccharide subunit of neoagarobiose (3,6-anhydro-l-galactose-α-(1,3)-d-galactose) that are β-(1,4)-linked. Here we present the crystal structure of a glycoside hydrolase family 50 exo-β-agarase, Aga50D, from the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The crystal structure of Aga50D to 1.9 Å resolution reveals a (β/α)8-barrel fold that is elaborated with a β-sandwich domain and extensive loops. The structures of catalytically inactivated Aga50D in complex with non-hydrolyzed neoagarotetraose (2.05 Å resolution) and neoagarooctaose (2.30 Å resolution) provide views of Michaelis complexes for a β-agarase. In these structures, the d-galactose residue in the -1 subsite is distorted into a (1)S3 skew boat conformation. The relative positioning of the putative catalytic residues are most consistent with a retaining catalytic mechanism. Additionally, the neoagarooctaose complex showed that this extended substrate made substantial interactions with the β-sandwich domain, which resembles a carbohydrate-binding module, thus creating additional plus (+) subsites and funneling the polymeric substrate through the tunnel-shaped active site. A synthesis of these results in combination with an additional neoagarobiose product complex suggests a potential exo-processive mode of action of Aga50D on the agarose double helix.
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Affiliation(s)
- Benjamin Pluvinage
- From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and
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Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J Biol Chem 2012; 287:30571-84. [PMID: 22778272 DOI: 10.1074/jbc.m112.377184] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Zobellia galactanivorans is an emerging model bacterium for the bioconversion of algal biomass. Notably, this marine Bacteroidetes possesses a complex agarolytic system comprising four β-agarases and five β-porphyranases, all belonging to the glycoside hydrolase family 16. Although β-agarases are specific for the neutral agarobiose moieties, the recently discovered β-porphyranases degrade the sulfated polymers found in various quantities in natural agars. Here, we report the biochemical and structural comparison of five β-porphyranases and β-agarases from Z. galactanivorans. The respective degradation patterns of two β-porphyranases and three β-agarases are analyzed by their action on defined hybrid oligosaccharides. In light of the high resolution crystal structures, the biochemical results allowed a detailed mapping of substrate specificities along the active site groove of the enzymes. Although PorA displays a strict requirement for C6-sulfate in the -2- and +1-binding subsites, PorB tolerates the presence of 3-6-anhydro-l-galactose in subsite -2. Both enzymes do not accept methylation of the galactose unit in the -1 subsite. The β-agarase AgaD requires at least four consecutive agarose units (DP8) and is highly intolerant to modifications, whereas for AgaB oligosaccharides containing C6-sulfate groups at the -4, +1, and +3 positions are still degraded. Together with a transcriptional analysis of the expression of these enzymes, the structural and biochemical results allow proposition of a model scheme for the agarolytic system of Z. galactanivorans.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Université Pierre et Marie Curie, Végétaux Marins et Biomolécules UMR 7139, Station Biologique de Roscoff, F 29682 Roscoff, France
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Hehemann JH, Smyth L, Yadav A, Vocadlo DJ, Boraston AB. Analysis of keystone enzyme in Agar hydrolysis provides insight into the degradation (of a polysaccharide from) red seaweeds. J Biol Chem 2012; 287:13985-95. [PMID: 22393053 DOI: 10.1074/jbc.m112.345645] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Agars are abundant polysaccharides from marine red algae, and their chemical structure consists of alternating D-galactose and 3,6-anhydro-L-galactose residues, the latter of which are presumed to make the polymer recalcitrant to degradation by most terrestrial bacteria. Here we study a family 117 glycoside hydrolase (BpGH117) encoded within a recently discovered locus from the human gut bacterium Bacteroides plebeius. Consistent with this locus being involved in agarocolloid degradation, we show that BpGH117 is an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase that removes the 3,6-anhydrogalactose from the non-reducing end of neoagaro-oligosaccharides. A Michaelis complex of BpGH117 with neoagarobiose reveals the distortion of the constrained 3,6-anhydro-L-galactose into a conformation that favors catalysis. Furthermore, this complex, supported by analysis of site-directed mutants, provides evidence for an organization of the active site and positioning of the catalytic residues that are consistent with an inverting mechanism of catalysis and suggests that a histidine residue acts as the general acid. This latter feature differs from the vast majority of glycoside hydrolases, which use a carboxylic acid, highlighting the alternative strategies that enzymes may utilize in catalyzing the cleavage of glycosidic bonds.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, British Columbia V8W 3P6, Canada
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Hehemann JH, Marsters C, Boraston AB. Ab initio
phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans
that is associated with carbohydrate metabolism. Proteins 2011; 79:2992-8. [DOI: 10.1002/prot.23126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 05/27/2011] [Accepted: 06/03/2011] [Indexed: 11/06/2022]
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Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut bacteroidetes: the food connection. Front Microbiol 2011; 2:93. [PMID: 21747801 PMCID: PMC3129010 DOI: 10.3389/fmicb.2011.00093] [Citation(s) in RCA: 648] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 04/14/2011] [Indexed: 12/21/2022] Open
Abstract
Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal, and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. LGT can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food-associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals’ symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects our health.
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Affiliation(s)
- François Thomas
- UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, UPMC University Paris 6, Roscoff, France
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Lammerts van Bueren A, Ficko-Blean E, Pluvinage B, Hehemann JH, Higgins M, Deng L, Ogunniyi A, Stroeher U, El Warry N, Burke R, Czjzek M, Paton J, Vocadlo D, Boraston A. The Conformation and Function of a Multimodular Glycogen-Degrading Pneumococcal Virulence Factor. Structure 2011; 19:640-51. [DOI: 10.1016/j.str.2011.03.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/22/2011] [Accepted: 03/03/2011] [Indexed: 11/28/2022]
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Gregg KJ, Zandberg WF, Hehemann JH, Whitworth GE, Deng L, Vocadlo DJ, Boraston AB. Analysis of a new family of widely distributed metal-independent alpha-mannosidases provides unique insight into the processing of N-linked glycans. J Biol Chem 2011; 286:15586-96. [PMID: 21388958 PMCID: PMC3083162 DOI: 10.1074/jbc.m111.223172] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/28/2011] [Indexed: 11/06/2022] Open
Abstract
The modification of N-glycans by α-mannosidases is a process that is relevant to a large number of biologically important processes, including infection by microbial pathogens and colonization by microbial symbionts. At present, the described mannosidases specific for α1,6-mannose linkages are very limited in number. Through structural and functional analysis of two sequence-related enzymes, one from Streptococcus pneumoniae (SpGH125) and one from Clostridium perfringens (CpGH125), a new glycoside hydrolase family, GH125, is identified and characterized. Analysis of SpGH125 and CpGH125 reveal them to have exo-α1,6-mannosidase activity consistent with specificity for N-linked glycans having their α1,3-mannose branches removed. The x-ray crystal structures of SpGH125 and CpGH125 obtained in apo-, inhibitor-bound, and substrate-bound forms provide both mechanistic and molecular insight into how these proteins, which adopt an (α/α)(6)-fold, recognize and hydrolyze the α1,6-mannosidic bond by an inverting, metal-independent catalytic mechanism. A phylogenetic analysis of GH125 proteins reveals this to be a relatively large and widespread family found frequently in bacterial pathogens, bacterial human gut symbionts, and a variety of fungi. Based on these studies we predict this family of enzymes will primarily comprise such exo-α1,6-mannosidases.
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Affiliation(s)
- Katie J. Gregg
- From the Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6 and
| | - Wesley F. Zandberg
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jan-Hendrik Hehemann
- From the Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6 and
| | - Garrett E. Whitworth
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Lehua Deng
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - David J. Vocadlo
- the Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Alisdair B. Boraston
- From the Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055 STN CSC, Victoria, British Columbia V8W 3P6 and
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Correc G, Hehemann JH, Czjzek M, Helbert W. Structural analysis of the degradation products of porphyran digested by Zobellia galactanivorans β-porphyranase A. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2010.07.060] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Hehemann JH, Correc G, Barbeyron T, Helbert W, Czjzek M, Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010; 464:908-12. [PMID: 20376150 DOI: 10.1038/nature08937] [Citation(s) in RCA: 681] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 02/19/2010] [Indexed: 11/09/2022]
Abstract
Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.
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Hehemann JH, Michel G, Barbeyron T, Czjzek M. Expression, purification and preliminary X-ray diffraction analysis of the catalytic module of a beta-agarase from the flavobacterium Zobellia galactanivorans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:413-7. [PMID: 20383011 PMCID: PMC2852333 DOI: 10.1107/s174430911000429x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 02/03/2010] [Indexed: 05/29/2023]
Abstract
Marine bacteria secrete specific glycoside hydrolases such as agarases to access polysaccharides from algal cell walls as a carbon and energy source. In an attempt to identify agarases with variable degradation patterns, a novel family GH16 beta-agarase from the marine bacterium Zobellia galactanivorans was expressed, purified and crystallized. The purified enzyme crystallized in two distinct forms that were grown by the hanging-drop vapour-diffusion method using polyethylene glycol as a precipitant. Hexagonal crystals belonging to space group P3(1)21 diffracted to 2.2 A resolution, whereas orthorhombic crystals belonging to space group P2(1)2(1)2(1) diffracted to 1.5 A resolution.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
| | - Gurvan Michel
- Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
| | - Tristan Barbeyron
- Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
| | - Mirjam Czjzek
- Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139 ‘Marine Plants and Biomolecules’, Station Biologique, F-29682 Roscoff CEDEX, Bretagne, France
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Ficko-Blean E, Gregg KJ, Adams JJ, Hehemann JH, Czjzek M, Smith SP, Boraston AB. Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens. J Biol Chem 2009; 284:9876-84. [PMID: 19193644 DOI: 10.1074/jbc.m808954200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.
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Affiliation(s)
- Elizabeth Ficko-Blean
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada
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Hehemann JH, Redecke L, Murugaiyan J, von Bergen M, Betzel C, Saborowski R. Autoproteolytic stability of a trypsin from the marine crab Cancer pagurus. Biochem Biophys Res Commun 2008; 370:566-71. [DOI: 10.1016/j.bbrc.2008.03.128] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 03/23/2008] [Indexed: 11/29/2022]
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Hehemann JH, Redecke L, Perbandt M, Saborowski R, Betzel C. Crystallization and preliminary X-ray diffraction studies of trypsin-like proteases from the gastric fluid of the marine crab Cancer pagurus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:242-5. [PMID: 17329824 PMCID: PMC2330177 DOI: 10.1107/s1744309107008524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 02/20/2007] [Indexed: 11/10/2022]
Abstract
The digestive fluid of the marine crab Cancer pagurus (Decapoda, Brachyura) contains highly stable proteases which display enhanced activity in aqueous mixtures of organic solvents. Three trypsins were isolated from the gastric fluid and two of them, C.p.TryII and C.p.TryIII, were purified to homogeneity by anion-exchange chromatography and crystallized by hanging-drop vapour diffusion. Diffraction data were collected at a synchrotron to 0.97 and 3.2 A resolution, respectively. The crystal of C.p.TryII belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 52.06, b = 62.00, c = 71.66 A. Based on the Matthews coefficient, one protein molecule per asymmetric unit is suggested. In contrast, crystals of C.p.TryIII, which belong to the cubic space group P2(1)3 with unit-cell parameters a = b = c = 215.4 A, are assumed to contain 12 molecules per asymmetric unit.
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Affiliation(s)
- Jan-Hendrik Hehemann
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Lars Redecke
- Center of Experimental Medicine, Institute of Biochemistry and Molecular Biology I, University Hospital Hamburg-Eppendorf, c/o DESY, 22603 Hamburg, Germany
| | - Markus Perbandt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Reinhard Saborowski
- Biologische Anstalt Helgoland, Alfred Wegener Institute for Polar and Marine Research, 27483 Helgoland, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
- Correspondence e-mail:
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