1
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Pudlo NA, Pereira GV, Parnami J, Cid M, Markert S, Tingley JP, Unfried F, Ali A, Varghese NJ, Kim KS, Campbell A, Urs K, Xiao Y, Adams R, Martin D, Bolam DN, Becher D, Eloe-Fadrosh EA, Schmidt TM, Abbott DW, Schweder T, Hehemann JH, Martens EC. Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host Microbe 2022; 30:314-328.e11. [PMID: 35240043 PMCID: PMC9096808 DOI: 10.1016/j.chom.2022.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 11/21/2020] [Revised: 11/03/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022]
Abstract
Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.
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Affiliation(s)
- Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jaagni Parnami
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Melissa Cid
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Frank Unfried
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Ahmed Ali
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kwi S Kim
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yao Xiao
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Adams
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duña Martin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Thomas Schweder
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jan Hendrik Hehemann
- Max Planck Institute for Marine Biology, Bremen, Germany; University of Bremen, Center for Marine Environmental Sciences (MARUM), 28359 Bremen, Germany.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Dürwald A, Zühlke MK, Schlüter R, Gebbe R, Bartosik D, Unfried F, Becher D, Schweder T. Reaching out in anticipation: bacterial membrane extensions represent a permanent investment in polysaccharide sensing and utilization. Environ Microbiol 2021; 23:3149-3163. [PMID: 33876569 DOI: 10.1111/1462-2920.15537] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 01/03/2023]
Abstract
Outer membrane extensions are common in many marine bacteria. However, the function of these surface enlargements or extracellular compartments is poorly understood. Using a combined approach of microscopy and subproteome analyses, we therefore examined Pseudoalteromonas distincta ANT/505, an Antarctic polysaccharide degrading gamma-proteobacterium. P. distincta produced outer membrane vesicles (MV) and vesicle chains (VC) on polysaccharide and non-polysaccharide carbon sources during the exponential and stationary growth phase. Surface structures of carbohydrate-grown cells were equipped with increased levels of highly substrate-specific proteins. At the same time, proteins encoded in all other polysaccharide degradation-related genomic regions were also detected in MV and VC samples under all growth conditions, indicating a basal expression. In addition, two alkaline phosphatases were highly abundant under non-limiting phosphate conditions. Surface structures may thus allow rapid sensing and fast responses in nutritionally deprived environments. It may also facilitate efficient carbohydrate processing and reduce loss of substrates and enzymes by diffusion as important adaptions to the aquatic ecosystem.
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Affiliation(s)
- Alexandra Dürwald
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, 17489, Germany
| | - Rebecca Gebbe
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
| | - Dörte Becher
- Institute of Marine Biotechnology, Greifswald, 17489, Germany.,Microbial Proteomics, Institute of Microbiology, University Greifswald, Greifswald, 17487, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, 17487, Germany.,Institute of Marine Biotechnology, Greifswald, 17489, Germany
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3
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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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4
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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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5
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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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6
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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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7
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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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8
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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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