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Páez-Watson T, Tomás-Martínez S, de Wit R, Keisham S, Tateno H, van Loosdrecht MCM, Lin Y. Sweet Secrets: Exploring Novel Glycans and Glycoconjugates in the Extracellular Polymeric Substances of " Candidatus Accumulibacter". ACS ES&T WATER 2024; 4:3391-3399. [PMID: 39144681 PMCID: PMC11320575 DOI: 10.1021/acsestwater.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 08/16/2024]
Abstract
Biological wastewater treatment relies on microorganisms that grow as flocs, biofilms, or granules for efficient separation of biomass from cleaned water. This biofilm structure emerges from the interactions between microbes that produce, and are embedded in, extracellular polymeric substances (EPS). The true composition and structure of the EPS responsible for dense biofilm formation are still obscure. We conducted a bottom-up approach utilizing advanced glycomic techniques to explore the glycan diversity in the EPS from a highly enriched "Candidatus Accumulibacter" granular sludge. Rare novel sugar monomers such as N-Acetylquinovosamine (QuiNAc) and 2-O-Methylrhamnose (2-OMe-Rha) were identified to be present in the EPS of both enrichments. Further, a high diversity in the glycoprotein structures of said EPS was identified by means of lectin based microarrays. We explored the genetic potential of "Ca. Accumulibacter" high quality metagenome assembled genomes (MAGs) to showcase the shortcoming of top-down bioinformatics based approaches at predicting EPS composition and structure, especially when dealing with glycans and glycoconjugates. This work suggests that more bottom-up research is necessary to understand the composition and complex structure of EPS in biofilms since genome based inference cannot directly predict glycan structures and glycoconjugate diversity.
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Affiliation(s)
- Timothy Páez-Watson
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Sergio Tomás-Martínez
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Roeland de Wit
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Sunanda Keisham
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hiroaki Tateno
- Cellular
and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Mark C. M. van Loosdrecht
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Yuemei Lin
- Department
of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, Lin YM, Lücker S, van Loosdrecht MCM, Laureni M. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. THE ISME JOURNAL 2022; 16:346-357. [PMID: 34341504 PMCID: PMC8776859 DOI: 10.1038/s41396-021-01073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.
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Affiliation(s)
- Martin Pabst
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | | | - Christopher E. Lawson
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Hugo B. C. Kleikamp
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Carol de Ram
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Rogier Louwen
- grid.5645.2000000040459992XDepartment of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yue Mei Lin
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mark C. M. van Loosdrecht
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Michele Laureni
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
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Guo W, Lakshminarayanan H, Rodriguez-Palacios A, Salata RA, Xu K, Draz MS. Glycan Nanostructures of Human Coronaviruses. Int J Nanomedicine 2021; 16:4813-4830. [PMID: 34290504 PMCID: PMC8289332 DOI: 10.2147/ijn.s302516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/22/2021] [Indexed: 12/18/2022] Open
Abstract
Human coronaviruses present a substantial global disease burden, causing damage to populations’ health, economy, and social well-being. Glycans are one of the main structural components of all microbes and organismic structures, including viruses—playing multiple essential roles in virus infection and immunity. Studying and understanding virus glycans at the nanoscale provide new insights into the diagnosis and treatment of viruses. Glycan nanostructures are considered potential targets for molecular diagnosis, antiviral therapeutics, and the development of vaccines. This review article describes glycan nanostructures (eg, glycoproteins and glycolipids) that exist in cells, subcellular structures, and microbes. We detail the structure, characterization, synthesis, and functions of virus glycans. Furthermore, we describe the glycan nanostructures of different human coronaviruses, such as human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), severe acute respiratory syndrome-associated coronavirus (SARS-CoV), human coronavirus NL63 (HCoV-NL63), human coronavirus HKU1 (HCoV-HKU1), the Middle East respiratory syndrome-associated coronavirus (MERS-CoV), and how glycan nanotechnology can be useful to prevent and combat human coronaviruses infections, along with possibilities that are not yet explored.
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Affiliation(s)
- Wanru Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Harini Lakshminarayanan
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA.,Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, Cleveland, OH, USA.,University Hospitals Research and Education Institute, University Hospital Cleveland Medical Center, Cleveland, OH, USA
| | - Robert A Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Mohamed S Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Jégouzo SAF, Nelson C, Hardwick T, Wong STA, Lau NKK, Neoh GKE, Castellanos-Rueda R, Huang Z, Mignot B, Hirdaramani A, Howitt A, Frewin K, Shen Z, Fox RJ, Wong R, Ando M, Emony L, Zhu H, Holder A, Werling D, Krishnan N, Robertson BD, Clements A, Taylor ME, Drickamer K. Mammalian lectin arrays for screening host-microbe interactions. J Biol Chem 2020; 295:4541-4555. [PMID: 32094229 PMCID: PMC7135977 DOI: 10.1074/jbc.ra120.012783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
Many members of the C-type lectin family of glycan-binding receptors have been ascribed roles in the recognition of microorganisms and serve as key receptors in the innate immune response to pathogens. Other mammalian receptors have become targets through which pathogens enter target cells. These receptor roles have often been documented with binding studies involving individual pairs of receptors and microorganisms. To provide a systematic overview of interactions between microbes and the large complement of C-type lectins, here we developed a lectin array and suitable protocols for labeling of microbes that could be used to probe this array. The array contains C-type lectins from cow, chosen as a model organism of agricultural interest for which the relevant pathogen–receptor interactions have not been previously investigated in detail. Screening with yeast cells and various strains of both Gram-positive and -negative bacteria revealed distinct binding patterns, which in some cases could be explained by binding to lipopolysaccharides or capsular polysaccharides, but in other cases they suggested the presence of novel glycan targets on many of the microorganisms. These results are consistent with interactions previously ascribed to the receptors, but they also highlight binding to additional sugar targets that have not previously been recognized. Our findings indicate that mammalian lectin arrays represent unique discovery tools for identifying both novel ligands and new receptor functions.
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Affiliation(s)
- Sabine A F Jégouzo
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Conor Nelson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Thomas Hardwick
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - S T Angel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Noel Kuan Kiat Lau
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Gaik Kin Emily Neoh
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Zhiyao Huang
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Benjamin Mignot
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Aanya Hirdaramani
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Annie Howitt
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kathryn Frewin
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zheng Shen
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rhys J Fox
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rachel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Momoko Ando
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lauren Emony
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Henderson Zhu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Nitya Krishnan
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Brian D Robertson
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Abigail Clements
- Department of Life Sciences and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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