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Ferreira MDS, Gonçalves DDS, Mendoza SR, de Oliveira GA, Pontes B, la Noval CRD, Honorato L, Ramos LFC, Nogueira FCS, Domont GB, Casadevall A, Nimrichter L, Peralta JM, Guimaraes AJ. β-1,3-Glucan recognition by Acanthamoeba castellanii as a putative mechanism of amoeba-fungal interactions. Appl Environ Microbiol 2024; 90:e0173623. [PMID: 38259076 PMCID: PMC10880599 DOI: 10.1128/aem.01736-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
In this study, we conducted an in-depth analysis to characterize potential Acanthamoeba castellanii (Ac) proteins capable of recognizing fungal β-1,3-glucans. Ac specifically anchors curdlan or laminarin, indicating the presence of surface β-1,3-glucan-binding molecules. Using optical tweezers, strong adhesion of laminarin- or curdlan-coated beads to Ac was observed, highlighting their adhesive properties compared to controls (characteristic time τ of 46.9 and 43.9 s, respectively). Furthermore, Histoplasma capsulatum (Hc) G217B, possessing a β-1,3-glucan outer layer, showed significant adhesion to Ac compared to a Hc G186 strain with an α-1,3-glucan outer layer (τ of 5.3 s vs τ 83.6 s). The addition of soluble β-1,3-glucan substantially inhibited this adhesion, indicating the involvement of β-1,3-glucan recognition. Biotinylated β-1,3-glucan-binding proteins from Ac exhibited higher binding to Hc G217B, suggesting distinct recognition mechanisms for laminarin and curdlan, akin to macrophages. These observations hinted at the β-1,3-glucan recognition pathway's role in fungal entrance and survival within phagocytes, supported by decreased fungal viability upon laminarin or curdlan addition in both phagocytes. Proteomic analysis identified several Ac proteins capable of binding β-1,3-glucans, including those with lectin/glucanase superfamily domains, carbohydrate-binding domains, and glycosyl transferase and glycosyl hydrolase domains. Notably, some identified proteins were overexpressed upon curdlan/laminarin challenge and also demonstrated high affinity to β-1,3-glucans. These findings underscore the complexity of binding via β-1,3-glucan and suggest the existence of alternative fungal recognition pathways in Ac.IMPORTANCEAcanthamoeba castellanii (Ac) and macrophages both exhibit the remarkable ability to phagocytose various extracellular microorganisms in their respective environments. While substantial knowledge exists on this phenomenon for macrophages, the understanding of Ac's phagocytic mechanisms remains elusive. Recently, our group identified mannose-binding receptors on the surface of Ac that exhibit the capacity to bind/recognize fungi. However, the process was not entirely inhibited by soluble mannose, suggesting the possibility of other interactions. Herein, we describe the mechanism of β-1,3-glucan binding by A. castellanii and its role in fungal phagocytosis and survival within trophozoites, also using macrophages as a model for comparison, as they possess a well-established mechanism involving the Dectin-1 receptor for β-1,3-glucan recognition. These shed light on a potential parallel evolution of pathways involved in the recognition of fungal surface polysaccharides.
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Affiliation(s)
- Marina da Silva Ferreira
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Imunologia e Inflamação, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Diego de Souza Gonçalves
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Susana Ruiz Mendoza
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Imunologia e Inflamação, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Gabriel Afonso de Oliveira
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Bruno Pontes
- Instituto de Ciências Biomédicas e Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Claudia Rodríguez-de la Noval
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Leandro Honorato
- Laboratório de Glicobiologia de Eucariotos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Luis Felipe Costa Ramos
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Fábio C. S. Nogueira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Gilberto B. Domont
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Leonardo Nimrichter
- Programa de Pós-Graduação em Imunologia e Inflamação, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
- Laboratório de Glicobiologia de Eucariotos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
- Rede Micologia RJ - Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Niterói, Rio de Janeiro, Brazil
| | - Jose Mauro Peralta
- Programa de Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
| | - Allan J. Guimaraes
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Imunologia e Inflamação, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Niterói, Rio de Janeiro, Brazil
- Rede Micologia RJ - Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Niterói, Rio de Janeiro, Brazil
- Pós-Graduação em Microbiologia e Parasitologia Aplicadas, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
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Ferreira MDS, Mendoza SR, Gonçalves DDS, Rodríguez-de la Noval C, Honorato L, Nimrichter L, Ramos LFC, Nogueira FCS, Domont GB, Peralta JM, Guimarães AJ. Recognition of Cell Wall Mannosylated Components as a Conserved Feature for Fungal Entrance, Adaptation and Survival Within Trophozoites of Acanthamoeba castellanii and Murine Macrophages. Front Cell Infect Microbiol 2022; 12:858979. [PMID: 35711659 PMCID: PMC9194641 DOI: 10.3389/fcimb.2022.858979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/28/2022] [Indexed: 01/09/2023] Open
Abstract
Acanthamoeba castellanii (Ac) is a species of free-living amoebae (FLAs) that has been widely applied as a model for the study of host-parasite interactions and characterization of environmental symbionts. The sharing of niches between Ac and potential pathogens, such as fungi, favors associations between these organisms. Through predatory behavior, Ac enhances fungal survival, dissemination, and virulence in their intracellular milieu, training these pathogens and granting subsequent success in events of infections to more evolved hosts. In recent studies, our group characterized the amoeboid mannose binding proteins (MBPs) as one of the main fungal recognition pathways. Similarly, mannose-binding lectins play a key role in activating antifungal responses by immune cells. Even in the face of similarities, the distinct impacts and degrees of affinity of fungal recognition for mannose receptors in amoeboid and animal hosts are poorly understood. In this work, we have identified high-affinity ligands for mannosylated fungal cell wall residues expressed on the surface of amoebas and macrophages and determined the relative importance of these pathways in the antifungal responses comparing both phagocytic models. Mannose-purified surface proteins (MPPs) from both phagocytes showed binding to isolated mannose/mannans and mannosylated fungal cell wall targets. Although macrophage MPPs had more intense binding when compared to the amoeba receptors, the inhibition of this pathway affects fungal internalization and survival in both phagocytes. Mass spectrometry identified several MPPs in both models, and in silico alignment showed highly conserved regions between spotted amoeboid receptors (MBP and MBP1) and immune receptors (Mrc1 and Mrc2) and potential molecular mimicry, pointing to a possible convergent evolution of pathogen recognition mechanisms.
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Affiliation(s)
- Marina da Silva Ferreira
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
- Pós-Graduação em Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Susana Ruiz Mendoza
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
- Pós-Graduação em Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diego de Souza Gonçalves
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
- Pós-Graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Claudia Rodríguez-de la Noval
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
| | - Leandro Honorato
- Programa de Pós-Graduação em Ciências (Microbiologia), Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leonardo Nimrichter
- Laboratório de Glicobiologia de Eucariotos, Instituto de Microbiologia Professor Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Rede Micologia RJ - FAPERJ, Rio de Janeiro, Brazil
| | - Luís Felipe Costa Ramos
- Laboratório de Química de Proteínas, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C. S. Nogueira
- Laboratório de Química de Proteínas, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B. Domont
- Laboratório de Química de Proteínas, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Mauro Peralta
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Allan J. Guimarães
- Laboratório de Bioquímica e Imunologia das Micoses, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
- Pós-Graduação em Imunologia e Inflamação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Rede Micologia RJ - FAPERJ, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Microbiologia e Parasitologia Aplicadas, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
- *Correspondence: Allan J. Guimarães,
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Muth T, Hartkopf F, Vaudel M, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics. Proteomics 2018; 18:e1700150. [PMID: 29968278 DOI: 10.1002/pmic.201700150] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/23/2018] [Indexed: 01/15/2023]
Abstract
In shotgun proteomics, peptide and protein identification is most commonly conducted using database search engines, the method of choice when reference protein sequences are available. Despite its widespread use the database-driven approach is limited, mainly because of its static search space. In contrast, de novo sequencing derives peptide sequence information in an unbiased manner, using only the fragment ion information from the tandem mass spectra. In recent years, with the improvements in MS instrumentation, various new methods have been proposed for de novo sequencing. This review article provides an overview of existing de novo sequencing algorithms and software tools ranging from peptide sequencing to sequence-to-protein mapping. Various use cases are described for which de novo sequencing was successfully applied. Finally, limitations of current methods are highlighted and new directions are discussed for a wider acceptance of de novo sequencing in the community.
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Affiliation(s)
- Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Felix Hartkopf
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
| | - Marc Vaudel
- K.G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020, Bergen, Norway.,Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5020, Bergen, Norway
| | - Bernhard Y Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, 13353, Berlin, Germany
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