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Mercurio K, Singh D, Walden E, Baetz K. Global analysis of Saccharomyces cerevisiae growth in mucin. G3 (BETHESDA, MD.) 2021; 11:jkab294. [PMID: 34849793 PMCID: PMC8527512 DOI: 10.1093/g3journal/jkab294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/03/2021] [Indexed: 11/12/2022]
Abstract
Metagenomic profiling of the human gut microbiome has discovered DNA from dietary yeasts like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected by common metagenomic methods are from dead dietary sources, or from live S. cerevisiae colonizing the gut similar to their close relative Candida albicans. While S. cerevisiae can adapt to minimal oxygen and acidic environments, it has not been explored whether this yeast can metabolize mucin, the large, gel-forming, highly glycosylated proteins representing a major source of carbon in the gut mucosa. We reveal that S. cerevisiae can utilize mucin as their main carbon source, as well as perform both a transcriptome analysis and a chemogenomic screen to identify biological pathways required for this yeast to grow optimally in mucin. In total, 739 genes demonstrate significant differential expression in mucin culture, and deletion of 21 genes impact growth in mucin. Both screens suggest that mitochondrial function is required for proper growth in mucin, and through secondary assays we determine that mucin exposure induces mitogenesis and cellular respiration. We further show that deletion of an uncharacterized ORF, YCR095W-A, led to dysfunction in mitochondrial morphology and oxygen consumption in mucin. Finally, we demonstrate that Yps7, an aspartyl protease and homolog to mucin-degrading proteins in C. albicans, is important for growth on mucin. Collectively, our work serves as the initial step toward establishing how this common dietary fungus can survive in the mucus environment of the human gut.
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Affiliation(s)
- Kevin Mercurio
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Dylan Singh
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Elizabeth Walden
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Kristin Baetz
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Multiple cellular responses guarantee yeast survival in presence of the cell membrane/wall interfering agent sodium dodecyl sulfate. Biochem Biophys Res Commun 2020; 527:276-282. [PMID: 32446380 DOI: 10.1016/j.bbrc.2020.03.163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 03/29/2020] [Indexed: 11/20/2022]
Abstract
Sodium dodecyl sulfate (SDS), a representative anionic surfactant, is a commonly used reagent in studies of the cell membrane and cell wall. However, the mechanisms through which SDS affects cellular functions have not yet been fully examined. Thus, to gain further insights into the cellular functions and responses to SDS, we tested a haploid library of Saccharomyces cerevisiae single-gene deletion mutants to identify genes required for tolerance to SDS. After two rounds of screening, we found 730 sensitive and 77 resistant mutants. Among the sensitive mutants, mitochondrial gene expression; the mitogen-activated protein kinase signaling pathway; the metabolic pathways involved in glycoprotein, lipid, purine metabolic process, oxidative phosphorylation, cellular amino acid biosynthesis and pentose phosphate pathway were found to be enriched. Additionally, we identified a set of transcription factors related to SDS responses. Among the resistant mutants, disruption of ribosome biogenesis and translation alleviated SDS-induced cytotoxicity. Collectively, our results provided new insights into the mechanisms through which SDS regulates the cell membrane or cell wall.
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Seifert GJ. On the Potential Function of Type II Arabinogalactan O-Glycosylation in Regulating the Fate of Plant Secretory Proteins. FRONTIERS IN PLANT SCIENCE 2020; 11:563735. [PMID: 33013983 PMCID: PMC7511660 DOI: 10.3389/fpls.2020.563735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/24/2020] [Indexed: 05/04/2023]
Abstract
In a plant-specific mode of protein glycosylation, various sugars and glycans are attached to hydroxyproline giving rise to a variety of diverse O-glycoproteins. The sub-family of arabinogalactan proteins is implicated in a multitude of biological functions, however, the mechanistic role of O-glycosylation on AGPs by type II arabinogalactans is largely elusive. Some models suggest roles of the O-glycans such as in ligand-receptor interactions and as localized calcium ion store. Structurally different but possibly analogous types of protein O-glycosylation exist in animal and yeast models and roles for O-glycans were suggested in determining the fate of O-glycoproteins by affecting intracellular sorting or proteolytic activation and degradation. At present, only few examples exist that describe how the fate of artificial and endogenous arabinogalactan proteins is affected by O-glycosylation with type II arabinogalactans. In addition to other roles, these glycans might act as a molecular determinant for cellular localization and protein lifetime of many endogenous proteins.
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Neubert P, Halim A, Zauser M, Essig A, Joshi HJ, Zatorska E, Larsen ISB, Loibl M, Castells-Ballester J, Aebi M, Clausen H, Strahl S. Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. Mol Cell Proteomics 2016; 15:1323-37. [PMID: 26764011 PMCID: PMC4824858 DOI: 10.1074/mcp.m115.057505] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 11/17/2022] Open
Abstract
O-Mannosylation is a vital protein modification conserved from fungi to humans. Yeast is a perfect model to study this post-translational modification, because in contrast to mammals O-mannosylation is the only type of O-glycosylation. In an essential step toward the full understanding of protein O-mannosylation we mapped the O-mannose glycoproteome in baker's yeast. Taking advantage of an O-glycan elongation deficient yeast strain to simplify sample complexity, we identified over 500 O-glycoproteins from all subcellular compartments for which over 2300 O-mannosylation sites were mapped by electron-transfer dissociation (ETD)-based MS/MS. In this study, we focus on the 293 O-glycoproteins (over 1900 glycosylation sites identified by ETD-MS/MS) that enter the secretory pathway and are targets of ER-localized protein O-mannosyltransferases. We find that O-mannosylation is not only a prominent modification of cell wall and plasma membrane proteins, but also of a large number of proteins from the secretory pathway with crucial functions in protein glycosylation, folding, quality control, and trafficking. The analysis of glycosylation sites revealed that O-mannosylation is favored in unstructured regions and β-strands. Furthermore, O-mannosylation is impeded in the proximity of N-glycosylation sites suggesting the interplay of these types of post-translational modifications. The detailed knowledge of the target proteins and their O-mannosylation sites opens for discovery of new roles of this essential modification in eukaryotes, and for a first glance on the evolution of different types of O-glycosylation from yeast to mammals.
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Affiliation(s)
- Patrick Neubert
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Adnan Halim
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Zauser
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Andreas Essig
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Hiren J Joshi
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Ewa Zatorska
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Ida Signe Bohse Larsen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Martin Loibl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Joan Castells-Ballester
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Markus Aebi
- ¶Institute of Microbiology, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Henrik Clausen
- §Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sabine Strahl
- From the ‡Centre for Organismal Studies (COS), Department of Cell Chemistry, Heidelberg University, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany;
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Landowski CP, Huuskonen A, Wahl R, Westerholm-Parvinen A, Kanerva A, Hänninen AL, Salovuori N, Penttilä M, Natunen J, Ostermeier C, Helk B, Saarinen J, Saloheimo M. Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei. PLoS One 2015; 10:e0134723. [PMID: 26309247 PMCID: PMC4550459 DOI: 10.1371/journal.pone.0134723] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
The filamentous fungus Trichoderma reesei has tremendous capability to secrete proteins. Therefore, it would be an excellent host for producing high levels of therapeutic proteins at low cost. Developing a filamentous fungus to produce sensitive therapeutic proteins requires that protease secretion is drastically reduced. We have identified 13 major secreted proteases that are related to degradation of therapeutic antibodies, interferon alpha 2b, and insulin like growth factor. The major proteases observed were aspartic, glutamic, subtilisin-like, and trypsin-like proteases. The seven most problematic proteases were sequentially removed from a strain to develop it for producing therapeutic proteins. After this the protease activity in the supernatant was dramatically reduced down to 4% of the original level based upon a casein substrate. When antibody was incubated in the six protease deletion strain supernatant, the heavy chain remained fully intact and no degradation products were observed. Interferon alpha 2b and insulin like growth factor were less stable in the same supernatant, but full length proteins remained when incubated overnight, in contrast to the original strain. As additional benefits, the multiple protease deletions have led to faster strain growth and higher levels of total protein in the culture supernatant.
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Affiliation(s)
| | - Anne Huuskonen
- VTT Technical Research Centre of Finland, Espoo, Finland
| | | | | | | | | | | | - Merja Penttilä
- VTT Technical Research Centre of Finland, Espoo, Finland
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