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Schiavone M, François JM, Zerbib D, Capp JP. Emerging relevance of cell wall components from non-conventional yeasts as functional ingredients for the food and feed industry. Curr Res Food Sci 2023; 7:100603. [PMID: 37840697 PMCID: PMC10568300 DOI: 10.1016/j.crfs.2023.100603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023] Open
Abstract
Non-conventional yeast species, or non-Saccharomyces yeasts, are increasingly recognized for their involvement in fermented foods. Many of them exhibit probiotic characteristics that are mainly due to direct contacts with other cell types through various molecular components of their cell wall. The biochemical composition and/or the molecular structure of the cell wall components are currently considered the primary determinant of their probiotic properties. Here we first present the techniques that are used to extract and analyze the cell wall components of food industry-related non-Saccharomyces yeasts. We then review the current understanding of the cell wall composition and structure of each polysaccharide from these yeasts. Finally, the data exploring the potential beneficial role of their cell wall components, which could be a source of innovative functional ingredients, are discussed. Such research would allow the development of high value-added products and provide the food industry with novel inputs beyond the well-established S. cerevisiae.
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Affiliation(s)
- Marion Schiavone
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Lallemand SAS, Blagnac, France
| | - Jean M. François
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Toulouse White Biotechnology (TWB), UMS INRAE/INSA/CNRS, Toulouse, France
| | - Didier Zerbib
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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2
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Characterization of putative mannoprotein in Kluyveromyces lactis for lactase production. Synth Syst Biotechnol 2023; 8:168-175. [PMID: 36733311 PMCID: PMC9880975 DOI: 10.1016/j.synbio.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/24/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023] Open
Abstract
Lactase is a member of the β-galactosidase family of enzymes that can hydrolyze lactose into galactose and glucose. However, extracellular lactase production was still restricted to the process of cell lysis. In this study, lactase-producing Kluyveromyces lactis JNXR-2101 was obtained using a rapid and sensitive method based on the fluorescent substrate 4-methylumbelliferyl-β-d-galactopyranoside. The purified enzyme was identified as a neutral lactase with an optimum pH of 9. To facilitate extracellular production of lactase, a putative mannoprotein KLLA0_E01057g of K. lactis was knocked out. It could effectively promote cell wall degradation and lactase production after lyticase treatment, which showed potential on other extracellular enzyme preparation. After optimizing the fermentation conditions, the lactase yield from mannoprotein-deficient K. lactis JNXR-2101ΔE01057g reached 159.62 U/mL in a 5-L fed-batch bioreactor.
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3
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The ploidy determination of the biotechnologically important yeast Candida utilis. J Appl Genet 2020; 61:275-286. [PMID: 31965459 DOI: 10.1007/s13353-020-00544-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 10/25/2022]
Abstract
Yeast Candida utilis is considered to be a potentially advantageous expression system for production of recombinant proteins utilizable for industrial and pharmaceutical purposes. As the scientific literature is not consistent in the ploidy of this yeast, in this work, we focused on resolving the problem via several methods such as the copy number determination of maltase gene by multiplex PCR, measuring α-glucosidase activity, the characterization of maltase gene copy number in deletion mutants using qPCR and flow cytometry. In context with the published data and results obtained in this study about the copy number of the maltase gene on C. utilis genome, we attempted to hypothesise and made conclusion about the ploidy of C. utilis. The results of this work, besides the biotechnological aspect, contribute to the elementary knowledge of C. utilis. The exact information about the ploidy or more specifically about the copy number of appropriate gene is essential for expression cassette dosage determination integrated into the chromosome of the host. In this study, we come to the conclusion that the maltase gene is present in C. utilis genome in four alleles, and in combination with flow cytometry, published information and the published genome sequences, the observations support the theory about tetraploidy of C. utilis.
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4
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Burgard J, Grünwald-Gruber C, Altmann F, Zanghellini J, Valli M, Mattanovich D, Gasser B. The secretome of Pichia pastoris in fed-batch cultivations is largely independent of the carbon source but changes quantitatively over cultivation time. Microb Biotechnol 2019; 13:479-494. [PMID: 31692260 PMCID: PMC7017826 DOI: 10.1111/1751-7915.13499] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/07/2019] [Indexed: 01/20/2023] Open
Abstract
The quantitative changes of the secretome of recombinant Pichia pastoris (Komagataella phaffii) CBS7435 over the time-course of methanol- or glucose-limited fed-batch cultures were investigated by LC-ESI-MS/MS to define the carbon source-specific secretomes under controlled bioreactor conditions. In both set-ups, no indication for elevated cell lysis was found. The quantitative data revealed that intact and viable P. pastoris cells secrete only a low number of endogenous proteins (in total 51), even during high cell density cultivation. Interestingly, no marked differences in the functional composition of the P. pastoris secretome between methanol- and glucose-grown cultures were observed with only few proteins being specifically affected by the carbon source. The 'core secretome' of 22 proteins present in all analysed carbon sources (glycerol, glucose and methanol) consists mainly of cell wall proteins. The quantitative analysis additionally revealed that most secretome proteins were already present after the batch phase, and depletion rather than accumulation occurred during the fed-batch processes. Among the changes over cultivation time, the depletion of both the extracellularly detected chaperones and the only two identified proteases (Pep4 and Yps1-1) during the methanol- or glucose-feed phase appear as most prominent.
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Affiliation(s)
- Jonas Burgard
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Chemistry, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jürgen Zanghellini
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Biotech University of Applied Sciences, Tulln, Austria
| | - Minoska Valli
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
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Abstract
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Secretory proteins are key modulators of host–pathogen interaction.
The human opportunistic fungal pathogen Candida glabrata lacks secreted proteolytic activity but possesses 11 glycosylphosphatidylinositol-anchored
aspartyl proteases, also referred to as Yapsins (CgYps1–11),
that are essential for its virulence. To delineate the role of CgYapsins
in interaction with host cells, we have profiled, through liquid chromatography-tandem
mass spectrometry (LC-MS/MS) approach, the total secretome of wild-type and Cgyps1-11Δ mutant.
The wild-type secretome consisted of 119 proteins
which were primarily involved in cell wall organization, carbohydrate
metabolism, proteolysis, and translation processes. Of eight CgYapsins
identified in the secretome, the release of two major CgYapsins, CgYps1
and CgYps7, to the medium was confirmed by Western analysis. Further,
comparative analysis revealed 20 common proteins, probably signifying
the core fungal secretome, among C. glabrata, Saccharomyces cerevisiae, and Candida albicans secretomes. Strikingly, the Cgyps1-11Δ secretome was 4.6-fold larger, and contained
65 differentially abundant proteins, as revealed by label-free quantitative
profiling, with 49 and 16 being high- and low-abundant proteins, respectively,
compared to the wild-type secretome. Importantly,
the CgMsb2 mucin, a putative CgYapsins’ substrate, was six-fold
underrepresented in the mutant secretome. Altogether, we demonstrate
for the first time that CgYapsins are both bona fide constituents
and key modulators of the C. glabrata secretome.
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Affiliation(s)
- Mubashshir Rasheed
- Laboratory of Fungal Pathogenesis , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500039 , India
| | - Naveen Kumar
- Laboratory of Fungal Pathogenesis , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500039 , India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis , Centre for DNA Fingerprinting and Diagnostics , Hyderabad , Telangana 500039 , India
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Araújo DS, de Sousa Lima P, Baeza LC, Parente AFA, Melo Bailão A, Borges CL, de Almeida Soares CM. Employing proteomic analysis to compare Paracoccidioides lutzii yeast and mycelium cell wall proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1304-1314. [PMID: 28844734 DOI: 10.1016/j.bbapap.2017.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 08/17/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022]
Abstract
Paracoccidioidomycosis is an important systemic mycosis caused by thermodimorphic fungi of the Paracoccidioides genus. During the infective process, the cell wall acts at the interface between the fungus and the host. In this way, the cell wall has a key role in growth, environment sensing and interaction, as well as morphogenesis of the fungus. Since the cell wall is absent in mammals, it may present molecules that are described as target sites for new antifungal drugs. Despite its importance, up to now few studies have been conducted employing proteomics in for the identification of cell wall proteins in Paracoccidioides spp. Here, a detailed proteomic approach, including cell wall-fractionation coupled to NanoUPLC-MSE, was used to study and compare the cell wall fractions from Paracoccidioides lutzii mycelia and yeast cells. The analyzed samples consisted of cell wall proteins extracted by hot SDS followed by extraction by mild alkali. In summary, 512 proteins constituting different cell wall fractions were identified, including 7 predicted GPI-dependent cell wall proteins that are potentially involved in cell wall metabolism. Adhesins previously described in Paracoccidioides spp. such as enolase, glyceraldehyde-3-phosphate dehydrogenase were identified. Comparing the proteins in mycelium and yeast cells, we detected some that are common to both fungal phases, such as Ecm33, and some specific proteins, as glucanase Crf1. All of those proteins were described in the metabolism of cell wall. Our study provides an important elucidation of cell wall composition of fractions in Paracoccidioides, opening a way to understand the fungus cell wall architecture.
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Affiliation(s)
- Danielle Silva Araújo
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil; Laboratório Interdisciplinar de Biologia, Universidade Estadual de Goiás, Itapuranga, Goiás, Brazil
| | - Lilian Cristiane Baeza
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Ana Flávia Alves Parente
- Laboratório de Bioquímica e Química de Proteínas, Instituto de Biologia, Campus Universitário Darci Ribeiro, Brasília, DF, Brazil
| | - Alexandre Melo Bailão
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, 74001-970 Goiânia, Goiás, Brazil.
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7
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Matthews CB, Wright C, Kuo A, Colant N, Westoby M, Love JC. Reexamining opportunities for therapeutic protein production in eukaryotic microorganisms. Biotechnol Bioeng 2017; 114:2432-2444. [DOI: 10.1002/bit.26378] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/19/2017] [Accepted: 07/03/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Catherine B. Matthews
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - Angel Kuo
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Noelle Colant
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
| | | | - J. Christopher Love
- Department of Chemical Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge Massachusetts
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8
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Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS. Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis. J Proteomics 2017; 156:63-74. [DOI: 10.1016/j.jprot.2017.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/13/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
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9
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Gómez-Molero E, Dekker HL, de Boer AD, de Groot PWJ. Identification of Secreted Candida Proteins Using Mass Spectrometry. Methods Mol Biol 2016; 1356:79-94. [PMID: 26519067 DOI: 10.1007/978-1-4939-3052-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Analysis of fungal secretomes using mass spectrometry is a useful technique in cell biology. Knowledge of the secretome of a human fungal pathogen may yield important information of host-pathogen interactions and may be useful for identifying vaccines candidates or diagnostic markers for antifungal strategies. In this chapter, with a main focus on sample preparation aspects, we describe the methodology that we apply for gel-independent batch identification and quantification of proteins that are secreted during growth in liquid cultures. Using these techniques with Candida and other yeast species, the majority of the identified proteins are classical secretory proteins and cell wall proteins containing N-terminal signal peptides for secretion, although dependent on sample preparation quality and the mass spectrometric analysis also usually, a number of nonsecretory proteins are identified.
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Affiliation(s)
- Emilia Gómez-Molero
- Regional Center for Biomedical Research, Albacete Science & Technology Park, University of Castilla-La Mancha, Calle Almansa 14, 02008, Albacete, Spain
| | - Henk L Dekker
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Albert D de Boer
- Regional Center for Biomedical Research, Albacete Science & Technology Park, University of Castilla-La Mancha, Calle Almansa 14, 02008, Albacete, Spain
| | - Piet W J de Groot
- Regional Center for Biomedical Research, Albacete Science & Technology Park, University of Castilla-La Mancha, Calle Almansa 14, 02008, Albacete, Spain.
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10
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Wang H, Zhang L, Shi G. Secretory expression of a phospholipase A2 from Lactobacillus casei DSM20011 in Kluyveromyces lactis. J Biosci Bioeng 2015; 120:601-7. [DOI: 10.1016/j.jbiosc.2015.03.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 03/09/2015] [Accepted: 03/31/2015] [Indexed: 11/29/2022]
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11
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Giardina BJ, Stanley BA, Chiang HL. Glucose induces rapid changes in the secretome of Saccharomyces cerevisiae. Proteome Sci 2014; 12:9. [PMID: 24520859 PMCID: PMC3927832 DOI: 10.1186/1477-5956-12-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/31/2014] [Indexed: 12/14/2022] Open
Abstract
Background Protein secretion is a fundamental process in all living cells. Proteins can either be secreted via the classical or non-classical pathways. In Saccharomyces cerevisiae, gluconeogenic enzymes are in the extracellular fraction/periplasm when cells are grown in media containing low glucose. Following a transfer of cells to high glucose media, their levels in the extracellular fraction are reduced rapidly. We hypothesized that changes in the secretome were not restricted to gluconeogenic enzymes. The goal of the current study was to use a proteomic approach to identify extracellular proteins whose levels changed when cells were transferred from low to high glucose media. Results We performed two iTRAQ experiments and identified 347 proteins that were present in the extracellular fraction including metabolic enzymes, proteins involved in oxidative stress, protein folding, and proteins with unknown functions. Most of these proteins did not contain typical ER-Golgi signal sequences. Moreover, levels of many of these proteins decreased upon a transfer of cells from media containing low to high glucose media. Using an extraction procedure and Western blotting, we confirmed that the metabolic enzymes (glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, glucose-6-phosphate dehydrogenase, pyruvate decarboxylase), proteins involved in oxidative stress (superoxide dismutase and thioredoxin), and heat shock proteins (Ssa1p, Hsc82p, and Hsp104p) were in the extracellular fraction during growth in low glucose and that the levels of these extracellular proteins were reduced when cells were transferred to media containing high glucose. These proteins were associated with membranes in vesicle-enriched fraction. We also showed that small vesicles were present in the extracellular fraction in cells grown in low glucose. Following a transfer from low to high glucose media for 30 minutes, 98% of these vesicles disappeared from the extracellular fraction. Conclusions Our data indicate that transferring cells from low to high glucose media induces a rapid decline in levels of a large number of extracellular proteins and the disappearance of small vesicles from the extracellular fraction. Therefore, we conclude that the secretome undergoes dynamic changes during transition from glucose-deficient to glucose-rich media. Most of these extracellular proteins do not contain typical ER signal sequences, suggesting that they are secreted via the non-classical pathway.
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Affiliation(s)
| | | | - Hui-Ling Chiang
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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12
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Ciesielska K, Van Bogaert I, Chevineau S, Li B, Groeneboer S, Soetaert W, Van de Peer Y, Devreese B. Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids. J Proteomics 2014; 98:159-74. [DOI: 10.1016/j.jprot.2013.12.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 12/30/2013] [Indexed: 01/25/2023]
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13
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Xiao X, Xie J, Cheng J, Li G, Yi X, Jiang D, Fu Y. Novel secretory protein Ss-Caf1 of the plant-pathogenic fungus Sclerotinia sclerotiorum is required for host penetration and normal sclerotial development. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:40-55. [PMID: 24299212 DOI: 10.1094/mpmi-05-13-0145-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To decipher the mechanism of pathogenicity in Sclerotinia sclerotiorum, a pathogenicity-defective mutant, Sunf-MT6, was isolated from a T-DNA insertional library. Sunf-MT6 could not form compound appressorium and failed to induce lesions on leaves of rapeseed though it could produce more oxalic acid than the wild-type strain. However, it could enter into host tissues via wounds and cause typical necrotic lesions. Furthermore, Sunf-MT6 produced fewer but larger sclerotia than the wild-type strain Sunf-M. A gene, named Ss-caf1, was disrupted by T-DNA insertion in Sunf-MT6. Gene complementation and knockdown experiments confirmed that the disruption of Ss-caf1 was responsible for the phenotypic changes of Sunf-MT6. Ss-caf1 encodes a secretory protein with a putative Ca(2+)-binding EF-hand motif. High expression levels of Ss-caf1 were observed at an early stage of compound appressorium formation and in immature sclerotia. Expression of Ss-caf1 without signal peptides in Nicotiana benthamiana via Tobacco rattle virus-based vectors elicited cell death. These results suggest that Ss-caf1 plays an important role in compound appressorium formation and sclerotial development of S. sclerotiorum. In addition, Ss-Caf1 has the potential to interact with certain host proteins or unknown substances in host cells, resulting in subsequent host cell death.
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14
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Girard V, Dieryckx C, Job C, Job D. Secretomes: The fungal strike force. Proteomics 2013; 13:597-608. [DOI: 10.1002/pmic.201200282] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Vincent Girard
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Cindy Dieryckx
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Claudette Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
| | - Dominique Job
- Bayer CropScience Joint Laboratory (UMR5240); CNRS, University Lyon1; Lyon; France
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15
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Brown KJ, Formolo CA, Seol H, Marathi RL, Duguez S, An E, Pillai D, Nazarian J, Rood BR, Hathout Y. Advances in the proteomic investigation of the cell secretome. Expert Rev Proteomics 2013; 9:337-45. [PMID: 22809211 DOI: 10.1586/epr.12.21] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Studies of the cell secretome have greatly increased in recent years owing to improvements in proteomic platforms, mass spectrometry instrumentation and to the increased interaction between analytical chemists, biologists and clinicians. Several secretome studies have been implemented in different areas of research, leading to the generation of a valuable secretome catalogs. Secreted proteins continue to be an important source of biomarkers and therapeutic target discovery and are equally valuable in the field of microbiology. Several discoveries have been achieved in vitro using cell culture systems, ex vivo using human tissue specimens and in vivo using animal models. In this review, some of the most recent advances in secretome studies and the fields that have benefited the most from this evolving technology are highlighted.
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Affiliation(s)
- Kristy J Brown
- Children's National Medical Center, Center for Genetic Medicine Research, 111 Michigan Avenue NW, Washington, DC 20010, USA
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16
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Sorgo AG, Heilmann CJ, Brul S, de Koster CG, Klis FM. Beyond the wall:Candida albicanssecret(e)s to survive. FEMS Microbiol Lett 2012; 338:10-7. [DOI: 10.1111/1574-6968.12049] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 01/12/2023] Open
Affiliation(s)
- Alice G. Sorgo
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam; The Netherlands
| | - Clemens J. Heilmann
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam; The Netherlands
| | - Stanley Brul
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam; The Netherlands
| | - Chris G. de Koster
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam; The Netherlands
| | - Frans M. Klis
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam; The Netherlands
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17
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Klis FM, de Koster CG, Brul S. A mass spectrometric view of the fungal wall proteome. Future Microbiol 2011; 6:941-51. [PMID: 21861624 DOI: 10.2217/fmb.11.72] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The walls of many fungal species consist of a polysaccharide network offering mechanical strength and functioning as a scaffold for covalently attached glycoproteins. The rapid advances in fungal genome sequencing and mass spectrometry have made it possible to study fungal wall proteomes in detail, both qualitatively and quantitatively. One of the surprising outcomes of these studies is the large variety of covalently attached proteins found in fungal walls. Another important result is that fungi can rapidly adapt the protein composition of their new walls to changes in environmental conditions. The wall proteome of the opportunistic human pathogen Candida albicans amply illustrates these properties. Finally, we discuss the relevance of our insights for the identification of new vaccine candidates.
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Affiliation(s)
- Frans M Klis
- Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
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18
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Navarrete M, Callegari E, Eyzaguirre J. The effect of acetylated xylan and sugar beet pulp on the expression and secretion of enzymes by Penicillium purpurogenum. Appl Microbiol Biotechnol 2011; 93:723-41. [DOI: 10.1007/s00253-011-3744-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 11/02/2011] [Accepted: 11/16/2011] [Indexed: 01/26/2023]
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19
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Buerth C, Heilmann CJ, Klis FM, de Koster CG, Ernst JF, Tielker D. Growth-dependent secretome of Candida utilis. MICROBIOLOGY-SGM 2011; 157:2493-2503. [PMID: 21680638 DOI: 10.1099/mic.0.049320-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recently, the food yeast Candida utilis has emerged as an excellent host for production of heterologous proteins. Since secretion of the recombinant product is advantageous for its purification, we characterized the secreted proteome of C. utilis. Cells were cultivated to the exponential or stationary growth phase, and the proteins in the medium were identified by MS. In parallel, a draft genome sequence of C. utilis strain DSM 2361 was determined by massively parallel sequencing. Comparisons of protein and coding sequences established that C. utilis is not a member of the CUG clade of Candida species. In total, we identified 37 proteins in the culture solution, 17 of which were exclusively present in the stationary phase, whereas three proteins were specific to the exponential growth phase. Identified proteins represented mostly carbohydrate-active enzymes associated with cell wall organization, while no proteolytic enzymes and only a few cytoplasmic proteins were detected. Remarkably, cultivation in xylose-based medium generated a protein pattern that diverged significantly from glucose-grown cells, containing the invertase Inv1 as the major extracellular protein, particularly in its highly glycosylated S-form (slow-migrating). Furthermore, cultivation without ammonium sulfate induced the secretion of the asparaginase Asp3. Comparisons of the secretome of C. utilis with those of Kluyveromyces lactis and Pichia pastoris, as well as with those of the human fungal pathogens Candida albicans and Candida glabrata, revealed a conserved set of 10 and six secretory proteins, respectively.
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Affiliation(s)
- Christoph Buerth
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
| | - Clemens J Heilmann
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Frans M Klis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris G de Koster
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joachim F Ernst
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
| | - Denis Tielker
- Molecular Mycology, Heinrich-Heine-University, Duesseldorf, Universitaetsstraße 1, 40225 Duesseldorf, Germany
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Development and validation of a medium for recombinant endo-β-1,4-xylanase production by Kluyveromyces lactis using a statistical experimental design. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0258-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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21
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Ganatra MB, Vainauskas S, Hong JM, Taylor TE, Denson JPM, Esposito D, Read JD, Schmeisser H, Zoon KC, Hartley JL, Taron CH. A set of aspartyl protease-deficient strains for improved expression of heterologous proteins in Kluyveromyces lactis. FEMS Yeast Res 2010; 11:168-78. [PMID: 21166768 PMCID: PMC3041862 DOI: 10.1111/j.1567-1364.2010.00703.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Secretion of recombinant proteins is a common strategy for heterologous protein expression using the yeast Kluyveromyces lactis. However, a common problem is degradation of a target recombinant protein by secretory pathway aspartyl proteases. In this study, we identified five putative pfam00026 aspartyl proteases encoded by the K. lactis genome. A set of selectable marker-free protease deletion mutants was constructed in the prototrophic K. lactis GG799 industrial expression strain background using a PCR-based dominant marker recycling method based on the Aspergillus nidulans acetamidase gene (amdS). Each mutant was assessed for its secretion of protease activity, its health and growth characteristics, and its ability to efficiently produce heterologous proteins. In particular, despite having a longer lag phase and slower growth compared with the other mutants, a Δyps1 mutant demonstrated marked improvement in both the yield and the quality of Gaussia princeps luciferase and the human chimeric interferon Hy3, two proteins that experienced significant proteolysis when secreted from the wild-type parent strain.
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Affiliation(s)
- Mehul B Ganatra
- Division of Gene Expression, New England Biolabs, Ipswich, MA 01938-2723, USA
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Backhaus K, Heilmann CJ, Sorgo AG, Purschke G, de Koster CG, Klis FM, Heinisch JJ. A systematic study of the cell wall composition of Kluyveromyces lactis. Yeast 2010; 27:647-60. [PMID: 20641021 DOI: 10.1002/yea.1781] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In many ascomycetous yeasts, the cell wall is composed of two main types of macromolecules: (a) polysaccharides, with a high content of beta-1,6- and beta-1,3-linked glucan chains and minor amounts of chitin; and (b) cell wall proteins of different types. Synthesis and maintenance of these macromolecules respond to environmental changes, which are sensed by the cell wall integrity (CWI) signal transduction pathway. We here present a first systematic analysis of the cell wall composition of the milk yeast, Kluyveromyces lactis. Electron microscopic analyses revealed that exponentially growing cells of K. lactis supplied with glucose as a carbon source have a wall thickness of 64 nm, as compared to 105 nm when growing on 3% ethanol. Despite their increased wall thickness, ethanol-grown cells were more sensitive to the presence of zymolyase in the growth medium. Mass spectrometric analysis identified 22 covalently linked cell wall proteins, including 19 GPI-modified proteins and two Pir wall proteins. Importantly, the composition of the cell wall glycoproteome depended on carbon source and growth phase. Our results clearly illustrate the dynamic nature of the cell wall of K. lactis and provide a firm base for studying its regulation.
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Affiliation(s)
- Katja Backhaus
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Osnabrück, Germany
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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