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Araújo GRDS, Pontes B, Frases S. Electron Microscopy of Cryptococcus neoformans: Processing Challenges to Avoid Artifacts. Methods Mol Biol 2024; 2775:141-153. [PMID: 38758316 DOI: 10.1007/978-1-0716-3722-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
This chapter describes methodological details for preparing specimens of Cryptococcus neoformans (although it can be applied to any species of the genus) and their subsequent analysis by scanning and transmission electron microscopy. Adaptations to conventional protocols for better preservation of the sample, as well as to avoid artifacts, are presented. The protocols may be used to examine both the surface ultrastructure and the interior of this pathogenic fungus in detail.
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Affiliation(s)
- Glauber R de S Araújo
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Bruno Pontes
- Laboratório de Pinças Ópticas Moysés Nussenzveig (LPO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rede Micologia RJ, FAPERJ, Rio de Janeiro, Brazil
| | - Susana Frases
- Laboratório de Biofísica de Fungos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rede Micologia RJ, FAPERJ, Rio de Janeiro, Brazil
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Abstract
In alcohol distilleries, the amount of distillery stillage generated can be up to 15 times larger than the amount of alcohol produced. The stillage has high concentrations of organics and nitrogen, a low pH, and a dark brown color. Currently, stillage is mainly used for soil fertilization. For this purpose, it requires thickening and is used seasonally, which creates storage problems and transport costs. To reduce environmental pollution, physicochemical and biological processes have been employed for the treatment of distillery stillage. However, according to bioeconomy principles, the stillage should be transformed into value-added products. Therefore, this review paper focuses on methods of stillage processing that enable energy recovery. Due to its high content of organic compounds, stillage is often used as a raw material for biogas production. Accordingly, anaerobic digestion of stillage is discussed, including an overview of the bioreactors used and the effects of operational parameters on organics removal and biogas production. The necessity of integrating anaerobic stillage treatment with other treatment processes is presented. As complex compounds that are present in the stillage (mainly polyphenols and melanoidin) are difficult to biodegrade and have antibacterial activities, the effect of their recovery on biogas production is described. Next, the possibility of converting distillery stillage to bioethanol and biohydrogen is presented. In addition, bioelectrochemical treatment of distillery stillage using microbial fuel cells is discussed. For all these treatment methods, current challenges and opportunities are given.
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Wang H, Li Q, Peng Y, Zhang Z, Kuang X, Hu X, Ayepa E, Han X, Abrha GT, Xiang Q, Yu X, Zhao K, Zou L, Gu Y, Li X, Li X, Chen Q, Zhang X, Liu B, Ma M. Cellular Analysis and Comparative Transcriptomics Reveal the Tolerance Mechanisms of Candida tropicalis Toward Phenol. Front Microbiol 2020; 11:544. [PMID: 32373081 PMCID: PMC7179700 DOI: 10.3389/fmicb.2020.00544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/12/2020] [Indexed: 12/03/2022] Open
Abstract
Phenol is a ubiquitous pollutant and can contaminate natural water resources. Hence, the removal of phenol from wastewater is of significant importance. A series of biological methods were used to remove phenol based on the natural ability of microorganisms to degrade phenol, but the tolerance mechanism of phenol-degraded strains to phenol are not very clear. Morphological observation on Candida tropicalis showed that phenol caused the reactive oxygen species (ROS) accumulation, damaging the mitochondrial and the endoplasmic reticulum. On the basis of transcriptome data and cell wall susceptibility analysis, it was found that C. tropicalis prevented phenol-caused cell damage through improvement of cell wall resistance, maintenance of high-fidelity DNA replication, intracellular protein homeostasis, organelle integrity, and kept the intracellular phenol concentration at a low level through cell-wall remodeling and removal of excess phenol via MDR/MXR transporters. The knowledge obtained will promote the genetic modification of yeast strains in general to tolerate the high concentrations of phenol and improve their efficiency of phenol degradation.
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Affiliation(s)
- Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuanyuan Peng
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zhengyue Zhang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaolin Kuang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiangdong Hu
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ellen Ayepa
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xuebing Han
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Getachew Tafere Abrha
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, China
| | - Xiaoying Li
- School of Forestry and Life Science, Chongqing University of Arts and Sciences, Chongqing, China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiaoping Zhang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteburg, Sweden.,State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Chengdu, China.,Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
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Cell surface display of proteins on filamentous fungi. Appl Microbiol Biotechnol 2019; 103:6949-6972. [PMID: 31359105 DOI: 10.1007/s00253-019-10026-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Protein display approaches have been useful to endow the cell surface of yeasts with new catalytic activities so that they can act as enhanced whole-cell biocatalysts. Despite their biotechnological potential, protein display technologies remain poorly developed for filamentous fungi. The lignocellulolytic character of some of them coupled to the cell surface biosynthesis of valuable molecules by a single or a cascade of several displayed enzymes is an appealing prospect. Cell surface protein display consists in the co-translational fusion of a functional protein (passenger) to an anchor one, usually a cell-wall-resident protein. The abundance, spacing, and local environment of the displayed enzymes-determined by the relationship of the anchor protein with the structure and dynamics of the engineered cell wall-are factors that influence the performance of display-based biocatalysts. The development of protein display strategies in filamentous fungi could be based on the field advances in yeasts; however, the unique composition, structure, and biology of filamentous fungi cell walls require the customization of the approach to those microorganisms. In this prospective review, the cellular bases, the design principles, and the available tools to foster the development of cell surface protein display technologies in filamentous fungi are discussed.
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Yuzbasheva EY, Gotovtsev PM, Mostova EB, Perkovskaya NI, Lomonosova MA, Butylin VV, Sineokii SP, Vasilov RG. Biodiesel production via enzymatic catalysis. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814080067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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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Sosinska GJ, de Koning LJ, de Groot PWJ, Manders EMM, Dekker HL, Hellingwerf KJ, de Koster CG, Klis FM. Mass spectrometric quantification of the adaptations in the wall proteome of Candida albicans in response to ambient pH. MICROBIOLOGY-SGM 2010; 157:136-146. [PMID: 20864472 DOI: 10.1099/mic.0.044206-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mucosal layers colonized by the pathogenic fungus Candida albicans differ widely in ambient pH. Because the properties and functions of wall proteins are probably pH dependent, we hypothesized that C. albicans adapts its wall proteome to the external pH. We developed an in vitro system that mimics colonization of mucosal surfaces by growing biomats at pH 7 and 4 on semi-solid agarose containing mucin as the sole nitrogen source. The biomats expanded radially for at least 8 days at a rate of ~30 μm h(-1). At pH 7, hyphal growth predominated and growth was invasive, whereas at pH 4 only yeast and pseudohyphal cells were present and growth was noninvasive. Both qualitative mass spectrometric analysis of the wall proteome by tandem mass spectrometry and relative quantification of individual wall proteins (pH 7/pH 4), using Fourier transform mass spectrometry (FT-MS) and a reference mixture of (15)N-labelled yeast and hyphal walls, identified similar sets of >20 covalently linked wall proteins. The adhesion proteins Als1 and Als3, Hyr1, the transglucosidase Phr1, the detoxification enzyme Sod5 and the mammalian transglutaminase substrate Hwp1 (immunological detection) were only present at pH 7, whereas at pH 4 the level of the transglucosidase Phr2 was >35-fold higher than at pH 7. Sixteen out of the 22 proteins identified by FT-MS showed a greater than twofold change. These results demonstrate that ambient pH strongly affects the wall proteome of C. albicans, show that our quantitative approach can give detailed insights into the dynamics of the wall proteome, and point to potential vaccine targets.
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Affiliation(s)
- Grazyna J Sosinska
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Leo J de Koning
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Piet W J de Groot
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Erik M M Manders
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Henk L Dekker
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- 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
| | - Frans M Klis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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de Boer AD, de Groot PWJ, Weindl G, Schaller M, Riedel D, Diez-Orejas R, Klis FM, de Koster CG, Dekker HL, Gross U, Bader O, Weig M. The Candida albicans cell wall protein Rhd3/Pga29 is abundant in the yeast form and contributes to virulence. Yeast 2010; 27:611-24. [DOI: 10.1002/yea.1790] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Klis FM, Brul S, De Groot PWJ. Covalently linked wall proteins in ascomycetous fungi. Yeast 2009; 27:489-93. [DOI: 10.1002/yea.1747] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Klis FM, Sosinska GJ, de Groot PWJ, Brul S. Covalently linked cell wall proteins of Candida albicans and their role in fitness and virulence. FEMS Yeast Res 2009; 9:1013-28. [PMID: 19624749 DOI: 10.1111/j.1567-1364.2009.00541.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The cell wall of Candida albicans consists of an internal skeletal layer and an external protein coat. This coat has a mosaic-like nature, containing c. 20 different protein species covalently linked to the skeletal layer. Most of them are GPI proteins. Coat proteins vary widely in function. Many of them are involved in the primary interactions between C. albicans and the host and mediate adhesive steps or invasion of host cells. Others are involved in biofilm formation and cell-cell aggregation. They further include iron acquisition proteins, superoxide dismutases, and yapsin-like aspartic proteases. In addition, several covalently linked carbohydrate-active enzymes are present, whose precise functions remain hitherto largely elusive. The expression levels of the genes that encode covalently linked cell wall proteins (CWPs) can vary enormously. They depend on the mode of growth and the combined inputs of several signaling pathways that sense environmental conditions. This is reflected in the unusually long intergenic regions of most of these genes. Finally, the precise location of several covalently linked CWPs is temporally and spatially regulated. We conclude that covalently linked CWPs of C. albicans play a crucial role in fitness and virulence and that their expression is tightly controlled.
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Affiliation(s)
- Frans M Klis
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1018 WV Amsterdam, The Netherlands.
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Richard ML, Plaine A. Comprehensive analysis of glycosylphosphatidylinositol-anchored proteins in Candida albicans. EUKARYOTIC CELL 2006; 6:119-33. [PMID: 17189485 PMCID: PMC1797948 DOI: 10.1128/ec.00297-06] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Mathias L Richard
- Laboratoire de Microbiologie et Génétique Moléculaire, INA P-G UMR-INRA1238 UMR-CNRS2585, 78850 Thiverval-Grignon, France.
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Bartnicki-García S. José Ruiz-Herrera - biographical sketch. FEMS Yeast Res 2006; 6:949-56. [PMID: 17042745 DOI: 10.1111/j.1567-1364.2006.00104.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Salomón Bartnicki-García
- Division of Experimental and Applied Biology, Center for Scientific Investigation & Higher Education of Ensenada (CICESE), Ensenada, Baja California, Mexico.
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Rast DM, Baumgartner D, Mayer C, Hollenstein GO. Cell wall-associated enzymes in fungi. PHYTOCHEMISTRY 2003; 64:339-366. [PMID: 12943752 DOI: 10.1016/s0031-9422(03)00350-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review compiles and discusses previous reports on the identity of wall-associated enzymes (WAEs) in fungi and addresses critically the widely different terminologies used in the literature to specify the type of bonding of WAEs to other entities of the cell wall compartment, the extracellular matrix (ECM). A facile and rapid fractionation protocol for catalytically active WAEs is presented, which uses crude cell walls as the experimental material, a variety of test enzymes (including representatives of polysaccharide synthases and hydrolases, phosphatases, gamma-glutamyltransferases, pyridine-nucleotide dehydrogenases and phenol-oxidising enzymes) and a combination of simple hydrophilic and hydrophobic extractants. The protocol provides four fully operationally defined classes of WAEs, with constituent members of each class displaying the same basic type of physicochemical interaction with binding partners in situ. The routine application of the protocol to different species and cell types could yield easily accessible data useful for building-up a general objective information retrieval system of WAEs, suitable as an heuristic basis both for the unravelling of the role and for the biotechnological potentialities of WAEs. A detailed account is given of the function played in the ECM by WAEs in the metabolism of chitin (chitin synthase, chitinase and beta-N-acetylhexosaminidase) and of phenols (tyrosinase).
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Affiliation(s)
- Dora M Rast
- Department of Plant Biology, University of Zürich, CH-8008 Zürich, Switzerland.
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