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Arribas V, Monteoliva L, Hernáez ML, Gil C, Molero G. Unravelling the Role of Candida albicans Prn1 in the Oxidative Stress Response through a Proteomics Approach. Antioxidants (Basel) 2024; 13:527. [PMID: 38790632 PMCID: PMC11118716 DOI: 10.3390/antiox13050527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Candida albicans Prn1 is a protein with an unknown function similar to mammalian Pirin. It also has orthologues in other pathogenic fungi, but not in Saccharomyces cerevisiae. Prn1 highly increases its abundance in response to H2O2 treatment; thus, to study its involvement in the oxidative stress response, a C. albicans prn1∆ mutant and the corresponding wild-type strain SN250 have been studied. Under H2O2 treatment, Prn1 absence led to a higher level of reactive oxygen species (ROS) and a lower survival rate, with a higher percentage of death by apoptosis, confirming its relevant role in oxidative detoxication. The quantitative differential proteomics studies of both strains in the presence and absence of H2O2 indicated a lower increase in proteins with oxidoreductase activity after the treatment in the prn1∆ strain, as well as an increase in proteasome-activating proteins, corroborated by in vivo measurements of proteasome activity, with respect to the wild type. In addition, remarkable differences in the abundance of some transcription factors were observed between mutant and wild-type strains, e.g., Mnl1 or Nrg1, an Mnl1 antagonist. orf19.4850, a protein orthologue to S. cerevisiae Cub1, has shown its involvement in the response to H2O2 and in proteasome function when Prn1 is highly expressed in the wild type.
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Affiliation(s)
- Victor Arribas
- University of Salamanca (USAL), 37008 Salamanca, Spain;
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), 28040 Madrid, Spain; (L.M.); (G.M.)
- Ramon y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - Lucia Monteoliva
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), 28040 Madrid, Spain; (L.M.); (G.M.)
- Ramon y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
| | - María Luisa Hernáez
- Proteomics Unit, Biological Techniques Center, Complutense University of Madrid (UCM), 28040 Madrid, Spain;
| | - Concha Gil
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), 28040 Madrid, Spain; (L.M.); (G.M.)
- Ramon y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
- Proteomics Unit, Biological Techniques Center, Complutense University of Madrid (UCM), 28040 Madrid, Spain;
| | - Gloria Molero
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), 28040 Madrid, Spain; (L.M.); (G.M.)
- Ramon y Cajal Health Research Institute (IRYCIS), 28034 Madrid, Spain
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Alhameed RA, Semreen MH, Hamad M, Giddey AD, Sulaiman A, Al Bataineh MT, Al-Hroub HM, Bustanji Y, Alzoubi KH, Soares NC. Multi-Omics Profiling of Candida albicans Grown on Solid Versus Liquid Media. Microorganisms 2023; 11:2831. [PMID: 38137975 PMCID: PMC10745582 DOI: 10.3390/microorganisms11122831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Candida albicans is a common pathogenic fungus that presents a challenge to healthcare facilities. It can switch between a yeast cell form that diffuses through the bloodstream to colonize internal organs and a filamentous form that penetrates host mucosa. Understanding the pathogen's strategies for environmental adaptation and, ultimately, survival, is crucial. As a complementary study, herein, a multi-omics analysis was performed using high-resolution timsTOF MS to compare the proteomes and metabolomes of Wild Type (WT) Candida albicans (strain DK318) grown on agar plates versus liquid media. Proteomic analysis revealed a total of 1793 proteins and 15,013 peptides. Out of the 1403 identified proteins, 313 proteins were significantly differentially abundant with a p-value < 0.05. Of these, 156 and 157 proteins were significantly increased in liquid and solid media, respectively. Metabolomics analysis identified 192 metabolites in total. The majority (42/48) of the significantly altered metabolites (p-value 0.05 FDR, FC 1.5), mainly amino acids, were significantly higher in solid media, while only 2 metabolites were significantly higher in liquid media. The combined multi-omics analysis provides insight into adaptative morphological changes supporting Candida albicans' life cycle and identifies crucial virulence factors during biofilm formation and bloodstream infection.
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Affiliation(s)
- Rouba Abdulsalam Alhameed
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Mohamad Hamad
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- College of Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Alexander D. Giddey
- Center for Applied and Translational Genomics, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates;
| | - Ashna Sulaiman
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Mohammad T. Al Bataineh
- Center for Biotechnology, Department of Molecular Biology and Genetics, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Hamza M. Al-Hroub
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
| | - Nelson C. Soares
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates; (R.A.A.); (M.H.); (A.S.); (H.M.A.-H.); (Y.B.); (K.H.A.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27227, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Faculdade de Lisboa, NOVA School, 1169-056 Lisbon, Portugal
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MH, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2023; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042 RENNES Cedex, France
| | - Nicolle H. Packer
- Macquarie University, Sydney, NSW 2109, Australia
- Griffith University’s Institute for Glycomics, Sydney, NSW 2109, Australia
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Michael H.A. Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States
| | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou 310024, Zhejiang Province, China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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The adaptive response to alternative carbon sources in the pathogen Candida albicans involves a remodeling of thiol- and glutathione-dependent redox status. Biochem J 2023; 480:197-217. [PMID: 36625375 DOI: 10.1042/bcj20220505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
Candida albicans is an opportunist pathogen responsible for a large spectrum of infections, from superficial mycosis to systemic diseases known as candidiasis. During infection in vivo, Candida albicans must adapt to host microenvironments and this adaptive response is crucial for the survival of this organism, as it facilitates the effective assimilation of alternative carbon sources others than glucose. We performed a global proteomic analysis on the global changes in protein abundance in response to changes in micronutrient levels, and, in parallel, explored changes in the intracellular redox and metabolic status of the cells. We show here that each of the carbon sources considered - glucose, acetate and lactate - induces a unique pattern of response in C. albicans cells, and that some conditions trigger an original and specific adaptive response involving the adaptation of metabolic pathways, but also a complete remodeling of thiol-dependent antioxidant defenses. Protein S-thiolation and the overproduction of reduced glutathione are two components of the response to high glucose concentration. In the presence of acetate, glutathione-dependent oxidative stress occurs, reduced thiol groups bind to proteins, and glutathione is exported out of the cells, these changes probably being triggered by an increase in glutathione-S-transferases. Overall, our results suggest that the role of cellular redox status regulation and defenses against oxidative stress, including the thiol- and glutathione-dependent response, in the adaptive response of C. albicans to alternative carbon sources should be reconsidered.
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Martínez-López R, Hernáez ML, Redondo E, Calvo G, Radau S, Pardo M, Gil C, Monteoliva L. Candida albicans Hyphal Extracellular Vesicles Are Different from Yeast Ones, Carrying an Active Proteasome Complex and Showing a Different Role in Host Immune Response. Microbiol Spectr 2022; 10:e0069822. [PMID: 35604172 PMCID: PMC9241596 DOI: 10.1128/spectrum.00698-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/13/2022] [Indexed: 12/20/2022] Open
Abstract
Candida albicans is the principal causative agent of lethal fungal infections, predominantly in immunocompromised hosts. Extracellular vesicles (EVs) have been described as crucial in the interaction of microorganisms with their host. Since the yeast-to-hypha transition is an important virulence trait with great impact in invasive candidiasis (IC), we have addressed the characterization of EVs secreted by hyphal cells (HEVs) from C. albicans, comparing them to yeast EVs (YEVs). YEVs comprised a larger population of bigger EVs with mainly cell wall proteins, while HEVs were smaller, in general, and had a much higher protein diversity. YEVs were able to rescue the sensitivity of a cell wall mutant against calcofluor white, presumably due to the larger amount of cell wall proteins they contained. On the other hand, HEVs also contained many cytoplasmic proteins related to protein metabolism and intracellular protein transport and the endosomal sorting complexes required for transport (ESCRT) pathway related to exosome biogenesis, pointing to an intracellular origin of HEVs. Interestingly, an active 20S proteasome complex was secreted exclusively in HEVs. Moreover, HEVs contained a greater number of virulence-related proteins. As for their immunogenic role, both types of EV presented immune reactivity with human sera from patients suffering invasive candidiasis; however, under our conditions, only HEVs showed a cytotoxic effect on human macrophages and could elicit the release of tumor necrosis factor alpha (TNF-α) by these macrophages. IMPORTANCE This first analysis of HEVs of C. albicans has shown clear differences between them and the YEVs of C. albicans, showing their relevance and possible use in the discovery of new diagnostic markers and treatment targets against C. albicans infections. The data obtained point to different mechanisms of biogenesis of YEVs and HEVs, as well as different involvements in cell biology and host interaction. YEVs played a more relevant role in cell wall maintenance, while HEVs were more closely related to virulence, as they had greater effects on human immune cells. Importantly, an active 20S proteosome complex was described as a fungal-EV cargo. A deeper study of its role and those of many other proteins exclusively detected in HEVs and involved in different relevant biological processes of this fungus could open up interesting new areas of research in the battle against C. albicans.
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Affiliation(s)
- Raquel Martínez-López
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, Spain
- Ramon y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | | | - Esther Redondo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, Spain
| | - Guillermo Calvo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, Spain
| | - Sonja Radau
- Thermo Fisher Scientific GmbH, Dreieich, Germany
| | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London, United Kingdom
| | - Concha Gil
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, Spain
- Ramon y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Proteomics Unit, Complutense University of Madrid, Madrid, Spain
| | - Lucía Monteoliva
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid (UCM), Madrid, Spain
- Ramon y Cajal Health Research Institute (IRYCIS), Madrid, Spain
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