1
|
Jiang J, Keniya MV, Puri A, Zhan X, Cheng J, Wang H, Lin G, Lee YK, Jaber N, Hassoun Y, Shor E, Shi Z, Lee SH, Xu M, Perlin DS, Dai W. Structural and Biophysical Dynamics of Fungal Plasma Membrane Proteins and Implications for Echinocandin Action in Candida glabrata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596243. [PMID: 38854035 PMCID: PMC11160696 DOI: 10.1101/2024.05.29.596243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Fungal plasma membrane proteins represent key therapeutic targets for antifungal agents, yet their structure and spatial distribution in the native context remain poorly characterized. Herein, we employ an integrative multimodal approach to elucidate the structural and functional organization of plasma membrane protein complexes in Candida glabrata , focusing on prominent and essential membrane proteins, the polysaccharide synthase β-(1,3)-glucan synthase (GS) and the proton pump Pma1. Cryo-electron tomography (cryo-ET) and live cell imaging reveal that GS and Pma1 are heterogeneously distributed into distinct plasma membrane microdomains. Treatment with caspofungin, an echinocandin antifungal that targets GS, alters the plasma membrane and disrupts the native distribution of GS and Pma1. Based on these findings, we propose a model for echinocandin action that considers how drug interactions with the plasma membrane environment lead to inhibition of GS. Our work underscores the importance of interrogating the structural and dynamic characteristics of fungal plasma membrane proteins in situ to understand function and facilitate precisely targeted development of novel antifungal therapies.
Collapse
|
2
|
Scott J, Amich J. The role of methionine synthases in fungal metabolism and virulence. Essays Biochem 2023; 67:853-863. [PMID: 37449444 DOI: 10.1042/ebc20230007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023]
Abstract
Methionine synthases (MetH) catalyse the methylation of homocysteine (Hcy) with 5-methyl-tetrahydrofolate (5, methyl-THF) acting as methyl donor, to form methionine (Met) and tetrahydrofolate (THF). This function is performed by two unrelated classes of enzymes that differ significantly in both their structures and mechanisms of action. The genomes of plants and many fungi exclusively encode cobalamin-independent enzymes (EC.2.1.1.14), while some fungi also possess proteins from the cobalamin-dependent (EC.2.1.1.13) family utilised by humans. Methionine synthase's function connects the methionine and folate cycles, making it a crucial node in primary metabolism, with impacts on important cellular processes such as anabolism, growth and synthesis of proteins, polyamines, nucleotides and lipids. As a result, MetHs are vital for the viability or virulence of numerous prominent human and plant pathogenic fungi and have been proposed as promising broad-spectrum antifungal drug targets. This review provides a summary of the relevance of methionine synthases to fungal metabolism, their potential as antifungal drug targets and insights into the structures of both classes of MetH.
Collapse
Affiliation(s)
- Jennifer Scott
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jorge Amich
- Manchester Fungal Infection Group, Division of Evolution, Infection, and Genomics, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
- Mycology Reference Laboratory (Laboratorio de Referencia e Investigación en Micología [LRIM]), National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| |
Collapse
|
3
|
Molecular targets for antifungals in amino acid and protein biosynthetic pathways. Amino Acids 2021; 53:961-991. [PMID: 34081205 PMCID: PMC8241756 DOI: 10.1007/s00726-021-03007-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 01/22/2023]
Abstract
Fungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems caused by fungal pathogens. There is a growing need for improvement of the availability of antifungal drugs, decreasing their prices and reducing side effects. Searching for novel approaches in this respect, amino acid and protein biosynthesis pathways appear to be competitive. The route that leads from amino acid biosynthesis to protein folding and its activation is rich in enzymes that are descriptive of fungi. Blocking the action of those enzymes often leads to avirulence or growth inhibition. In this review, we want to trace the principal processes of fungi vitality. We present the data of genes encoding enzymes involved in amino acid and protein biosynthesis, potential molecular targets in antifungal chemotherapy, and describe the impact of inhibitors on fungal organisms.
Collapse
|
4
|
Targeting Methionine Synthase in a Fungal Pathogen Causes a Metabolic Imbalance That Impacts Cell Energetics, Growth, and Virulence. mBio 2020; 11:mBio.01985-20. [PMID: 33051366 PMCID: PMC7554668 DOI: 10.1128/mbio.01985-20] [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] [Indexed: 02/07/2023] Open
Abstract
Fungal pathogens are responsible for millions of life-threatening infections on an annual basis worldwide. The current repertoire of antifungal drugs is very limited and, worryingly, resistance has emerged and already become a serious threat to our capacity to treat fungal diseases. The first step to develop new drugs is often to identify molecular targets in the pathogen whose inhibition during infection can prevent its growth. However, the current models are not suitable to validate targets in established infections. Here, we have characterized the promising antifungal target methionine synthase in great detail, using the prominent fungal pathogen Aspergillus fumigatus as a model. We have uncovered the underlying reason for its essentiality and confirmed its druggability. Furthermore, we have optimized the use of a genetic system to show a beneficial effect of targeting methionine synthase in established infections. Therefore, we believe that antifungal drugs to target methionine synthase should be pursued and additionally, we provide a model that permits gaining information about the validity of antifungal targets in established infections. There is an urgent need to develop novel antifungals to tackle the threat fungal pathogens pose to human health. Here, we have performed a comprehensive characterization and validation of the promising target methionine synthase (MetH). We show that in Aspergillus fumigatus the absence of this enzymatic activity triggers a metabolic imbalance that causes a reduction in intracellular ATP, which prevents fungal growth even in the presence of methionine. Interestingly, growth can be recovered in the presence of certain metabolites, which shows that metH is a conditionally essential gene and consequently should be targeted in established infections for a more comprehensive validation. Accordingly, we have validated the use of the tetOFF genetic model in fungal research and improved its performance in vivo to achieve initial validation of targets in models of established infection. We show that repression of metH in growing hyphae halts growth in vitro, which translates into a beneficial effect when targeting established infections using this model in vivo. Finally, a structure-based virtual screening of methionine synthases reveals key differences between the human and fungal structures and unravels features in the fungal enzyme that can guide the design of novel specific inhibitors. Therefore, methionine synthase is a valuable target for the development of new antifungals.
Collapse
|
5
|
Wang Y, Weisenhorn E, MacDiarmid CW, Andreini C, Bucci M, Taggart J, Banci L, Russell J, Coon JJ, Eide DJ. The cellular economy of the Saccharomyces cerevisiae zinc proteome. Metallomics 2018; 10:1755-1776. [PMID: 30358795 PMCID: PMC6291366 DOI: 10.1039/c8mt00269j] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is an essential cofactor for many proteins. A key mechanism of zinc homeostasis during deficiency is "zinc sparing" in which specific zinc-binding proteins are repressed to reduce the cellular requirement. In this report, we evaluated zinc sparing across the zinc proteome of Saccharomyces cerevisiae. The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. Protein abundance was determined by mass spectrometry. In zinc-replete cells, we detected over 2500 proteins among which 229 were zinc proteins. Based on copy number estimates and binding stoichiometries, a replete cell contains ∼9 million zinc-binding sites on proteins. During zinc deficiency, many zinc proteins decreased in abundance and the zinc-binding requirement decreased to ∼5 million zinc atoms per cell. Many of these effects were due at least in part to changes in mRNA levels rather than simply protein degradation. Measurements of cellular zinc content showed that the level of zinc atoms per cell dropped from over 20 million in replete cells to only 1.7 million in deficient cells. These results confirmed the ability of replete cells to store excess zinc and suggested that the majority of zinc-binding sites on proteins in deficient cells are either unmetalated or mismetalated. Our analysis of two abundant zinc proteins, Fba1 aldolase and Met6 methionine synthetase, supported that hypothesis. Thus, we have discovered widespread zinc sparing mechanisms and obtained evidence of a high accumulation of zinc proteins that lack their cofactor during deficiency.
Collapse
Affiliation(s)
- Yirong Wang
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Sahu U, Rajendra VKH, Kapnoor SS, Bhagavat R, Chandra N, Rangarajan PN. Methionine synthase is localized to the nucleus in Pichia pastoris and Candida albicans and to the cytoplasm in Saccharomyces cerevisiae. J Biol Chem 2017; 292:14730-14746. [PMID: 28701466 DOI: 10.1074/jbc.m117.783019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/10/2017] [Indexed: 11/06/2022] Open
Abstract
Methionine synthase (MS) catalyzes methylation of homocysteine, the last step in the biosynthesis of methionine, which is essential for the regeneration of tetrahydrofolate and biosynthesis of S-adenosylmethionine. Here, we report that MS is localized to the nucleus of Pichia pastoris and Candida albicans but is cytoplasmic in Saccharomyces cerevisiae The P. pastoris strain carrying a deletion of the MET6 gene encoding MS (Ppmet6) exhibits methionine as well as adenine auxotrophy indicating that MS is required for methionine as well as adenine biosynthesis. Nuclear localization of P. pastoris MS (PpMS) was abrogated by the deletion of 107 C-terminal amino acids or the R742A mutation. In silico analysis of the PpMS structure indicated that PpMS may exist in a dimer-like configuration in which Arg-742 of a monomer forms a salt bridge with Asp-113 of another monomer. Biochemical studies indicate that R742A as well as D113R mutations abrogate nuclear localization of PpMS and its ability to reverse methionine auxotrophy of Ppmet6 Thus, association of two PpMS monomers through the interaction of Arg-742 and Asp-113 is essential for catalytic activity and nuclear localization. When PpMS is targeted to the cytoplasm employing a heterologous nuclear export signal, it is expressed at very low levels and is unable to reverse methionine and adenine auxotrophy of Ppmet6 Thus, nuclear localization is essential for the stability and function of MS in P. pastoris. We conclude that nuclear localization of MS is a unique feature of respiratory yeasts such as P. pastoris and C. albicans, and it may have novel moonlighting functions in the nucleus.
Collapse
Affiliation(s)
- Umakant Sahu
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Vinod K H Rajendra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Shankar S Kapnoor
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Raghu Bhagavat
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Nagasuma Chandra
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pundi N Rangarajan
- From the Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
7
|
Uranga CC, Ghassemian M, Hernández-Martínez R. Novel proteins from proteomic analysis of the trunk disease fungus Lasiodiplodia theobromae (Botryosphaeriaceae). BIOCHIMIE OPEN 2017; 4:88-98. [PMID: 29450146 PMCID: PMC5802045 DOI: 10.1016/j.biopen.2017.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/02/2017] [Indexed: 11/21/2022]
Abstract
Many basic science questions remain regarding protein functions in the pathogen: host interaction, especially in the trunk disease fungi family, the Botryosphaeriaceae, which are a global problem for economically important plants, especially fruiting trees. Proteomics is a highly useful technology for studying protein expression and for discovering novel proteins in unsequenced and poorly annotated organisms. Current fungal proteomics approaches involve 2D SDS-PAGE and extensive, complex, protein extraction methodologies. In this work, a modified Folch extraction was applied to protein extraction to perform both de novo peptide sequencing and peptide fragmentation analysis/protein identification of the plant and human fungal pathogen Lasiodiplodia theobromae. Both bioinformatics approaches yielded novel peptide sequences from proteins produced by L. theobromae in the presence of exogenous triglycerides and glucose. These proteins and the functions they may possess could be targeted for further functional characterization and validation efforts, due to their potential uses in biotechnology and as new paradigms for understanding fungal biochemistry, such as the finding of allergenic enolases, as well as various novel proteases, including zinc metalloproteinases homologous to those found in snake venom. This work contributes to genomic annotation efforts, which, hand in hand with genomic sequencing, will help improve fungal bioinformatics databases for future studies of Botryosphaeriaceae. All data, including raw data, are available via the ProteomeXchange data repository with identifier PXD005283. This is the first study of its kind in Botryosphaeriaceae.
Collapse
Affiliation(s)
- Carla C. Uranga
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, 22860 Ensenada, B.C., Mexico
| | - Majid Ghassemian
- University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Rufina Hernández-Martínez
- Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Carretera Ensenada-Tijuana 3918, Zona Playitas, 22860 Ensenada, B.C., Mexico
| |
Collapse
|
8
|
Lakshman DK, Roberts DP, Garrett WM, Natarajan SS, Darwish O, Alkharouf N, Pain A, Khan F, Jambhulkar PP, Mitra A. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:3101-3110. [PMID: 27019116 DOI: 10.1021/acs.jafc.5b05735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. This study used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions, the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.
Collapse
Affiliation(s)
- Dilip K Lakshman
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Daniel P Roberts
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Wesley M Garrett
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Savithiry S Natarajan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Nadim Alkharouf
- Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
| | - Arnab Pain
- Pathogen Genomics, KAUST , Thuwal, Saudi Arabia 23955
| | - Farooq Khan
- Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | | | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska , Lincoln, Nebraska 68583, United States
| |
Collapse
|
9
|
Wheatley RW, Ng KK, Kapoor M. Fungal cobalamin-independent methionine synthase: Insights from the model organism, Neurospora crassa. Arch Biochem Biophys 2016; 590:125-137. [DOI: 10.1016/j.abb.2015.11.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/10/2015] [Accepted: 11/21/2015] [Indexed: 10/22/2022]
|
10
|
Ubhi DK, Robertus JD. The Cobalamin-Independent Methionine Synthase Enzyme Captured in a Substrate-Induced Closed Conformation. J Mol Biol 2015; 427:901-909. [DOI: 10.1016/j.jmb.2014.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/19/2014] [Accepted: 12/21/2014] [Indexed: 10/24/2022]
|