1
|
Schuntermann DB, Jaskolowski M, Reynolds NM, Vargas-Rodriguez O. The central role of transfer RNAs in mistranslation. J Biol Chem 2024; 300:107679. [PMID: 39154912 DOI: 10.1016/j.jbc.2024.107679] [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: 04/25/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
Transfer RNAs (tRNA) are essential small non-coding RNAs that enable the translation of genomic information into proteins in all life forms. The principal function of tRNAs is to bring amino acid building blocks to the ribosomes for protein synthesis. In the ribosome, tRNAs interact with messenger RNA (mRNA) to mediate the incorporation of amino acids into a growing polypeptide chain following the rules of the genetic code. Accurate interpretation of the genetic code requires tRNAs to carry amino acids matching their anticodon identity and decode the correct codon on mRNAs. Errors in these steps cause the translation of codons with the wrong amino acids (mistranslation), compromising the accurate flow of information from DNA to proteins. Accumulation of mutant proteins due to mistranslation jeopardizes proteostasis and cellular viability. However, the concept of mistranslation is evolving, with increasing evidence indicating that mistranslation can be used as a mechanism for survival and acclimatization to environmental conditions. In this review, we discuss the central role of tRNAs in modulating translational fidelity through their dynamic and complex interplay with translation factors. We summarize recent discoveries of mistranslating tRNAs and describe the underlying molecular mechanisms and the specific conditions and environments that enable and promote mistranslation.
Collapse
Affiliation(s)
- Dominik B Schuntermann
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Mateusz Jaskolowski
- Department of Biology, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Noah M Reynolds
- School of Integrated Sciences, Sustainability, and Public Health, University of Illinois Springfield, Springfield, Illinois, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
| |
Collapse
|
2
|
Correia I, Oliveira C, Reis A, Guimarães AR, Aveiro S, Domingues P, Bezerra AR, Vitorino R, Moura G, Santos MAS. A Proteogenomic Pipeline for the Analysis of Protein Biosynthesis Errors in the Human Pathogen Candida albicans. Mol Cell Proteomics 2024; 23:100818. [PMID: 39047911 DOI: 10.1016/j.mcpro.2024.100818] [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: 11/24/2023] [Revised: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024] Open
Abstract
Candida albicans is a diploid pathogen known for its ability to live as a commensal fungus in healthy individuals but causing both superficial infections and disseminated candidiasis in immunocompromised patients where it is associated with high morbidity and mortality. Its success in colonizing the human host is attributed to a wide range of virulence traits that modulate interactions between the host and the pathogen, such as optimal growth rate at 37 °C, the ability to switch between yeast and hyphal forms, and a remarkable genomic and phenotypic plasticity. A fascinating aspect of its biology is a prominent heterogeneous proteome that arises from frequent genomic rearrangements, high allelic variation, and high levels of amino acid misincorporations in proteins. This leads to increased morphological and physiological phenotypic diversity of high adaptive potential, but the scope of such protein mistranslation is poorly understood due to technical difficulties in detecting and quantifying amino acid misincorporation events in complex protein samples. We have developed and optimized mass spectrometry and bioinformatics pipelines capable of identifying rare amino acid misincorporation events at the proteome level. We have also analyzed the proteomic profile of an engineered C. albicans strain that exhibits high level of leucine misincorporation at protein CUG sites and employed an in vivo quantitative gain-of-function fluorescence reporter system to validate our LC-MS/MS data. C. albicans misincorporates amino acids above the background level at protein sites of diverse codons, particularly at CUG, confirming our previous data on the quantification of leucine incorporation at single CUG sites of recombinant reporter proteins, but increasing misincorporation of Leucine at these sites does not alter the translational fidelity of the other codons. These findings indicate that the C. albicans statistical proteome exceeds prior estimates, suggesting that its highly plastic phenome may also be modulated by environmental factors due to translational ambiguity.
Collapse
Affiliation(s)
- Inês Correia
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal.
| | - Carla Oliveira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Ana Rita Guimarães
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Susana Aveiro
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Pedro Domingues
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ana Rita Bezerra
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Gabriela Moura
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal
| | - Manuel A S Santos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences (DCM), University of Aveiro, Aveiro, Portugal; Multidisciplinary Institute of Ageing (MIA-Portugal), University of Coimbra, Coimbra, Portugal.
| |
Collapse
|
3
|
Lin Y, Jung H, Bulman CA, Ng J, Vinck R, O'Beirne C, Zhong S, Moser MS, Tricoche N, Peguero R, Li RW, Urban JF, Le Pape P, Pagniez F, Moretto M, Weil T, Lustigman S, Cariou K, Mitreva M, Sakanari JA, Gasser G. Discovery of New Broad-Spectrum Anti-Infectives for Eukaryotic Pathogens Using Bioorganometallic Chemistry. J Med Chem 2023; 66:15867-15882. [PMID: 38009931 DOI: 10.1021/acs.jmedchem.3c01333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Drug resistance observed with many anti-infectives clearly highlights the need for new broad-spectrum agents to treat especially neglected tropical diseases (NTDs) caused by eukaryotic parasitic pathogens, including fungal infections. Herein, we show that the simple modification of one of the most well-known antifungal drugs, fluconazole, with organometallic moieties not only improves the activity of the parent drug but also broadens the scope of application of the new derivatives. These compounds were highly effective in vivo against pathogenic fungal infections and potent against parasitic worms such as Brugia, which causes lymphatic filariasis and Trichuris, one of the soil-transmitted helminths that infects millions of people globally. Notably, the identified molecular targets indicate a mechanism of action that differs greatly from that of the parental antifungal drug, including targets involved in biosynthetic pathways that are absent in humans, offering great potential to expand our armamentarium against drug-resistant fungal infections and neglected tropical diseases (NTDs) targeted for elimination by 2030.
Collapse
Affiliation(s)
- Yan Lin
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Hyeim Jung
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Christina A Bulman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - James Ng
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Robin Vinck
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Cillian O'Beirne
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Shuai Zhong
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Matthew S Moser
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Nancy Tricoche
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Ricardo Peguero
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Robert W Li
- United States Department of Agricultural Research Service (USDA-ARS), Animal Parasitic Diseases Laboratory, Beltsville, Maryland 20705, United States
| | - Joseph F Urban
- United States Department of Agriculture, Diet, Genomics and Immunology Laboratory, Beltsville, Maryland 20705, United States
| | - Patrice Le Pape
- Nantes Université, CHU de Nantes, Cibles et Médicaments des Infections et de l'Immunité, IICiMed, UR 1155, F-44000 Nantes, France
| | - Fabrice Pagniez
- Nantes Université, CHU de Nantes, Cibles et Médicaments des Infections et de l'Immunité, IICiMed, UR 1155, F-44000 Nantes, France
| | - Marco Moretto
- Fondazione Edmund Mach Via E. Mach 1, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Tobias Weil
- Fondazione Edmund Mach Via E. Mach 1, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Sara Lustigman
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Kevin Cariou
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, United States
| | - Judy A Sakanari
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| |
Collapse
|
4
|
Lockhart SR, Chowdhary A, Gold JAW. The rapid emergence of antifungal-resistant human-pathogenic fungi. Nat Rev Microbiol 2023; 21:818-832. [PMID: 37648790 DOI: 10.1038/s41579-023-00960-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.
Collapse
Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
5
|
Choudhary S, Mundodi V, Smith AD, Kadosh D. Genome-wide translational response of Candida albicans to fluconazole treatment. Microbiol Spectr 2023; 11:e0257223. [PMID: 37610232 PMCID: PMC10580883 DOI: 10.1128/spectrum.02572-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 08/24/2023] Open
Abstract
Azoles are commonly used for the treatment of fungal infections, and the ability of human fungal pathogens to rapidly respond to azole treatment is critical for the development of antifungal resistance. While the roles of genetic mutations, chromosomal rearrangements, and transcriptional mechanisms in azole resistance have been well-characterized, very little is known about post-transcriptional and translational mechanisms that drive this process. In addition, most previous genome-wide studies have focused on transcriptional responses to azole treatment and likely serve as inaccurate proxies for changes in protein expression due to extensive post-transcriptional and translational regulation. In this study, we use ribosome profiling to provide the first picture of the global translational response of a major human fungal pathogen, Candida albicans, to treatment with fluconazole (Flu), one of the most widely used azole drugs. We identify sets of genes showing significantly altered translational efficiency, including genes associated with a variety of biological processes such as the cell cycle, DNA repair, cell wall/cell membrane biosynthesis, transport, signaling, DNA- and RNA-binding activities, and protein synthesis. We observe both similarities and differences among the most highly represented gene categories (as defined by gene ontology) that are regulated by fluconazole at the translational vs transcriptional levels. Importantly, however, very few genes that are translationally regulated by fluconazole are also controlled transcriptionally under this condition. Our findings suggest that C. albicans possesses distinct translational mechanisms that are important for the response to antifungal treatment, which could eventually be targeted by novel antifungal therapies. IMPORTANCE Azoles are one of the most commonly used drug classes to treat human fungal pathogens. While point mutations, chromosomal rearrangements, and transcriptional mechanisms that drive azole resistance have been well-characterized, we know very little about the role of translational mechanisms. In this study, we determined the global translational profile of genes that are expressed in the major human fungal pathogen Candida albicans in response to fluconazole, one of the most widely used azole drugs. We find both similarities and differences among the most highly represented categories of genes regulated by fluconazole at the transcriptional and translational levels. Interestingly, however, many of the specific genes that are regulated by fluconazole at the translational level do not appear to be controlled by transcriptional mechanisms under this condition. Our results suggest that distinct C. albicans translational mechanisms control the response to antifungals and could eventually be targeted in the development of new therapies.
Collapse
Affiliation(s)
- Saket Choudhary
- Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Vasanthakrishna Mundodi
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Andrew D. Smith
- Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - David Kadosh
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| |
Collapse
|
6
|
Sharma C, Kadosh D. Post-transcriptional control of antifungal resistance in human fungal pathogens. Crit Rev Microbiol 2023; 49:469-484. [PMID: 35634915 PMCID: PMC9766424 DOI: 10.1080/1040841x.2022.2080527] [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: 01/12/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 11/03/2022]
Abstract
Global estimates suggest that over 300 million individuals of all ages are affected by serious fungal infections every year, culminating in about 1.7 million deaths. The societal and economic burden on the public health sector due to opportunistic fungal pathogens is quite significant, especially among immunocompromised patients. Despite the high clinical significance of these infectious agents, treatment options are limited with only three major classes of antifungal drugs approved for use. Clinical management of fungal diseases is further compromised by the emergence of antifungal resistant strains. Transcriptional and genetic mechanisms that control drug resistance in human fungal pathogens are well-studied and include drug target alteration, upregulation of drug efflux pumps as well as changes in drug affinity and abundance of target proteins. In this review, we highlight several recently discovered novel post-transcriptional mechanisms that control antifungal resistance, which involve regulation at the translational, post-translational, epigenetic, and mRNA stability levels. The discovery of many of these novel mechanisms has opened new avenues for the development of more effective antifungal treatment strategies and new insights, perspectives, and future directions that will facilitate this process are discussed.
Collapse
Affiliation(s)
- Cheshta Sharma
- Department of Microbiology, Immunology and Molecular Genetics University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - David Kadosh
- Department of Microbiology, Immunology and Molecular Genetics University of Texas Health Science Center at San Antonio, San Antonio, TX
| |
Collapse
|
7
|
Ibba M. The Pros of changing tRNA identity. J Biol Chem 2023; 299:104974. [PMID: 37380073 PMCID: PMC10365949 DOI: 10.1016/j.jbc.2023.104974] [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] [Accepted: 06/23/2023] [Indexed: 06/30/2023] Open
Abstract
The notion that errors in protein synthesis are universally harmful to the cell has been questioned by findings that suggest such mistakes may sometimes be beneficial. However, how often these beneficial mistakes arise from programmed changes in gene expression as opposed to reduced accuracy of the translation machinery is still unclear. A new study published in JBC shows that some bacteria have beneficially evolved the ability to mistranslate specific parts of the genetic code, a trait that allows improved antibiotic resistance.
Collapse
Affiliation(s)
- Michael Ibba
- Schmid College of Science and Technology, Chapman University, Orange, California, USA.
| |
Collapse
|
8
|
Wang WY, Cai HQ, Qu SY, Lin WH, Liang CC, Liu H, Xie ZX, Yuan YJ. Genomic Variation-Mediating Fluconazole Resistance in Yeast. Biomolecules 2022; 12:biom12060845. [PMID: 35740970 PMCID: PMC9221393 DOI: 10.3390/biom12060845] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal infections pose a serious and growing threat to public health. These infections can be treated with antifungal drugs by killing hazardous fungi in the body. However, the resistance can develop over time when fungi are exposed to antifungal drugs by generating genomic variations, including mutation, aneuploidy, and loss of heterozygosity. The variations could reduce the binding affinity of a drug to its target or block the pathway through which drugs exert their activity. Here, we review genomic variation-mediating fluconazole resistance in the yeast Candida, with the hope of highlighting the functional consequences of genomic variations for the antifungal resistance.
Collapse
|
9
|
Ribeiro GF, Denes E, Heaney H, Childers DS. What 'Omics Can Tell Us About Antifungal Adaptation. FEMS Yeast Res 2021; 21:6484793. [PMID: 34958354 PMCID: PMC8755904 DOI: 10.1093/femsyr/foab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/22/2021] [Indexed: 12/01/2022] Open
Abstract
Invasive candidiasis, the most frequent healthcare-associated invasive fungal infection, is commonly caused by Candida albicans. However, in recent years other antifungal-resistant Candida species—namely Candida glabrata and Candidaauris—have emerged as a serious matter of concern. Much of our understanding of the mechanisms regulating antifungal resistance and tolerance relies on studies utilizing C. albicans, C. glabrataand the model yeast Saccharomyces cerevisiae. ‘Omics studies have been used to describe alterations in metabolic, genomic and transcriptomic expression profiles upon antifungal treatment of fungal cells. The physiological changes identified by these approaches could significantly affect fungal fitness in the host and survival during antifungal challenge, as well as provide further understanding of clinical resistance. Thus, this review aims to comparatively address ‘omics data for C. albicans, C. glabrata andS. cerevisiae published from 2000 to 2021 to identify what these technologies can tell us regarding cellular responses to antifungal therapy. We will also highlight possible effects on pathogen survival and identify future avenues for antifungal research.
Collapse
Affiliation(s)
- Gabriela Fior Ribeiro
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Eszter Denes
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Helen Heaney
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| | - Delma S Childers
- University of Aberdeen, Institute of Medical Sciences, Aberdeen Fungal Group, Aberdeen, UK, AB25 2ZD
| |
Collapse
|
10
|
Accounting for the Biological Complexity of Pathogenic Fungi in Phylogenetic Dating. J Fungi (Basel) 2021; 7:jof7080661. [PMID: 34436200 PMCID: PMC8400180 DOI: 10.3390/jof7080661] [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: 07/04/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
In the study of pathogen evolution, temporal dating of phylogenies provides information on when species and lineages may have diverged in the past. When combined with spatial and epidemiological data in phylodynamic models, these dated phylogenies can also help infer where and when outbreaks occurred, how pathogens may have spread to new geographic locations and/or niches, and how virulence or drug resistance has developed over time. Although widely applied to viruses and, increasingly, to bacterial pathogen outbreaks, phylogenetic dating is yet to be widely used in the study of pathogenic fungi. Fungi are complex organisms with several biological processes that could present issues with appropriate inference of phylogenies, clock rates, and divergence times, including high levels of recombination and slower mutation rates although with potentially high levels of mutation rate variation. Here, we discuss some of the key methodological challenges in accurate phylogeny reconstruction for fungi in the context of the temporal analyses conducted to date and make recommendations for future dating studies to aid development of a best practices roadmap in light of the increasing threat of fungal outbreaks and antifungal drug resistance worldwide.
Collapse
|
11
|
Rubbiani R, Weil T, Tocci N, Mastrobuoni L, Jeger S, Moretto M, Ng J, Lin Y, Hess J, Ferrari S, Kaech A, Young L, Spencer J, Moore AL, Cariou K, Renga G, Pariano M, Romani L, Gasser G. In vivo active organometallic-containing antimycotic agents. RSC Chem Biol 2021; 2:1263-1273. [PMID: 34458840 PMCID: PMC8341145 DOI: 10.1039/d1cb00123j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022] Open
Abstract
Fungal infections represent a global problem, notably for immunocompromised patients in hospital, COVID-19 patient wards and care home settings, and the ever-increasing emergence of multidrug resistant fungal strains is a sword of Damocles hanging over many healthcare systems. Azoles represent the mainstay of antifungal drugs, and their mode of action involves the binding mode of these molecules to the fungal lanosterol 14α-demethylase target enzyme. In this study, we have prepared and characterized four novel organometallic derivatives of the frontline antifungal drug fluconazole (1a-4a). Very importantly, enzyme inhibition and chemogenomic profiling demonstrated that lanosterol 14α-demethylase, as for fluconazole, was the main target of the most active compound of the series, (N-(ferrocenylmethyl)-2-(2,4-difluorophenyl)-2-hydroxy-N-methyl-3-(1H-1,2,4-triazol-1-yl)propan-1-aminium chloride, 2a). Transmission electron microscopy (TEM) studies suggested that 2a induced a loss in cell wall integrity as well as intracellular features ascribable to late apoptosis or necrosis. The impressive activity of 2a was further confirmed on clinical isolates, where antimycotic potency up to 400 times higher than fluconazole was observed. Also, 2a showed activity towards azole-resistant strains. This finding is very interesting since the primary target of 2a is the same as that of fluconazole, emphasizing the role played by the organometallic moiety. In vivo experiments in a mice model of Candida infections revealed that 2a reduced the fungal growth and dissemination but also ameliorated immunopathology, a finding suggesting that 2a is active in vivo with added activity on the host innate immune response.
Collapse
Affiliation(s)
- Riccardo Rubbiani
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Tobias Weil
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1 38010 San Michele all'Adige Italy
| | - Noemi Tocci
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1 38010 San Michele all'Adige Italy
| | - Luciano Mastrobuoni
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Severin Jeger
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Marco Moretto
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1 38010 San Michele all'Adige Italy
| | - James Ng
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Yan Lin
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Jeannine Hess
- Department of Chemistry, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Luke Young
- Department of Chemistry, School of Life Sciences, University of Sussex Brighton BN1 9QJ UK
| | - John Spencer
- Department of Chemistry, School of Life Sciences, University of Sussex Brighton BN1 9QJ UK
| | - Anthony L Moore
- Biochemistry & Biomedicine, School of Life Sciences, University of Sussex Brighton BN1 9QG UK
| | - Kevin Cariou
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| | - Giorgia Renga
- University of Perugia, Department of Medicine and Surgery, Piazzale Lucio Severi - Polo Unico Sant'Andrea delle Fratte 06132 Perugia Italy
| | - Marilena Pariano
- University of Perugia, Department of Medicine and Surgery, Piazzale Lucio Severi - Polo Unico Sant'Andrea delle Fratte 06132 Perugia Italy
| | - Luigina Romani
- University of Perugia, Department of Medicine and Surgery, Piazzale Lucio Severi - Polo Unico Sant'Andrea delle Fratte 06132 Perugia Italy
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France
| |
Collapse
|
12
|
Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic Cryptococcus. Microorganisms 2021; 9:microorganisms9081579. [PMID: 34442658 PMCID: PMC8398696 DOI: 10.3390/microorganisms9081579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022] Open
Abstract
To better understand the potential factors contributing to genome instability and phenotypic diversity, we conducted mutation accumulation (MA) experiments for 120 days for 7 diploid cryptococcal hybrids under fluconazole (10 MA lines each) and non-fluconazole conditions (10 MA lines each). The genomic DNA content, loss of heterozygosity (LOH) rate, growth ability, and fluconazole susceptibility were determined for all 140 evolved cultures. Compared to that of their ancestral clones, the evolved clones showed: (i) genomic DNA content changes ranging from ~22% less to ~27% more, and (ii) reduced, similar, and increased phenotypic values for each tested trait, with most evolved clones displaying increased growth at 40 °C and increased fluconazole resistance. Aside from the ancestral multi-locus genotypes (MLGs) and heterozygosity patterns (MHPs), 77 unique MLGs and 70 unique MPHs were identified among the 140 evolved cultures at day 120. The average LOH rates of the MA lines in the absence and presence of fluconazole were similar at 1.27 × 10−4 and 1.38 × 10−4 LOH events per MA line per mitotic division, respectively. While LOH rates varied among MA lines from different ancestors, there was no apparent correlation between the genetic divergence of the parental haploid genomes within ancestral clones and LOH rates. Together, our results suggest that hybrids between diverse lineages of the human pathogenic Cryptococcus can generate significant genotypic and phenotypic diversities during asexual reproduction.
Collapse
|
13
|
Bezerra AR, Oliveira C, Correia I, Guimarães AR, Sousa G, Carvalho MJ, Moura G, Santos MAS. The role of non-standard translation in Candida albicans pathogenesis. FEMS Yeast Res 2021; 21:6280978. [PMID: 34021562 PMCID: PMC8178436 DOI: 10.1093/femsyr/foab032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.
Collapse
Affiliation(s)
- Ana Rita Bezerra
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Oliveira
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Inês Correia
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana Rita Guimarães
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gonçalo Sousa
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria João Carvalho
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Gabriela Moura
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Manuel A S Santos
- Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| |
Collapse
|
14
|
Ponde NO, Lortal L, Ramage G, Naglik JR, Richardson JP. Candida albicans biofilms and polymicrobial interactions. Crit Rev Microbiol 2021; 47:91-111. [PMID: 33482069 PMCID: PMC7903066 DOI: 10.1080/1040841x.2020.1843400] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/05/2020] [Accepted: 10/25/2020] [Indexed: 12/16/2022]
Abstract
Candida albicans is a common fungus of the human microbiota. While generally a harmless commensal in healthy individuals, several factors can lead to its overgrowth and cause a range of complications within the host, from localized superficial infections to systemic life-threatening disseminated candidiasis. A major virulence factor of C. albicans is its ability to form biofilms, a closely packed community of cells that can grow on both abiotic and biotic substrates, including implanted medical devices and mucosal surfaces. These biofilms are extremely hard to eradicate, are resistant to conventional antifungal treatment and are associated with high morbidity and mortality rates, making biofilm-associated infections a major clinical challenge. Here, we review the current knowledge of the processes involved in C. albicans biofilm formation and development, including the central processes of adhesion, extracellular matrix production and the transcriptional network that regulates biofilm development. We also consider the advantages of the biofilm lifestyle and explore polymicrobial interactions within multispecies biofilms that are formed by C. albicans and selected microbial species.
Collapse
Affiliation(s)
- Nicole O. Ponde
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, United Kingdom
| | - Léa Lortal
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, United Kingdom
| | - Gordon Ramage
- School of Medicine, Dentistry & Nursing, Glasgow Dental School and Hospital, Faculty of Medicine, University of Glasgow, G2 3JZ, United Kingdom
| | - Julian R. Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, United Kingdom
| | - Jonathan P. Richardson
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, SE1 9RT, United Kingdom
| |
Collapse
|
15
|
Ryu HY, Ahn SH, Hochstrasser M. SUMO and cellular adaptive mechanisms. Exp Mol Med 2020; 52:931-939. [PMID: 32591648 PMCID: PMC7338444 DOI: 10.1038/s12276-020-0457-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin family member SUMO is a covalent regulator of proteins that functions in response to various stresses, and defects in SUMO-protein conjugation or deconjugation have been implicated in multiple diseases. The loss of the Ulp2 SUMO protease, which reverses SUMO-protein modifications, in the model eukaryote Saccharomyces cerevisiae is severely detrimental to cell fitness and has emerged as a useful model for studying how cells adapt to SUMO system dysfunction. Both short-term and long-term adaptive mechanisms are triggered depending on the length of time cells spend without this SUMO chain-cleaving enzyme. Such short-term adaptations include a highly specific multichromosome aneuploidy and large changes in ribosomal gene transcription. While aneuploid ulp2Δ cells survive, they suffer severe defects in growth and stress resistance. Over many generations, euploidy is restored, transcriptional programs are adjusted, and specific genetic changes that compensate for the loss of the SUMO protease are observed. These long-term adapted cells grow at normal rates with no detectable defects in stress resistance. In this review, we examine the connections between SUMO and cellular adaptive mechanisms more broadly. Cellular stress caused by disrupting attachment of the ubiquitous small ubiquitin-like modifier (SUMO) proteins, which are present in most organisms and regulate numerous DNA processes and stress responses by attaching to key proteins, results in some remarkable adaptations. Mark Hochstrasser at Yale University, New Haven, USA, and co-workers review how this “sumoylation” is reversed by protease enzymes, and how imbalances between sumoylation and desumoylation may be linked to diseases including cancer. When certain SUMO proteases are deliberately disrupted, the cells quickly become aneuploid, i.e., carry an abnormal number of chromosomes. These cells show severe growth defects, but over many generations they regain the normal number of chromosomes. They also undergo genetic changes that promote alternative mechanisms that compensate for losing the SUMO protease and facilitate the same efficient stress responses as the original cells.
Collapse
Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.,Brain Science and Engineering Institute, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seong Hoon Ahn
- Department of Molecular and Life Science, College of Science and Convergence Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| |
Collapse
|
16
|
Salazar SB, Simões RS, Pedro NA, Pinheiro MJ, Carvalho MFNN, Mira NP. An Overview on Conventional and Non-Conventional Therapeutic Approaches for the Treatment of Candidiasis and Underlying Resistance Mechanisms in Clinical Strains. J Fungi (Basel) 2020; 6:E23. [PMID: 32050673 PMCID: PMC7151124 DOI: 10.3390/jof6010023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023] Open
Abstract
Fungal infections and, in particular, those caused by species of the Candida genus, are growing at an alarming rate and have high associated rates of mortality and morbidity. These infections, generally referred as candidiasis, range from common superficial rushes caused by an overgrowth of the yeasts in mucosal surfaces to life-threatening disseminated mycoses. The success of currently used antifungal drugs to treat candidiasis is being endangered by the continuous emergence of resistant strains, specially among non-albicans Candida species. In this review article, the mechanisms of action of currently used antifungals, with emphasis on the mechanisms of resistance reported in clinical isolates, are reviewed. Novel approaches being taken to successfully inhibit growth of pathogenic Candida species, in particular those based on the exploration of natural or synthetic chemicals or on the activity of live probiotics, are also reviewed. It is expected that these novel approaches, either used alone or in combination with traditional antifungals, may contribute to foster the identification of novel anti-Candida therapies.
Collapse
Affiliation(s)
- Sara B. Salazar
- Department of Bioengineering, Institute of Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (S.B.S.); (R.S.S.); (N.A.P.); (M.J.P.)
| | - Rita S. Simões
- Department of Bioengineering, Institute of Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (S.B.S.); (R.S.S.); (N.A.P.); (M.J.P.)
| | - Nuno A. Pedro
- Department of Bioengineering, Institute of Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (S.B.S.); (R.S.S.); (N.A.P.); (M.J.P.)
| | - Maria Joana Pinheiro
- Department of Bioengineering, Institute of Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (S.B.S.); (R.S.S.); (N.A.P.); (M.J.P.)
| | - Maria Fernanda N. N. Carvalho
- Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal;
| | - Nuno P. Mira
- Department of Bioengineering, Institute of Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (S.B.S.); (R.S.S.); (N.A.P.); (M.J.P.)
| |
Collapse
|
17
|
Franco A, Tocci N, Guella G, Dell’Agli M, Sangiovanni E, Perenzoni D, Vrhovsek U, Mattivi F, Manca G. Myrtle Seeds ( Myrtus communis L.) as a Rich Source of the Bioactive Ellagitannins Oenothein B and Eugeniflorin D 2. ACS OMEGA 2019; 4:15966-15974. [PMID: 31592467 PMCID: PMC6776983 DOI: 10.1021/acsomega.9b02010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
The increasing popularity of "Mirto" liqueur, produced from Myrtus communis berries, has led to the planting of domesticated cultivars, expanding myrtle berry production. To promote the use of cultivated berries, the content in the nutraceutical compounds ellagitannins has been investigated both in spontaneous and cultivated fruits. Oenothein B and eugeniflorin D2, characterized by 1H and 13C NMR, were isolated and quantified using ultrahigh-performance liquid chromatography-diode array detector-tandem mass spectrometry (UPLC-DAD-MS/MS). The antifungal and anti-inflammatory activities of oenothein B were assayed in vitro. Large amounts of oenothein B and eugeniflorin D2 were detected in seeds (12 ± 2.4 and 5.8 ± 1.2 mg/g). The oenothein B concentration in liqueurs was 194 ± 22 mg/L. This macrocyclic ellagitannin dimer showed anti-Candida (minimal inhibitory concentration <8-64 μg/mL) and anti-inflammatory properties. Cultivated myrtle berries are a source of nutraceutical compounds. The high concentration of oenothein B in liqueur suggests a possible contribution to the organoleptic and biological properties of the beverage.
Collapse
Affiliation(s)
- Andrea
M. Franco
- Department
of Economics and Business (DiSea), Laboratory of Commodity Science
Technology and Quality, University of Sassari, Via Muroni 25, 07100 Sassari, Italy
| | - Noemi Tocci
- Department
of Economics and Business (DiSea), Laboratory of Commodity Science
Technology and Quality, University of Sassari, Via Muroni 25, 07100 Sassari, Italy
- Centre
for Research and Innovation, Department of Food Quality and Nutrition, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Graziano Guella
- Department
of Physics, Bioorganic Chemistry Laboratory, University of Trento, Via Sommarive 14, 38123 Povo, TN, Italy
| | - Mario Dell’Agli
- Department
of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Enrico Sangiovanni
- Department
of Pharmacological and Biomolecular Sciences (DiSFeB), Università degli Studi di Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Daniele Perenzoni
- Centre
for Research and Innovation, Department of Food Quality and Nutrition, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Urska Vrhovsek
- Centre
for Research and Innovation, Department of Food Quality and Nutrition, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Fulvio Mattivi
- Centre
for Research and Innovation, Department of Food Quality and Nutrition, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
- Department
of Physics, Bioorganic Chemistry Laboratory, University of Trento, Via Sommarive 14, 38123 Povo, TN, Italy
| | - Gavina Manca
- Department
of Economics and Business (DiSea), Laboratory of Commodity Science
Technology and Quality, University of Sassari, Via Muroni 25, 07100 Sassari, Italy
| |
Collapse
|
18
|
Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS. tRNA Deregulation and Its Consequences in Cancer. Trends Mol Med 2019; 25:853-865. [PMID: 31248782 DOI: 10.1016/j.molmed.2019.05.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.
Collapse
Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - A Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Pathology, Medical Faculty of Porto, Porto, Portugal.
| | - Manuel A S Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.
| |
Collapse
|
19
|
Zimmerman SM, Kon Y, Hauke AC, Ruiz BY, Fields S, Phizicky EM. Conditional accumulation of toxic tRNAs to cause amino acid misincorporation. Nucleic Acids Res 2018; 46:7831-7843. [PMID: 30007351 PMCID: PMC6125640 DOI: 10.1093/nar/gky623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/22/2018] [Accepted: 07/01/2018] [Indexed: 12/16/2022] Open
Abstract
To develop a system for conditional amino acid misincorporation, we engineered tRNAs in the yeast Saccharomyces cerevisiae to be substrates of the rapid tRNA decay (RTD) pathway, such that they accumulate when RTD is turned off. We used this system to test the effects on growth of a library of tRNASer variants with all possible anticodons, and show that many are lethal when RTD is inhibited and the tRNA accumulates. Using mass spectrometry, we measured serine misincorporation in yeast containing each of six tRNA variants, and for five of them identified hundreds of peptides with serine substitutions at the targeted amino acid sites. Unexpectedly, we found that there is not a simple correlation between toxicity and the level of serine misincorporation; in particular, high levels of serine misincorporation can occur at cysteine residues without obvious growth defects. We also showed that toxic tRNAs can be used as a tool to identify sequence variants that reduce tRNA function. Finally, we generalized this method to another tRNA species, and generated conditionally toxic tRNATyr variants in a similar manner. This method should facilitate the study of tRNA biology and provide a tool to probe the effects of amino acid misincorporation on cellular physiology.
Collapse
Affiliation(s)
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Alayna C Hauke
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| | - Bianca Y Ruiz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY 14642, USA
| |
Collapse
|
20
|
Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen. Proc Natl Acad Sci U S A 2018; 115:E8688-E8697. [PMID: 30150418 PMCID: PMC6140516 DOI: 10.1073/pnas.1806002115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Candida albicans is a heterozygous diploid yeast that is a commensal of the human gastrointestinal tract and a prevalent opportunistic pathogen. Here, whole-genome sequencing was performed on multiple C. albicans isolates passaged both in vitro and in vivo to characterize the complete spectrum of mutations arising in laboratory culture and in the mammalian host. We establish that, independent of culture niche, microevolution is primarily driven by de novo base substitutions and frequent short-tract loss-of-heterozygosity events. An average base-substitution rate of ∼1.2 × 10-10 per base pair per generation was observed in vitro, with higher rates inferred during host infection. Large-scale chromosomal changes were relatively rare, although chromosome 7 trisomies frequently emerged during passaging in a gastrointestinal model and was associated with increased fitness for this niche. Multiple chromosomal features impacted mutational patterns, with mutation rates elevated in repetitive regions, subtelomeric regions, and in gene families encoding cell surface proteins involved in host adhesion. Strikingly, de novo mutation rates were more than 800-fold higher in regions immediately adjacent to emergent loss-of-heterozygosity tracts, indicative of recombination-induced mutagenesis. Furthermore, genomes showed biased patterns of mutations suggestive of extensive purifying selection during passaging. These results reveal how both cell-intrinsic and cell-extrinsic factors influence C. albicans microevolution, and provide a quantitative picture of genome dynamics in this heterozygous diploid species.
Collapse
|
21
|
Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia. Nat Commun 2018; 9:2470. [PMID: 29941885 PMCID: PMC6018213 DOI: 10.1038/s41467-018-04926-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/05/2018] [Indexed: 11/23/2022] Open
Abstract
Tolerance to antifungal drug concentrations above the minimal inhibitory concentration (MIC) is rarely quantified, and current clinical recommendations suggest it should be ignored. Here, we quantify antifungal tolerance in Candida albicans isolates as the fraction of growth above the MIC, and find that it is distinct from susceptibility/resistance. Instead, tolerance is due to the slow growth of subpopulations of cells that overcome drug stress more efficiently than the rest of the population, and correlates inversely with intracellular drug accumulation. Many adjuvant drugs used in combination with fluconazole, a widely used fungistatic drug, reduce tolerance without affecting resistance. Accordingly, in an invertebrate infection model, adjuvant combination therapy is more effective than fluconazole in treating infections with highly tolerant isolates and does not affect infections with low tolerance isolates. Furthermore, isolates recovered from immunocompetent patients with persistent candidemia display higher tolerance than isolates readily cleared by fluconazole. Thus, tolerance correlates with, and may help predict, patient responses to fluconazole therapy. The authors show that antifungal tolerance, defined as the fraction of growth of a fungal pathogen above the minimal inhibitory concentration, is due to the slow growth of subpopulations of cells that overcome drug stress, and that high tolerance is often associated with persistent infections.
Collapse
|
22
|
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun 2018; 9:1887. [PMID: 29760453 PMCID: PMC5951914 DOI: 10.1038/s41467-018-04374-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/12/2018] [Indexed: 11/08/2022] Open
Abstract
The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the ‘universal’ leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNASer(CAG) and an ancestral tRNALeu(CAG) to read CUG, but only tRNASer(CAG) is used in standard growth conditions. The coexistence of these alloacceptor tRNA genes indicates that the genetic code transition occurred via an ambiguous translation phase. We propose that the three parallel reassignments of CUG were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tRNALeu(CAG). The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.
Collapse
|
23
|
Tocci N, Perenzoni D, Iamonico D, Fava F, Weil T, Mattivi F. Extracts From Hypericum hircinum subsp. majus Exert Antifungal Activity Against a Panel of Sensitive and Drug-Resistant Clinical Strains. Front Pharmacol 2018; 9:382. [PMID: 29755350 PMCID: PMC5932341 DOI: 10.3389/fphar.2018.00382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/03/2018] [Indexed: 12/27/2022] Open
Abstract
During the last two decades incidences of fungal infections dramatically increased and the often accompanying failure of available antifungal therapies represents a substantial clinical problem. The urgent need for novel antimycotics called particular attention to the study of natural products. The genus Hypericum includes many species that are used in the traditional medicine to treat pathological states like inflammations and infections caused by fungi. However, despite the diffused use of Hypericum-based products the antifungal potential of the genus is still poorly investigated. In this study five Hypericum species autochthonous of Central and Eastern Europe were evaluated regarding their polyphenolic content, their toxicological safety and their antifungal potential against a broad panel of clinical fungal isolates. LC-MS analysis led to the identification and quantification of 52 compounds, revealing that Hypericum extracts are rich sources of flavonols, benzoates and cinnamates, and of flavan-3-ols. An in-depth screen of the biological activity of crude extracts clearly unveiled H. hircinum subsp. majus as a promising candidate species for the search of novel antifungals. H. hircinum is diffused in the Mediterranean basin from Spain to Turkey where it is traditionally used to prepare a herbal tea indicated for the treatment of respiratory tract disorders, several of which are caused by fungi. Noteworthy, the infusion of H. hircinum subsp. majus excreted broad antifungal activity against Penicillium, Aspergillus and non-albicans Candida isolates comprising strains both sensitive and resistant to fluconazole. Additionally, it showed no cytotoxicity on human cells and the chemical characterization of the H. hircinum subsp. majus infusion revealed high amounts of the metabolite hyperoside. These results scientifically support the traditional use of H. hircinum extracts for the treatment of respiratory tract infections and suggest the presence of exploitable antifungal principles for further investigations aimed at developing novel antifungal therapies.
Collapse
Affiliation(s)
- Noemi Tocci
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Daniele Perenzoni
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Duilio Iamonico
- Laboratory of Phytogeography and Applied Geobotany, Section Environment and Landscape, Department of Planning, Design, and Technology of Architecture, Sapienza University of Rome, Rome, Italy
| | - Francesca Fava
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Tobias Weil
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Fulvio Mattivi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Centre Agriculture Food Environment, University of Trento, Trento, Italy
| |
Collapse
|
24
|
Modulation of the Fungal-Host Interaction by the Intra-Species Diversity of C. albicans. Pathogens 2018; 7:pathogens7010011. [PMID: 29342100 PMCID: PMC5874737 DOI: 10.3390/pathogens7010011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/09/2023] Open
Abstract
The incidence of human infections caused by the opportunistic fungal pathogen Candida albicans is on the rise due to increasing numbers of immunosuppressed patients. The importance of the immune system in preventing overgrowth of the colonizing fungus and thereby limiting infection is well recognized and host protective mechanisms widely investigated. Only recently, it was recognized that the natural diversity in the fungal species could also influence the outcome of the interaction between the fungus and the host. C. albicans strain-specific differences are complex and their regulation at the genomic, genetic, and epigenetic level and by environmental factors is only partially understood. In this review, we provide an overview of the natural diversity of C. albicans and discuss how it impacts host-fungal interactions and thereby affects the balance between commensalism versus disease.
Collapse
|