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Brejová B, Hodorová V, Mutalová S, Cillingová A, Tomáška Ľ, Vinař T, Nosek J. Chromosome-level Genome Assembly of the Yeast Lodderomyces beijingensis Reveals the Genetic Nature of Metabolic Adaptations and Identifies Subtelomeres as Hotspots for Amplification of Mating Type Loci. DNA Res 2024:dsae014. [PMID: 38686638 DOI: 10.1093/dnares/dsae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Lodderomyces beijingensis is an ascosporic ascomycetous yeast. In contrast to related species Lodderomyces elongisporus, which is a recently emerging human pathogen, L. beijingensis is associated with insects. To provide an insight into its genetic makeup, we investigated the genome of its type strain, CBS 14171. We demonstrate that this yeast is diploid and describe the high contiguity nuclear genome assembly consisting of eight chromosome-sized contigs with a total size of about 15.1 Mbp. We find that the genome sequence contains multiple copies of the mating type loci and codes for essential components of the mating pheromone response pathway, however, the missing orthologs of several genes involved in the meiotic program raise questions about the mode of sexual reproduction. We also show that L. beijingensis genome codes for the 3-oxoadipate pathway enzymes, which allow the assimilation of protocatechuate. In contrast, the GAL gene cluster underwent a decay resulting in an inability of L. beijingensis to utilize galactose. Moreover, we find that the 56.5 kbp long mitochondrial DNA is structurally similar to known linear mitochondrial genomes terminating on both sides with covalently closed single-stranded hairpins. Finally, we discovered a new double-stranded RNA mycovirus from the Totiviridae family and characterize its genome sequence.
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Affiliation(s)
- Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University Bratislava, 842 48 Bratislava, Slovak Republic
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Sofia Mutalová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University Bratislava, 842 48 Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
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Červenák F, Sepšiová R, Peška V, Nosek J, Tomáška Ľ. Primary Scientific Literature Represents an Essential Source of Telomeric Repeat Sequences. Microbiol Spectr 2023; 11:e0123023. [PMID: 37310973 PMCID: PMC10433822 DOI: 10.1128/spectrum.01230-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Affiliation(s)
- Filip Červenák
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Vratislav Peška
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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Brejová B, Vozáriková V, Agarský I, Derková H, Fedor M, Harmanová D, Kiss L, Korman A, Pašen M, Brázdovič F, Vinař T, Nosek J, Tomáška Ľ. y-mtPTM: Yeast Mitochondrial Post-Translational Modification Database. Genetics 2023:7161925. [PMID: 37183478 DOI: 10.1093/genetics/iyad087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/02/2023] [Accepted: 05/12/2023] [Indexed: 05/16/2023] Open
Abstract
One powerful strategy of how to increase the complexity of cellular proteomes is through post-translational modifications (PTMs) of proteins. Currently there are approximately 400 types of PTMs, the different combinations of which yield a large variety of protein isoforms with distinct biochemical properties. Although mitochondrial proteins undergoing PTMs were identified nearly six decades ago, studies on the roles and extent of PTMs on mitochondrial functions lagged behind the other cellular compartments. The application of mass spectrometry for the characterization of the mitochondrial proteome as well as for the detection of various PTMs resulted in the identification of thousands of amino acid positions that can be modified by different chemical groups. However, the data on mitochondrial PTMs are scattered in several datasets, and the available databases do not contain a complete list of modified residues. To integrate information on PTMs of the mitochondrial proteome of the yeast Saccharomyces cerevisiae, we built the y-mtPTM (Yeast Mitochondrial Post-Translational Modification) Database (http://compbio.fmph.uniba.sk/y-mtptm/). It lists nearly 20,000 positions on mitochondrial proteins affected by approximately twenty various PTMs, with phosphorylated, succinylated, acetylated and ubiquitylated sites being the most abundant. A simple search of a protein of interest reveals the modified amino acid residues, their position within the primary sequence as well as on its 3D structure and links to the source reference(s). The database will serve yeast mitochondrial researchers as a comprehensive platform to investigate the functional significance of the PTMs of mitochondrial proteins.
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Affiliation(s)
- Bronislava Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ivan Agarský
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Hana Derková
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Matej Fedor
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Dominika Harmanová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Lukáš Kiss
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Andrej Korman
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Martin Pašen
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Filip Brázdovič
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
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Cillingová A, Tóth R, Mojáková A, Zeman I, Vrzoňová R, Siváková B, Baráth P, Neboháčová M, Klepcová Z, Brázdovič F, Lichancová H, Hodorová V, Brejová B, Vinař T, Mutalová S, Vozáriková V, Mutti G, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J. Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources. PLoS Genet 2022; 18:e1009815. [PMID: 35255079 PMCID: PMC8929692 DOI: 10.1371/journal.pgen.1009815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/17/2022] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in β-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates.
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Affiliation(s)
- Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Renáta Tóth
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Anna Mojáková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Igor Zeman
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Romana Vrzoňová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Zuzana Klepcová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Brázdovič
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Hana Lichancová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sofia Mutalová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Giacomo Mutti
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Atilla Gácser
- HCEMM-USZ Department of Microbiology, University of Szeged, Szeged, Hungary
- MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- * E-mail:
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Mixão V, del Olmo V, Hegedűsová E, Saus E, Pryszcz L, Cillingová A, Nosek J, Gabaldón T. Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex. DNA Res 2022; 29:6570588. [PMID: 35438177 PMCID: PMC9046093 DOI: 10.1093/dnares/dsac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Indexed: 01/27/2023] Open
Abstract
Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C. metapsilosis isolates sequenced thus far are hybrids, and most of the parental lineages remain unidentified. This led to the hypothesis that hybrids with pathogenic potential were formed by the hybridization of non-pathogenic lineages that thrive in the environment. In a search for the missing hybrid parentals, and aiming to get a better understanding of the evolution of the species complex, we sequenced, assembled and analysed the genome of five close relatives isolated from the environment: Candida jiufengensis, Candida pseudojiufengensis, Candida oxycetoniae, Candida margitis and Candida theae. We found that the linear conformation of mitochondrial genomes in Candida species emerged multiple times independently. Furthermore, our analyses discarded the possible involvement of these species in the mentioned hybridizations, but identified C. theae as an additional hybrid in the species complex. Importantly, C. theae was recently associated with a case of infection, and we also uncovered the hybrid nature of this clinical isolate. Altogether, our results reinforce the hypothesis that hybridization is widespread among Candida species, and potentially contributes to the emergence of lineages with opportunistic pathogenic behaviour.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Valentina del Olmo
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Eva Hegedűsová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Leszek Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Andrea Cillingová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- ICREA, Barcelona 08010, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Barcelona, Spain
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Kovacech B, Fialova L, Filipcik P, Skrabana R, Zilkova M, Paulenka-Ivanovova N, Kovac A, Palova D, Rolkova GP, Tomkova K, Csokova NT, Markova K, Skrabanova M, Sinska K, Basheer N, Majerova P, Hanes J, Parrak V, Prcina M, Cehlar O, Cente M, Piestansky J, Fresser M, Novak M, Slavikova M, Borsova K, Cabanova V, Brejova B, Vinař T, Nosek J, Klempa B, Eyer L, Hönig V, Palus M, Ruzek D, Vyhlidalova T, Strakova P, Mrazkova B, Zudova D, Koubkova G, Novosadova V, Prochazka J, Sedlacek R, Zilka N, Kontsekova E. Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. EBioMedicine 2022; 76:103818. [PMID: 35078012 PMCID: PMC8782626 DOI: 10.1016/j.ebiom.2022.103818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence of new SARS-CoV-2 variants of concern B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) that harbor mutations in the viral S protein raised concern about activity of current vaccines and therapeutic antibodies. Independent studies have shown that mutant variants are partially or completely resistant against some of the therapeutic antibodies authorized for emergency use. METHODS We employed hybridoma technology, ELISA-based and cell-based S-ACE2 interaction assays combined with authentic virus neutralization assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize the new variants of SARS-CoV-2. FINDINGS AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). In addition, AX677 is able to bind Omicron Spike protein just like the wild type Spike. The combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. Prophylactic administration of AX290 and AX677, either individually or in combination, effectively reduced viral burden and inflammation in the lungs, and prevented disease in a mouse model of SARS-CoV-2 infection. INTERPRETATION The virus-neutralizing properties were fully reproduced in chimeric mouse-human versions of the antibodies, which may represent a promising tool for COVID-19 therapy. FUNDING The study was funded by AXON Neuroscience SE and AXON COVIDAX a.s.
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Affiliation(s)
- Branislav Kovacech
- AXON COVIDAX a. s.; Bratislava, 811 02, Slovakia; AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia.
| | - Lubica Fialova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Peter Filipcik
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Monika Zilkova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Andrej Kovac
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Denisa Palova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | | | - Natalia Turic Csokova
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Karina Markova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michaela Skrabanova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Kristina Sinska
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Neha Basheer
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Petra Majerova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Jozef Hanes
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Vojtech Parrak
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michal Prcina
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Ondrej Cehlar
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Martin Cente
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Michal Fresser
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Monika Slavikova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Kristina Borsova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia; Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Viktoria Cabanova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Bronislava Brejova
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Tomas Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Ludek Eyer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Tereza Vyhlidalova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic
| | - Petra Strakova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Blanka Mrazkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Dagmar Zudova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Gizela Koubkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Vendula Novosadova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Norbert Zilka
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia.
| | - Eva Kontsekova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
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7
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Brejová B, Boršová K, Hodorová V, Čabanová V, Gafurov A, Fričová D, Neboháčová M, Vinař T, Klempa B, Nosek J. Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols. PLoS One 2021; 16:e0259277. [PMID: 34714886 PMCID: PMC8555800 DOI: 10.1371/journal.pone.0259277] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
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Affiliation(s)
- Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Kristína Boršová
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Viktória Čabanová
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Askar Gafurov
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Dominika Fričová
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
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8
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Boršová K, Paul ED, Kováčová V, Radvánszka M, Hajdu R, Čabanová V, Sláviková M, Ličková M, Lukáčiková Ľ, Belák A, Roussier L, Kostičová M, Líšková A, Maďarová L, Štefkovičová M, Reizigová L, Nováková E, Sabaka P, Koščálová A, Brejová B, Staroňová E, Mišík M, Vinař T, Nosek J, Čekan P, Klempa B. Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay. Sci Rep 2021; 11:20494. [PMID: 34650153 PMCID: PMC8516907 DOI: 10.1038/s41598-021-99661-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
The emergence of a novel SARS-CoV-2 B.1.1.7 variant sparked global alarm due to increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack genomic surveillance programs and failed assays detect unrelated variants containing similar mutations as B.1.1.7, we used allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop an RT-qPCR test that accurately and rapidly differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing and conducted a country-wide surveillance study of B.1.1.7 prevalence in Slovakia. Our multiplexed RT-qPCR test showed 97% clinical sensitivity and retesting 6,886 SARS-CoV-2 positive samples obtained during three campaigns performed within one month, revealed pervasive spread of B.1.1.7 with an average prevalence of 82%. Labs can easily implement this test to rapidly scale B.1.1.7 surveillance efforts and it is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.
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Affiliation(s)
- Kristína Boršová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Rockville, MD, USA
| | - Viera Kováčová
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Rockville, MD, USA
| | - Monika Radvánszka
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Rockville, MD, USA
| | - Roman Hajdu
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., One Research Court, Rockville, MD, USA
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Viktória Čabanová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Ličková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ľubomíra Lukáčiková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Andrej Belák
- Institute of Ethnology and Social Anthropology, Slovak Academy of Sciences, Bratislava, Slovakia
- Intervention Team, Ministry of Health, Bratislava, Slovakia
| | - Lucia Roussier
- Intervention Team, Ministry of Health, Bratislava, Slovakia
| | - Michaela Kostičová
- Intervention Team, Ministry of Health, Bratislava, Slovakia
- Institute of Social Medicine and Medical Ethics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anna Líšková
- Department of Clinical Microbiology, Nitra Faculty Hospital, Nitra, Slovakia
| | - Lucia Maďarová
- Regional Authority of Public Health, Banská Bystrica, Slovakia
| | - Mária Štefkovičová
- Regional Authority of Public Health, Trenčín, Slovakia
- Faculty of Healthcare, Alexander Dubček University of Trenčín, Trenčín, Slovakia
| | - Lenka Reizigová
- Regional Authority of Public Health, Trenčín, Slovakia
- Department of Laboratory Medicine, Faculty of Healthcare and Social Work, Trnava University, Trnava, Slovakia
| | - Elena Nováková
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Sabaka
- Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Alena Koščálová
- Department of Infectology and Geographical Medicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
- Department of Infectious Diseases, Slovak Medical University, Bratislava, Slovakia
| | - Broňa Brejová
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Edita Staroňová
- National Influenza Centre, National Public Health Authority of Slovak Republic in Bratislava, Bratislava, Slovakia
| | - Matej Mišík
- Institute for Healthcare Analyses, Ministry of Health, Bratislava, Slovakia
| | - Tomáš Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
- MultiplexDX, Inc., One Research Court, Rockville, MD, USA.
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
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9
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Brejová B, Boršová K, Hodorová V, Čabanová V, Reizigová L, Paul ED, Čekan P, Klempa B, Nosek J, Vinař T. A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020. Virus Genes 2021; 57:556-560. [PMID: 34448987 PMCID: PMC8390540 DOI: 10.1007/s11262-021-01866-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/13/2021] [Indexed: 01/17/2023]
Abstract
SARS-CoV-2 mutants carrying the ∆H69/∆V70 deletion in the amino-terminal domain of the Spike protein emerged independently in at least six lineages of the virus (namely, B.1.1.7, B.1.1.298, B.1.160, B.1.177, B.1.258, B.1.375). We analyzed SARS-CoV-2 samples collected from various regions of Slovakia between November and December 2020 that were presumed to contain B.1.1.7 variant due to drop-out of the Spike gene target in an RT-qPCR test caused by this deletion. Sequencing of these samples revealed that although in some cases the samples were indeed confirmed as B.1.1.7, a substantial fraction of samples contained another ∆H69/∆V70 carrying mutant belonging to the lineage B.1.258, which has been circulating in Central Europe since August 2020, long before the import of B.1.1.7. Phylogenetic analysis shows that the early sublineage of B.1.258 acquired the N439K substitution in the receptor-binding domain (RBD) of the Spike protein and, later on, also the deletion ∆H69/∆V70 in the Spike N-terminal domain (NTD). This variant was particularly common in several European countries including the Czech Republic and Slovakia but has been quickly replaced by B.1.1.7 early in 2021.
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Affiliation(s)
- Broňa Brejová
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48, Bratislava, Slovak Republic
| | - Kristína Boršová
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovak Republic
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Viktória Hodorová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Viktória Čabanová
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovak Republic
| | - Lenka Reizigová
- Regional Authority of Public Health, Trenčín, Slovak Republic
- Department of Laboratory Medicine, Faculty of Healthcare and Social Work, Trnava University, Trnava, Slovak Republic
| | - Evan D Paul
- MultiplexDX, s.r.o., Comenius University in Bratislava Science Park, Ilkovičova 8, 841 04, Bratislava, Slovak Republic
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University in Bratislava Science Park, Ilkovičova 8, 841 04, Bratislava, Slovak Republic
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05, Bratislava, Slovak Republic.
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Tomáš Vinař
- Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynská dolina, 842 48, Bratislava, Slovak Republic
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10
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Mixão V, Hegedűsová E, Saus E, Pryszcz LP, Cillingová A, Nosek J, Gabaldón T. Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations. DNA Res 2021; 28:6299387. [PMID: 34129020 PMCID: PMC8311171 DOI: 10.1093/dnares/dsab006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/14/2021] [Indexed: 01/14/2023] Open
Abstract
Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32.
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Affiliation(s)
- Verónica Mixão
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Eva Hegedűsová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Andrea Cillingová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Jozef Nosek
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovak Republic
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Jordi Girona, 29, 08034 Barcelona, Spain.,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
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11
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Vrzoňová R, Tóth R, Siváková B, Moťovská A, Gaplovská-Kyselá K, Baráth P, Tomáška Ľ, Gácser A, Gabaldón T, Nosek J, Neboháčová M. OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway. FEMS Yeast Res 2021; 21:6293844. [PMID: 34089318 DOI: 10.1093/femsyr/foab034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.
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Affiliation(s)
- Romana Vrzoňová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Barbara Siváková
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Anna Moťovská
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Katarína Gaplovská-Kyselá
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Department of Genetics, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.,MTA-SZTE Lendület Mycobiome Research Group, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Institute for Research in Biomedicine (IRB), Jordi Girona 29, 08034 Barcelona, Spain.,Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona 29, 08034 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jozef Nosek
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Martina Neboháčová
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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12
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Schikora-Tamarit MÀ, Marcet-Houben M, Nosek J, Gabaldón T. Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi. Open Biol 2021; 11:200362. [PMID: 33906412 PMCID: PMC8080010 DOI: 10.1098/rsob.200362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.
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Affiliation(s)
- Miquel Àngel Schikora-Tamarit
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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13
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Monakhova N, Korduláková J, Vocat A, Egorova A, Lepioshkin A, Salina EG, Nosek J, Repková E, Zemanová J, Jurdáková H, Górová R, Roh J, Degiacomi G, Sammartino JC, Pasca MR, Cole ST, Mikušová K, Makarov V. Design and Synthesis of Pyrano[3,2- b]indolones Showing Antimycobacterial Activity. ACS Infect Dis 2021; 7:88-100. [PMID: 33352041 DOI: 10.1021/acsinfecdis.0c00622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Latent Mycobacterium tuberculosis infection presents one of the largest challenges for tuberculosis control and novel antimycobacterial drug development. A series of pyrano[3,2-b]indolone-based compounds was designed and synthesized via an original eight-step scheme. The synthesized compounds were evaluated for their in vitro activity against M. tuberculosis strains H37Rv and streptomycin-starved 18b (SS18b), representing models for replicating and nonreplicating mycobacteria, respectively. Compound 10a exhibited good activity with MIC99 values of 0.3 and 0.4 μg/mL against H37Rv and SS18b, respectively, as well as low toxicity, acceptable intracellular activity, and satisfactory metabolic stability and was selected as the lead compound for further studies. An analysis of 10a-resistant M. bovis mutants disclosed a cross-resistance with pretomanid and altered relative amounts of different forms of cofactor F420 in these strains. Complementation experiments showed that F420-dependent glucose-6-phosphate dehydrogenase and the synthesis of mature F420 were important for 10a activity. Overall these studies revealed 10a to be a prodrug that is activated by an unknown F420-dependent enzyme in mycobacteria.
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Affiliation(s)
- Natalia Monakhova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | | | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Anna Egorova
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Alexander Lepioshkin
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Elena G. Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | | | | | | | | | | | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové 50005, Czech Republic
| | - Giulia Degiacomi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - José Camilla Sammartino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Maria Rosalia Pasca
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia 27100, Italy
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | | | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russian Federation
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14
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Frankovsky J, Vozáriková V, Nosek J, Tomáška Ľ. Mitochondrial protein phosphorylation in yeast revisited. Mitochondrion 2021; 57:148-162. [PMID: 33412333 DOI: 10.1016/j.mito.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is one of the best-known post-translational modifications occurring in all domains of life. In eukaryotes, protein phosphorylation affects all cellular compartments including mitochondria. High-throughput techniques of mass spectrometry combined with cell fractionation and biochemical methods yielded thousands of phospho-sites on hundreds of mitochondrial proteins. We have compiled the information on mitochondrial protein kinases and phosphatases and their substrates in Saccharomyces cerevisiae and provide the current state-of-the-art overview of mitochondrial protein phosphorylation in this model eukaryote. Using several examples, we describe emerging features of the yeast mitochondrial phosphoproteome and present challenges lying ahead in this exciting field.
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Affiliation(s)
- Jan Frankovsky
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
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15
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Abstract
In virtually every eukaryotic species, the ends of nuclear chromosomes are protected by telomeres, nucleoprotein structures counteracting the end-replication problem and suppressing recombination and undue DNA repair. Although in most cases, the primary structure of telomeric DNA is conserved, there are several exceptions to this rule. One is represented by the telomeric repeats of ascomycetous yeasts, which encompass a great variety of sequences, whose evolutionary origin has been puzzling for several decades. At present, the key questions concerning the driving force behind their rapid evolution and the means of co-evolution of telomeric repeats and telomere-binding proteins remain largely unanswered. Previously published studies addressed mostly the general concepts of the evolutionary origin of telomeres, key properties of telomeric proteins as well as the molecular mechanisms of telomere maintenance; however, the evolutionary process itself has not been analyzed thoroughly. Here, we aimed to inspect the evolution of telomeres in ascomycetous yeasts from the subphyla Saccharomycotina and Taphrinomycotina, with special focus on the evolutionary origin of species-specific telomeric repeats. We analyzed the sequences of telomeric repeats from 204 yeast species classified into 20 families and as a result, we propose a step-by-step model, which integrates the diversity of telomeric repeats, telomerase RNAs, telomere-binding protein complexes and explains a propensity of certain species to generate the repeat heterogeneity within a single telomeric array.
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Affiliation(s)
- Filip Červenák
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Bratislava, Slovakia
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16
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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17
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Jurikova K, Gajarsky M, Hajikazemi M, Nosek J, Prochazkova K, Paeschke K, Trantirek L, Tomaska L. Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae. J Biol Chem 2020; 295:8958-8971. [PMID: 32385108 PMCID: PMC7335780 DOI: 10.1074/jbc.ra120.012914] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The ends of eukaryotic chromosomes typically contain a 3' ssDNA G-rich protrusion (G-overhang). This overhang must be protected against detrimental activities of nucleases and of the DNA damage response machinery and participates in the regulation of telomerase, a ribonucleoprotein complex that maintains telomere integrity. These functions are mediated by DNA-binding proteins, such as Cdc13 in Saccharomyces cerevisiae, and the propensity of G-rich sequences to form various non-B DNA structures. Using CD and NMR spectroscopies, we show here that G-overhangs of S. cerevisiae form distinct Hoogsteen pairing-based secondary structures, depending on their length. Whereas short telomeric oligonucleotides form a G-hairpin, their longer counterparts form parallel and/or antiparallel G-quadruplexes (G4s). Regardless of their topologies, non-B DNA structures exhibited impaired binding to Cdc13 in vitro as demonstrated by electrophoretic mobility shift assays. Importantly, whereas G4 structures formed relatively quickly, G-hairpins folded extremely slowly, indicating that short G-overhangs, which are typical for most of the cell cycle, are present predominantly as single-stranded oligonucleotides and are suitable substrates for Cdc13. Using ChIP, we show that the occurrence of G4 structures peaks at the late S phase, thus correlating with the accumulation of long G-overhangs. We present a model of how time- and length-dependent formation of non-B DNA structures at chromosomal termini participates in telomere maintenance.
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Affiliation(s)
- Katarina Jurikova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martin Gajarsky
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mona Hajikazemi
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Prochazkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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18
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Abstract
Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.
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Affiliation(s)
- Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia.
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovakia
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19
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Červenák F, Juríková K, Devillers H, Kaffe B, Khatib A, Bonnell E, Sopkovičová M, Wellinger RJ, Nosek J, Tzfati Y, Neuvéglise C, Tomáška Ľ. Identification of telomerase RNAs in species of the Yarrowia clade provides insights into the co-evolution of telomerase, telomeric repeats and telomere-binding proteins. Sci Rep 2019; 9:13365. [PMID: 31527614 PMCID: PMC6746865 DOI: 10.1038/s41598-019-49628-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/29/2019] [Indexed: 12/17/2022] Open
Abstract
Telomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia clade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5′-TTNNNNAGGG-3′, with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5′-TTAGGG-3′. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts.
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Affiliation(s)
- Filip Červenák
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Katarína Juríková
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Binyamin Kaffe
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel
| | - Areej Khatib
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel
| | - Erin Bonnell
- Department of Microbiology and Infectiology, RNA Group, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Martina Sopkovičová
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Raymund J Wellinger
- Department of Microbiology and Infectiology, RNA Group, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Jerusalem, 91904, Israel.
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Ľubomír Tomáška
- Departments of Genetics and Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, Mlynská dolina, 84215, Bratislava, Slovakia.
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20
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Tomaska L, Nosek J, Kar A, Willcox S, Griffith JD. A New View of the T-Loop Junction: Implications for Self-Primed Telomere Extension, Expansion of Disease-Related Nucleotide Repeat Blocks, and Telomere Evolution. Front Genet 2019; 10:792. [PMID: 31475042 PMCID: PMC6702307 DOI: 10.3389/fgene.2019.00792] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022] Open
Abstract
Telomere loops (t-loops) are formed at the ends of chromosomes in species ranging from humans to worms, plants, and with genetic manipulation, some yeast. Recent in vitro studies demonstrated that transcription of telomeric DNA leads to highly efficient t-loop formation. It was also shown that both DNA termini are inserted into the preceding DNA to generate a highly stable t-loop junction. Furthermore, some telomeric RNA remains present at the junction, potentially acting as a plug to further protect and stabilize the t-loop. Modeling the loop junction reveals two mechanisms by which the canonical chromosomal replication factors could extend the telomere in the absence of telomerase. One mechanism would utilize the annealed 3’ terminus as a de novo replication origin. In vitro evidence for the ability of the t-loop to prime telomere extension using the T7 replication factors is presented. A second mechanism would involve resolution of the Holliday junction present in the t-loop bubble by factors such as GEN1 to generate a rolling circle template at the extreme terminus of the telomere. This could lead to large expansions of the telomeric tract. Here, we propose that telomeres evolved as terminal elements containing long arrays of short nucleotide repeats due to the ability of such arrays to fold back into loops and self-prime their replicative extension. In this view, telomerase may have evolved later to provide a more precise mechanism of telomere maintenance. Both pathways have direct relevance to the alternative lengthening of telomeres (ALT) pathway. This view also provides a possible mechanism for the very large repeat expansions observed in nucleotide repeat diseases such as Fragile X syndrome, myotonic dystrophy, familial amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). The evolution of telomeres is discussed in the framework of these models.
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Affiliation(s)
- Lubomir Tomaska
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Departments of Genetics and Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Anirban Kar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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21
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Tomáška Ĺ, Nosek J, Sepšiová R, Červenák F, Juríková K, Procházková K, Neboháčová M, Willcox S, Griffith JD. Commentary: Single-stranded telomere-binding protein employs a dual rheostat for binding affinity and specificity that drives function. Front Genet 2019; 9:742. [PMID: 30697232 PMCID: PMC6341069 DOI: 10.3389/fgene.2018.00742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/22/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ĺubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Regina Sepšiová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Červenák
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarína Juríková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martina Neboháčová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, United States
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22
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Říha I, Třeška V, Nosek J, Šmíd D, Slunečko R. Rare causes of acute appendicitis. Rozhl Chir 2019; 98:189-193. [PMID: 31159539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
INTRODUCTION A clinical diagnosis of acute appendicitis does not necessarily imply only inflammatory changes found upon histopathological examination. Even though appendiceal tumors are very rare, accounting for less than 4% of all gastrointestinal tumors‚ they need to be taken into account and require the right choices regarding subsequent onco-surgical management. METHODS 1036 appendectomies were performed and 38 (3.7%) rare appendiceal tumor cases were identified at the department of Surgery in Pilsen from 1 January 2008 to 1 October 2018. The following text presents the difficult nature of the initial diagnosis, current therapy and principles of follow-up care in this relatively rare group of patients. CONCLUSION Appendiceal tumors are very rare. Depending on the histopathological type of tumor, it is necessary to choose adequate therapy and also provide proper follow up care.
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Brejová B, Lichancová H, Brázdovič F, Hegedűsová E, Forgáčová Jakúbková M, Hodorová V, Džugasová V, Baláž A, Zeiselová L, Cillingová A, Neboháčová M, Raclavský V, Tomáška Ľ, Lang BF, Vinař T, Nosek J. Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus. Curr Genet 2018; 65:539-560. [PMID: 30456648 DOI: 10.1007/s00294-018-0904-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 01/12/2023]
Abstract
The yeast Magnusiomyces capitatus is an opportunistic human pathogen causing rare yet severe infections, especially in patients with hematological malignancies. Here, we report the 20.2 megabase genome sequence of an environmental strain of this species as well as the genome sequences of eight additional isolates from human and animal sources providing an insight into intraspecies variation. The distribution of single-nucleotide variants is indicative of genetic recombination events, supporting evidence for sexual reproduction in this heterothallic yeast. Using RNAseq-aided annotation, we identified genes for 6518 proteins including several expanded families such as kexin proteases and Hsp70 molecular chaperones. Several of these families are potentially associated with the ability of M. capitatus to infect and colonize humans. For the purpose of comparative analysis, we also determined the genome sequence of a closely related yeast, Magnusiomyces ingens. The genome sequences of M. capitatus and M. ingens exhibit many distinct features and represent a basis for further comparative and functional studies.
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Affiliation(s)
- Bronislava Brejová
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
| | - Hana Lichancová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Filip Brázdovič
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Eva Hegedűsová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Viktória Hodorová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Vladimíra Džugasová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrej Baláž
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Lucia Zeiselová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Andrea Cillingová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martina Neboháčová
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Vladislav Raclavský
- Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ľubomír Tomáška
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Tomáš Vinař
- Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Nosek
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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24
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Affiliation(s)
- Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- * E-mail:
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
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25
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Cillingová A, Zeman I, Tóth R, Neboháčová M, Dunčková I, Hölcová M, Jakúbková M, Gérecová G, Pryszcz LP, Tomáška Ľ, Gabaldón T, Gácser A, Nosek J. Eukaryotic transporters for hydroxyderivatives of benzoic acid. Sci Rep 2017; 7:8998. [PMID: 28827635 PMCID: PMC5566891 DOI: 10.1038/s41598-017-09408-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
Several yeast species catabolize hydroxyderivatives of benzoic acid. However, the nature of carriers responsible for transport of these compounds across the plasma membrane is currently unknown. In this study, we analyzed a family of genes coding for permeases belonging to the major facilitator superfamily (MFS) in the pathogenic yeast Candida parapsilosis. Our results revealed that these transporters are functionally equivalent to bacterial aromatic acid: H+ symporters (AAHS) such as GenK, MhbT and PcaK. We demonstrate that the genes HBT1 and HBT2 encoding putative transporters are highly upregulated in C. parapsilosis cells assimilating hydroxybenzoate substrates and the corresponding proteins reside in the plasma membrane. Phenotypic analyses of knockout mutants and hydroxybenzoate uptake assays provide compelling evidence that the permeases Hbt1 and Hbt2 transport the substrates that are metabolized via the gentisate (3-hydroxybenzoate, gentisate) and 3-oxoadipate pathway (4-hydroxybenzoate, 2,4-dihydroxybenzoate and protocatechuate), respectively. Our data support the hypothesis that the carriers belong to the AAHS family of MFS transporters. Phylogenetic analyses revealed that the orthologs of Hbt permeases are widespread in the subphylum Pezizomycotina, but have a sparse distribution among Saccharomycotina lineages. Moreover, these analyses shed additional light on the evolution of biochemical pathways involved in the catabolic degradation of hydroxyaromatic compounds.
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Affiliation(s)
- Andrea Cillingová
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Igor Zeman
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Renáta Tóth
- Department of Microbiology, University of Szeged, Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Martina Neboháčová
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Ivana Dunčková
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Mária Hölcová
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Michaela Jakúbková
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Gabriela Gérecová
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic.,Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, 1030, Vienna, Austria
| | - Leszek P Pryszcz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Doctor Aiguader 88, 08003, Barcelona, Spain.,International Institute of Molecular and Cell Biology in Warsaw, 4 Trojdena Street, 02-109, Warsaw, Poland
| | - Ľubomír Tomáška
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Doctor Aiguader 88, 08003, Barcelona, Spain.,Departament de Ciències Experimentals I de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Szeged, Közép fasor 52, H-6726, Szeged, Hungary
| | - Jozef Nosek
- Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic.
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26
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Abstract
Telomeric sequences constitute only a small fraction of the whole genome yet they are crucial for ensuring genomic stability. This function is in large part mediated by protein complexes recruited to telomeric sequences by specific telomere-binding proteins (TBPs). Although the principal tasks of nuclear telomeres are the same in all eukaryotes, TBPs in various taxa exhibit a surprising diversity indicating their distinct evolutionary origin. This diversity is especially pronounced in ascomycetous yeasts where they must have co-evolved with rapidly diversifying sequences of telomeric repeats. In this article we (i) provide a historical overview of the discoveries leading to the current list of TBPs binding to double-stranded (ds) regions of telomeres, (ii) describe examples of dsTBPs highlighting their diversity in even closely related species, and (iii) speculate about possible evolutionary trajectories leading to a long list of various dsTBPs fulfilling the same general role(s) in their own unique ways.
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Affiliation(s)
- Filip Červenák
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Katarína Juríková
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Regina Sepšiová
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Martina Neboháčová
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - Jozef Nosek
- b Department of Biochemistry , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
| | - L'ubomír Tomáška
- a Department of Genetics , Comenius University in Bratislava, Faculty of Natural Sciences , Bratislava , Slovakia
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27
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Zeman I, Neboháčová M, Gérecová G, Katonová K, Jánošíková E, Jakúbková M, Centárová I, Dunčková I, Tomáška L, Pryszcz LP, Gabaldón T, Nosek J. Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis. G3 (Bethesda) 2016; 6:4047-4058. [PMID: 27707801 PMCID: PMC5144973 DOI: 10.1534/g3.116.034389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/01/2016] [Indexed: 12/23/2022]
Abstract
The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. The orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. Our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exception of the mitochondrially targeted 3-oxoadipate CoA-transferase (Osc1p) and 3-oxoadipyl-CoA thiolase (Oct1p) catalyzing the last two reactions of the 3-oxoadipate pathway. The cellular localization of the enzymes indicates that degradation of hydroxyaromatic compounds requires a shuttling of intermediates, cofactors, and products of the corresponding biochemical reactions between cytosol and mitochondria. Indeed, we found that yeast cells assimilating hydroxybenzoates increase the expression of genes SFC1, LEU5, YHM2, and MPC1 coding for succinate/fumarate carrier, coenzyme A carrier, oxoglutarate/citrate carrier, and the subunit of pyruvate carrier, respectively. A phylogenetic analysis uncovered distinct evolutionary trajectories for sparsely distributed gene clusters coding for enzymes of both pathways. Whereas the 3-oxoadipate pathway appears to have evolved by vertical descent combined with multiple losses, the gentisate pathway shows a striking pattern suggestive of horizontal gene transfer to the evolutionarily distant Mucorales.
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Affiliation(s)
- Igor Zeman
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Martina Neboháčová
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Gabriela Gérecová
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Kornélia Katonová
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Eva Jánošíková
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Michaela Jakúbková
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Ivana Centárová
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Ivana Dunčková
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - L'ubomír Tomáška
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
| | - Leszek P Pryszcz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain
- Departament de Ciències Experimentals I de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, 842 15, Slovak Republic
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28
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Abstract
Mgm101 has well-characterized activity for the repair and replication of the mitochondrial genome. Recent work has demonstrated a further role for Mgm101 in nuclear DNA metabolism, contributing to an S-phase specific DNA interstrand cross-link repair pathway that acts redundantly with a pathway controlled by Pso2 exonuclease. Due to involvement of FANCM, FANCJ and FANCP homologues (Mph1, Chl1 and Slx4), this pathway has been described as a Fanconi anemia-like pathway. In this pathway, Mgm101 physically interacts with the DNA helicase Mph1 and the MutSα (Msh2/Msh6) heterodimer, but its precise role is yet to be elucidated. Data presented here suggests that Mgm101 functionally overlaps with Rad52, supporting previous suggestions that, based on protein structure and biochemical properties, Mgm101 and Rad52 belong to a family of proteins with similar function. In addition, our data shows that this overlap extends to the function of both proteins at telomeres, where Mgm101 is required for telomere elongation during chromosome replication in rad52 defective cells. We hypothesize that Mgm101 could, in Rad52-like manner, preferentially bind single-stranded DNAs (such as at stalled replication forks, broken chromosomes and natural chromosome ends), stabilize them and mediate single-strand annealing-like homologous recombination event to prevent them from converting into toxic structures.
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Affiliation(s)
- Jana Rendeková
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
| | - Thomas A Ward
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Lucia Šimoničová
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter H Thomas
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Jozef Nosek
- d Department of Biochemistry , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Ľubomír Tomáška
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter J McHugh
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Miroslav Chovanec
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
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29
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Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T. Correction: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet 2016; 12:e1006202. [PMID: 27415787 PMCID: PMC4945001 DOI: 10.1371/journal.pgen.1006202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1005626.].
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30
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Sepsiova R, Necasova I, Willcox S, Prochazkova K, Gorilak P, Nosek J, Hofr C, Griffith JD, Tomaska L. Evolution of Telomeres in Schizosaccharomyces pombe and Its Possible Relationship to the Diversification of Telomere Binding Proteins. PLoS One 2016; 11:e0154225. [PMID: 27101289 PMCID: PMC4839565 DOI: 10.1371/journal.pone.0154225] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 04/11/2016] [Indexed: 11/30/2022] Open
Abstract
Telomeres of nuclear chromosomes are usually composed of an array of tandemly repeated sequences that are recognized by specific Myb domain containing DNA-binding proteins (telomere-binding proteins, TBPs). Whereas in many eukaryotes the length and sequence of the telomeric repeat is relatively conserved, telomeric sequences in various yeasts are highly variable. Schizosaccharomyces pombe provides an excellent model for investigation of co-evolution of telomeres and TBPs. First, telomeric repeats of S. pombe differ from the canonical mammalian type TTAGGG sequence. Second, S. pombe telomeres exhibit a high degree of intratelomeric heterogeneity. Third, S. pombe contains all types of known TBPs (Rap1p [a version unable to bind DNA], Tay1p/Teb1p, and Taz1p) that are employed by various yeast species to protect their telomeres. With the aim of reconstructing evolutionary paths leading to a separation of roles between Teb1p and Taz1p, we performed a comparative analysis of the DNA-binding properties of both proteins using combined qualitative and quantitative biochemical approaches. Visualization of DNA-protein complexes by electron microscopy revealed qualitative differences of binding of Teb1p and Taz1p to mammalian type and fission yeast telomeres. Fluorescence anisotropy analysis quantified the binding affinity of Teb1p and Taz1p to three different DNA substrates. Additionally, we carried out electrophoretic mobility shift assays using mammalian type telomeres and native substrates (telomeric repeats, histone-box sequences) as well as their mutated versions. We observed relative DNA sequence binding flexibility of Taz1p and higher binding stringency of Teb1p when both proteins were compared directly to each other. These properties may have driven replacement of Teb1p by Taz1p as the TBP in fission yeast.
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Affiliation(s)
- Regina Sepsiova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Ivona Necasova
- Chromatin Molecular Complexes, Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Katarina Prochazkova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Peter Gorilak
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Ctirad Hofr
- Chromatin Molecular Complexes, Central European Institute of Technology, Masaryk University, Brno, CZ-62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Lubomir Tomaska
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
- * E-mail:
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31
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Pevala V, Truban D, Bauer JA, Košťan J, Kunová N, Bellová J, Brandstetter M, Marini V, Krejčí L, Tomáška Ľ, Nosek J, Kutejová E. The structure and DNA-binding properties of Mgm101 from a yeast with a linear mitochondrial genome. Nucleic Acids Res 2016; 44:2227-39. [PMID: 26743001 PMCID: PMC4797282 DOI: 10.1093/nar/gkv1529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/14/2022] Open
Abstract
To study the mechanisms involved in the maintenance of a linear mitochondrial genome we investigated the biochemical properties of the recombination protein Mgm101 from Candida parapsilosis. We show that CpMgm101 complements defects associated with the Saccharomyces cerevisiae mgm101-1(ts) mutation and that it is present in both the nucleus and mitochondrial nucleoids of C. parapsilosis. Unlike its S. cerevisiae counterpart, CpMgm101 is associated with the entire nucleoid population and is able to bind to a broad range of DNA substrates in a non-sequence specific manner. CpMgm101 is also able to catalyze strand annealing and D-loop formation. CpMgm101 forms a roughly C-shaped trimer in solution according to SAXS. Electron microscopy of a complex of CpMgm101 with a model mitochondrial telomere revealed homogeneous, ring-shaped structures at the telomeric single-stranded overhangs. The DNA-binding properties of CpMgm101, together with its DNA recombination properties, suggest that it can play a number of possible roles in the replication of the mitochondrial genome and the maintenance of its telomeres.
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Affiliation(s)
- Vladimír Pevala
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Dominika Truban
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Július Košťan
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9 (VBC 5), 1030 Vienna, Austria
| | - Nina Kunová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Jana Bellová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Marlene Brandstetter
- Electron Microscopy Facility of the Campus Science Support Facilities GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lumír Krejčí
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Eva Kutejová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia Institute of Microbiology of the CAS, v. v. i., 142 20 Prague, Czech Republic
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32
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Černá M, Opatrný V, Nosek J, Geiger J, Třeška V, Boudová L, Buriánek V. [Coincidence of colonic lymphoma and gallstone ileus - case report]. Rozhl Chir 2016; 95:377-382. [PMID: 27653308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Primary colonic lymphoma is a very rare malignant disease of the gastrointestinal tract, accounting for 14% of all malignant diseases in this location. It is classified in the group of extranodal lymphomas; its long-term asymptomatic progression makes it different from common colorectal carcinomas making its diagnosis very difficult, more often accidental. Gallstone ileus is quite an uncommon complication of cholecystolithiasis diagnosed with difficulty. Up to 50% of cases are diagnosed during surgery. The obturated location depends on the size of the stone, location of the conjunction between the biliary and gastrointestinal tracts, and also on any preexisting stenosis due to another unknown pathology. CASE REPORT We present a case of an 86-year-old man treated for acute diverticulitis with typical clinical symptoms. Following further examination (colonoscopy, computed tomography) revealed a tumour-like infiltration in the sigmoid colon wall and a voluminous polyp was suspected according to the colonoscopy. Computed tomography described an obstruction by a biliary stone tumbling through the cholecystocolonic fistula. Subsequent biopsy supported the suspected malignant etiology. The patient underwent resection of the sigmoid colon sec. Hartmann; an infiltration was found in the subhepatic space, which corresponded to the described fistulisation between the biliary tract and the colon. A large 40 mm gallstone was found in the resected sigmoid colon over the stenosis and the bowel wall showed diffuse thickening with several polyps; final histopathological assessment confirmed malignant lymphoma of the plasmocytoma type. No serious complications occurred in the postoperative period; after healing, the patient was transferred to hematooncology care. CONCLUSION The article describes the presence of two rare diseases - colonic lymphoma and gallstone ileus. Clearly, without the biliary stone obstruction in the preexisting tumorous stenosis in the sigmoid colon, the malignant hematooncology disease would not have been diagnosed. KEY WORDS primary colonic lymphoma - gallstone ileus - complication of the cholecystolithiasis - extranodal lymphoma - acute diverticulitis.
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Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T. The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis. PLoS Genet 2015; 11:e1005626. [PMID: 26517373 PMCID: PMC4627764 DOI: 10.1371/journal.pgen.1005626] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/05/2015] [Indexed: 01/17/2023] Open
Abstract
Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into the recent evolution of C. metapsilosis and the genetic basis of its virulence, we sequenced the genome of 11 clinical isolates from various locations, which we compared to each other and to the available genomes of the two remaining members of the complex: C. orthopsilosis and C. parapsilosis. Unexpectedly, we found compelling genomic evidence that C. metapsilosis is a highly heterozygous hybrid species, with all sequenced clinical strains resulting from the same past hybridization event involving two parental lineages that were approximately 4.5% divergent in sequence. This result indicates that the parental species are non-pathogenic, but that hybridization between them formed a new opportunistic pathogen, C. metapsilosis, that has achieved a worldwide distribution. We show that these hybrids are diploid and we identified strains carrying loci for both alternative mating types, which supports mating as the initial mechanism for hybrid formation. We trace the aftermath of this hybridization at the genomic level, and reconstruct the evolutionary relationships among the different strains. Recombination and introgression -resulting in loss of heterozygosis- between the two subgenomes have been rampant, and includes the partial overwriting of the MTLa mating locus in all strains. Collectively, our results shed light on the recent genomic evolution within the C. parapsilosis sensu lato complex, and argue for a re-definition of species within this clade, with at least five distinct homozygous lineages, some of which having the ability to form hybrids.
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Affiliation(s)
- Leszek P. Pryszcz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Tibor Németh
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Ester Saus
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Hegedűsová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Kenneth H. Wolfe
- UCD Conway Institute, School of Medicine & Medical Science, University College Dublin, Dublin, Ireland
| | - Attila Gacser
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Kubačková D, Nosek J, Třeška V, Vacek V, Pizingerová K. [Intestinal volvulus caused by the ingestion of magnet balls: unexpected risk in children]. Rozhl Chir 2015; 94:204-206. [PMID: 26112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
INTRODUCTION The occurrence of swallowed foreign bodies in the digestive system is a common problem in children with the highest incidence in children aged six months to five years. Most swallowed objects leave the human body per vias naturales while 10-20% of swallowed foreign bodies need to be removed with an endoscope. Serious and life-threatening situations are caused by the ingestion of foreign bodies in about 1% of all cases. CASE REPORT The authors present a case of a two-year-old girl diagnosed with acute abdomen for which she was operated on. A small bowel volvulus and several intestinal fistulas were found intraoperatively. The cause of this finding was the ingestion of magnetic balls and a swallowed metal body drawn to them by magnetic force. CONCLUSION If more than one magnetic body is ingested, it is necessary to admit the patient to hospital and to remove these foreign bodies using an endoscope. The position of the magnets which is not changing in a location inaccessible for an endoscope during 2448 hours is an indication for urgent operation.
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35
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Gérecová G, Neboháčová M, Zeman I, Pryszcz LP, Tomáška Ľ, Gabaldón T, Nosek J. Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans. FEMS Yeast Res 2015; 15:fov006. [DOI: 10.1093/femsyr/fov006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2015] [Indexed: 12/15/2022] Open
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Amoaku W, Cackett P, Tyagi A, Mahmood U, Nosek J, Mennie G, Rumney N. Redesigning services for the management of vitreomacular traction and macular hole. Eye (Lond) 2015; 28 Suppl 1:S1-10. [PMID: 25008433 PMCID: PMC4097190 DOI: 10.1038/eye.2014.125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Vitreomacular traction (VMT) and VMT with macular hole (MH) are serious conditions, being associated with visual disturbance, for example, metamorphopsia, and diminished visual acuity (VA). Pars plana vitrectomy is the routine treatment for symptomatic VMT and VMT+MH. However, ocriplasmin has demonstrated favourable efficacy and safety in specific patient groups with VMT/MH and is now recommended as a treatment option for certain patients by the National Institute of Health and Care Excellence. This means that services for managing patients with VMT/MH may need to be revised, as patients can now potentially receive treatment earlier in the course of the disease. VMT triage clinics could provide a more efficient way of managing VMT/MH patients. Patient assessment should always include high-definition optical coherence tomography, as this is the most accurate means of assessing abnormalities in the vitreoretinal (VR) interface, and an accurate measurement of best-corrected VA. It has been proposed that patients with VMT+MH be managed as a routine 6-week referral, with the complete patient journey—from initial referral to treatment—taking no longer than 6 months. It is important that patients are entered onto VR surgical lists so that there is no delay if ocriplasmin treatment is unsuccessful. Patients will need appropriate counselling about the expected outcomes and possible side effects of ocriplasmin treatment. One-year follow-up data should be collected by treatment centres in order to evaluate the new VMT service.
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Affiliation(s)
- W Amoaku
- Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - P Cackett
- Princess Alexandra Eye Pavilion, Edinburgh, UK
| | - A Tyagi
- Birmingham and Midlands Eye Centre and Sandwell General Hospital, Birmingham, UK
| | - U Mahmood
- University Hospital of North Staffordshire, Stoke-on-Trent, UK
| | - J Nosek
- Wolverhampton Eye Infirmary, Wolverhampton, UK
| | - G Mennie
- Gloucestershire Clinical Commissioning Group, Brockworth, UK
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Simonicova L, Dudekova H, Ferenc J, Prochazkova K, Nebohacova M, Dusinsky R, Nosek J, Tomaska L. Saccharomyces cerevisiae as a model for the study of extranuclear functions of mammalian telomerase. Curr Genet 2015; 61:517-27. [PMID: 25567623 DOI: 10.1007/s00294-014-0472-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/25/2014] [Accepted: 12/28/2014] [Indexed: 10/24/2022]
Abstract
The experimental evidence from the last decade made telomerase a prominent member of a family of moonlighting proteins performing different functions at various cellular loci. However, the study of extratelomeric functions of the catalytic subunit of mammalian telomerase (TERT) is often complicated by the fact that it is sometimes difficult to distinguish them from its role(s) at the chromosomal ends. Here, we present an experimental model for studying the extranuclear function(s) of mammalian telomerase in the yeast Saccharomyces cerevisiae. We demonstrate that the catalytic subunit of mammalian telomerase protects the yeast cells against oxidative stress and affects the stability of the mitochondrial genome. The advantage of using S. cerevisiae to study of mammalian telomerase is that (1) mammalian TERT does not interfere with its yeast counterpart in the maintenance of telomeres, (2) yeast telomerase is not localized in mitochondria and (3) it does not seem to be involved in the protection of cells against oxidative stress and stabilization of mtDNA. Thus, yeast cells can be used as a 'test tube' for reconstitution of mammalian TERT extranuclear function(s).
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Affiliation(s)
- Lucia Simonicova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic
| | - Henrieta Dudekova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic
| | - Jaroslav Ferenc
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic
| | - Katarina Prochazkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic
| | - Martina Nebohacova
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina, CH-1, 84215, Bratislava, Slovak Republic
| | - Roman Dusinsky
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina, CH-1, 84215, Bratislava, Slovak Republic
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina, B-1, 84215, Bratislava, Slovak Republic.
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Ivan B, Lajdova D, Abelovska L, Balazova M, Nosek J, Tomaska L. Mdm31 protein mediates sensitivity to potassium ionophores but does not regulate mitochondrial morphology or phospholipid trafficking inSchizosaccharomyces pombe. Yeast 2015; 32:345-54. [DOI: 10.1002/yea.3062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 11/20/2014] [Accepted: 11/28/2014] [Indexed: 01/31/2023] Open
Affiliation(s)
- Branislav Ivan
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Dana Lajdova
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Lenka Abelovska
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Maria Balazova
- Institute of Animal Biochemistry and Genetics; Slovak Academy of Sciences; Ivanka pri Dunaji Slovakia
| | - Jozef Nosek
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
| | - Lubomir Tomaska
- Departments of Biochemistry and Genetics; Comenius University, Faculty of Natural Sciences; Bratislava Slovakia
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Gerhold JM, Sedman T, Visacka K, Slezakova J, Tomaska L, Nosek J, Sedman J. Replication intermediates of the linear mitochondrial DNA of Candida parapsilosis suggest a common recombination based mechanism for yeast mitochondria. J Biol Chem 2014; 289:22659-22670. [PMID: 24951592 DOI: 10.1074/jbc.m114.552828] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Variation in the topology of mitochondrial DNA (mtDNA) in eukaryotes evokes the question if differently structured DNAs are replicated by a common mechanism. RNA-primed DNA synthesis has been established as a mechanism for replicating the circular animal/mammalian mtDNA. In yeasts, circular mtDNA molecules were assumed to be templates for rolling circle DNA-replication. We recently showed that in Candida albicans, which has circular mapping mtDNA, recombination driven replication is a major mechanism for replicating a complex branched mtDNA network. Careful analyses of C. albicans-mtDNA did not reveal detectable amounts of circular DNA molecules. In the present study we addressed the question of how the unit sized linear mtDNA of Candida parapsilosis terminating at both ends with arrays of tandem repeats (mitochondrial telomeres) is replicated. Originally, we expected to find replication intermediates diagnostic of canonical bi-directional replication initiation at the centrally located bi-directional promoter region. However, we found that the linear mtDNA of Candida parapsilosis also employs recombination for replication initiation. The most striking findings were that the mitochondrial telomeres appear to be hot spots for recombination driven replication, and that stable RNA:DNA hybrids, with a potential role in mtDNA replication, are also present in the mtDNA preparations.
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Affiliation(s)
- Joachim M Gerhold
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and.
| | - Tiina Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and
| | - Katarina Visacka
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Judita Slezakova
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, and
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Juhan Sedman
- Department of Biochemistry, Institute of Molecular and Cell Biology, University of Tartu, Riia 23c, 51014 Tartu, Estonia and
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Kollár R, Bod'ová K, Nosek J, Tomáška L. Mathematical model of alternative mechanism of telomere length maintenance. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:032701. [PMID: 24730869 DOI: 10.1103/physreve.89.032701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 06/03/2023]
Abstract
Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres-nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.
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Affiliation(s)
- Richard Kollár
- Department of Applied Mathematics and Statistics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia
| | - Katarína Bod'ová
- Department of Applied Mathematics and Statistics, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia and Institute of Science and Technology, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15 Bratislava, Slovakia
| | - L'ubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15 Bratislava, Slovakia
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Affiliation(s)
- Jozef Nosek
- Departments of Biochemistry and Genetics; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava-Staré Mesto, Slovak Republic
| | - Lubomir Tomaska
- Departments of Biochemistry and Genetics; Faculty of Natural Sciences; Comenius University in Bratislava; Bratislava-Staré Mesto, Slovak Republic
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Rupert K, Nosek J, Polák M, Třeška V. [Chronic abdominal pain with a rare cause]. Rozhl Chir 2013; 92:569-572. [PMID: 24295479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The authors use a case report of a female patient with chronic abdominal pain progressing postprandially as an example to demonstrate the complexity of the diagnostic process in patients with these complaints, as well as a surprising peroperative finding in which a small neuroendocrine tumour of the small intestine was the cause of the difficulties. The ensuing discussion also deals with other possible causes of chronic abdominal pain associated with eating disorders.
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Hegedusova E, Brejova B, Tomaska L, Sipiczki M, Nosek J. Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Curr Genet 2013; 60:49-59. [PMID: 24071901 DOI: 10.1007/s00294-013-0410-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/08/2013] [Accepted: 09/14/2013] [Indexed: 11/25/2022]
Abstract
Jaminaea angkorensis is an anamorphic basidiomycetous yeast species originally isolated from decaying leaves in Cambodia. Taxonomically, J. angkorensis is affiliated with Microstromatales (Exobasidiomycetes, Ustilaginomycotina, Basidiomycota) and represents a basal phylogenetic lineage of this fungal order. To perform a comparative analysis of J. angkorensis with other basidiomycetes, we determined and analyzed its complete mitochondrial DNA sequence. The mitochondrial genome is represented by 29,999 base pairs long, circular DNA containing 32 % guanine and cytosine residues. Its genetic organization is relatively compact and comprises typical genes for 15 conserved proteins involved in oxidative phosphorylation (atp6, 8, and 9; cob; cox1, 2, and 3; and nad1, 2, 3, 4, 4L, 5, and 6) and translation (rps3), two ribosomal RNAs (rnl and rns) and twenty-two transfer RNAs (trnA-Y). Although the gene content is similar to other basidiomycetes, the gene orders in the examined species exhibit only a limited synteny, reflecting their phylogenetic distances and extensive genome rearrangements. In addition, a comparative analysis of basidiomycete mitochondrial genomes indicates that stop-to-tryptophan reassignment of the UGA codon was accompanied by structural alterations of tRNA-Trp(CCA). These results provide an insight into the evolution of the genetic code in fungal mitochondria.
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Affiliation(s)
- Eva Hegedusova
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH-1, 842 15, Bratislava, Slovak Republic
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44
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Valach M, Pryszcz LP, Tomaska L, Gacser A, Gabaldón T, Nosek J. Mitochondrial genome variability within the Candida parapsilosis species complex. Mitochondrion 2012; 12:514-9. [DOI: 10.1016/j.mito.2012.07.109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 04/05/2012] [Accepted: 07/13/2012] [Indexed: 01/15/2023]
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Visacka K, Hofr C, Willcox S, Necasova I, Pavlouskova J, Sepsiova R, Wimmerova M, Simonicova L, Nosek J, Fajkus J, Griffith JD, Tomaska L. Synergism of the two Myb domains of Tay1 protein results in high affinity binding to telomeres. J Biol Chem 2012; 287:32206-15. [PMID: 22815473 DOI: 10.1074/jbc.m112.385591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Double-stranded regions of the telomeres are recognized by proteins containing Myb-like domains conferring specificity toward telomeric repeats. Although biochemical and structural studies revealed basic molecular principles involved in DNA binding, relatively little is known about evolutionary pathways leading to various types of Myb domain-containing proteins in divergent species of eukaryotes. Recently we identified a novel type of telomere-binding protein YlTay1p from the yeast Yarrowia lipolytica containing two Myb domains (Myb1, Myb2) very similar to the Myb domain of mammalian TRF1 and TRF2. In this study we prepared mutant versions of YlTay1p lacking Myb1, Myb2, or both Myb domains and found that YlTay1p carrying either Myb domain exhibits preferential affinity to both Y. lipolytica (GGGTTAGTCA)(n) and human (TTAGGG)(n) telomeric sequences. Quantitative measurements of the protein binding to telomeric DNA revealed that the presence of both Myb domains is required for a high affinity of YlTay1p to either telomeric repeat. Additionally, we performed detailed thermodynamic analysis of the YlTay1p interaction with its cognate telomeric DNA, which is to our knowledge the first energetic description of a full-length telomeric-protein binding to DNA. Interestingly, when compared with human TRF1 and TRF2 proteins, YlTay1p exhibited higher affinity not only for Y. lipolytica telomeres but also for human telomeric sequences. The duplication of the Myb domain region in YlTay1p thus produces a synergistic effect on its affinity toward the cognate telomeric sequence, alleviating the need for homodimerization observed in TRF-like proteins possessing a single Myb domain.
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Affiliation(s)
- Katarina Visacka
- Department of Genetics and Biochemistry, Comenius University, Faculty of Natural Sciences, Mlynska dolina, 842 15 Bratislava, Slovakia
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Nosek J, Tomáska L. A new tool for an old problem: synchronizing fission yeast cells during meiosis using an ATP analog-sensitive protein kinase. Cell Cycle 2012; 11:1755-6. [PMID: 22510556 PMCID: PMC3372390 DOI: 10.4161/cc.20314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jozef Nosek
- Comenius University in Bratislava, Bratislava, Slovak Republic.
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Bódis E, Nosek J, Oertel N, Tóth B, Hornung E, Sousa R. Spatial distribution of bivalves in relation to environmental conditions (middle Danube catchment, Hungary). COMMUNITY ECOL 2011. [DOI: 10.1556/comec.12.2011.2.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Holesova Z, Jakubkova M, Zavadiakova I, Zeman I, Tomaska L, Nosek J. Gentisate and 3-oxoadipate pathways in the yeast Candida parapsilosis: identification and functional analysis of the genes coding for 3-hydroxybenzoate 6-hydroxylase and 4-hydroxybenzoate 1-hydroxylase. Microbiology (Reading) 2011; 157:2152-2163. [PMID: 21474535 DOI: 10.1099/mic.0.048215-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The pathogenic yeast Candida parapsilosis degrades various hydroxy derivatives of benzenes and benzoates by the gentisate and 3-oxoadipate pathways. We identified the genes MNX1, MNX2, MNX3, GDX1, HDX1 and FPH1 that code for enzymes involved in these pathways in the complete genome sequence of C. parapsilosis. Next, we demonstrated that MNX1, MNX2, MNX3 and GDX1 are inducible and transcriptionally controlled by hydroxyaromatic substrates present in cultivation media. Our results indicate that MNX1 and MNX2 code for flavoprotein monooxygenases catalysing the first steps in the 3-oxoadipate and gentisate pathways, respectively (i.e. 4-hydroxybenzoate 1-hydroxylase and 3-hydroxybenzoate 6-hydroxylase). Moreover, we found that the two pathways differ by their intracellular localization. The enzymes of the 3-oxoadipate pathway, Mnx1p and Mnx3p, localize predominantly in the cytosol. In contrast, intracellular localization of the components of the gentisate pathway, Mnx2p and Gdx1p, depends on the substrate in the cultivation medium. In cells growing on glucose these proteins localize in the cytosol, whereas in media containing hydroxyaromatic compounds they associate with mitochondria. Finally, we showed that the overexpression of MNX1 or MNX2 increases the tolerance of C. parapsilosis cells to the antifungal drug terbinafine.
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Affiliation(s)
- Zuzana Holesova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina B-1, 842 15 Bratislava, Slovak Republic
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Michaela Jakubkova
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Ivana Zavadiakova
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina B-1, 842 15 Bratislava, Slovak Republic
| | - Igor Zeman
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina CH-1, 842 15 Bratislava, Slovak Republic
| | - Lubomir Tomaska
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina B-1, 842 15 Bratislava, Slovak Republic
| | - Jozef Nosek
- Department of Biochemistry, Comenius University in Bratislava, Faculty of Natural Sciences, Mlynska dolina CH-1, 842 15 Bratislava, Slovak Republic
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50
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Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J. Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Res 2011; 39:4202-19. [PMID: 21266473 PMCID: PMC3105423 DOI: 10.1093/nar/gkq1345] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry, Comenius University, Mlynska dolina CH-1, 842 15 Bratislava, Slovak republic
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