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Lim J, Kim W, Kim J, Lee J. Telomeric repeat evolution in the phylum Nematoda revealed by high-quality genome assemblies and subtelomere structures. Genome Res 2023; 33:gr.278124.123. [PMID: 37918961 PMCID: PMC10760449 DOI: 10.1101/gr.278124.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Telomeres are composed of tandem arrays of telomeric-repeat motifs (TRMs) and telomere-binding proteins (TBPs), which are responsible for ensuring end-protection and end-replication of chromosomes. TRMs are highly conserved owing to the sequence specificity of TBPs, although significant alterations in TRM have been observed in several taxa, except Nematoda. We used public whole-genome sequencing data sets to analyze putative TRMs of 100 nematode species and determined that three distinct branches included specific novel TRMs, suggesting that evolutionary alterations in TRMs occurred in Nematoda. We focused on one of the three branches, the Panagrolaimidae family, and performed a de novo assembly of four high-quality draft genomes of the canonical (TTAGGC) and novel TRM (TTAGAC) isolates; the latter genomes revealed densely clustered arrays of the novel TRM. We then comprehensively analyzed the subtelomeric regions of the genomes to infer how the novel TRM evolved. We identified DNA damage-repair signatures in subtelomeric sequences that were representative of consequences of telomere maintenance mechanisms by alternative lengthening of telomeres. We propose a hypothetical scenario in which TTAGAC-containing units are clustered in subtelomeric regions and pre-existing TBPs capable of binding both canonical and novel TRMs aided the evolution of the novel TRM in the Panagrolaimidae family.
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Affiliation(s)
- Jiseon Lim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Wonjoo Kim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Jun Kim
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea;
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, South Korea
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2
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Liang L, Wang Z, Qu L, Huang W, Guo S, Guan X, Zhang W, Sun F, Yuan H, Zou H, Liu H, Yu Z. Single-molecule multiplexed profiling of protein-DNA complexes using magnetic tweezers. J Biol Chem 2021; 296:100327. [PMID: 33493518 PMCID: PMC7949110 DOI: 10.1016/j.jbc.2021.100327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 01/14/2023] Open
Abstract
Epigenetics, such as the dynamic interplay between DNA methylation and demethylation, play diverse roles in critical cellular events. Enzymatic activity at CpG sites, where cytosines are methylated or demethylated, is known to be influenced by the density of CpGs, methylation states, and the flanking sequences of a CpG site. However, how the relevant enzymes are recruited to and recognize their target DNA is less clear. Moreover, although DNA-binding epigenetic enzymes are ideal targets for therapeutic intervention, these targets have been rarely exploited. Single-molecule techniques offer excellent capabilities to probe site-specific protein-DNA interactions and unravel the dynamics. Here, we develop a single-molecule approach that allows multiplexed profiling of protein-DNA complexes using magnetic tweezers. When a DNA hairpin with multiple binding sites is unzipping, strand separation pauses at the positions bound by a protein. We can thus measure site-specific binding probabilities and dissociation time directly. Taking the TET1 CXXC domain as an example, we show that TET1 CXXC binds multiple CpG motifs with various flanking nucleotides or different methylation patterns in an AT-rich DNA. We are able to establish for the first time, at nanometer resolution, that TET1 CXXC prefers G/C flanked CpG motif over C/G, A/T, or T/A flanked ones. CpG methylation strengthens TET1 CXXC recruitment but has little effect on dissociation time. Finally, we demonstrate that TET1 CXXC can distinguish five CpG clusters in a CpG island with crowded binding motifs. We anticipate that the feasibility of single-molecule multiplexed profiling assays will contribute to the understanding of protein-DNA interactions.
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Affiliation(s)
- Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Lihua Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Shuang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Xiangchen Guan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Zhang
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Fuping Sun
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Hongrui Yuan
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Huiru Zou
- Central Laboratory of Tianjin Stomatological Hospital, The Affiliated Stomatological Hospital of Nankai University, Tianjin, China
| | - Haitao Liu
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China.
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3
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Červenák F, Sepšiová R, Nosek J, Tomáška Ľ. Step-by-Step Evolution of Telomeres: Lessons from Yeasts. Genome Biol Evol 2020; 13:6127219. [PMID: 33537752 PMCID: PMC7857110 DOI: 10.1093/gbe/evaa268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 12/23/2022] Open
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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4
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Tomáška Ľ, Cesare AJ, AlTurki TM, Griffith JD. Twenty years of t-loops: A case study for the importance of collaboration in molecular biology. DNA Repair (Amst) 2020; 94:102901. [PMID: 32620538 DOI: 10.1016/j.dnarep.2020.102901] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Collaborative studies open doors to breakthroughs otherwise unattainable by any one laboratory alone. Here we describe the initial collaboration between the Griffith and de Lange laboratories that led to thinking about the telomere as a DNA template for homologous recombination, the proposal of telomere looping, and the first electron micrographs of t-loops. This was followed by collaborations that revealed t-loops across eukaryotic phyla. The Griffith and Tomáška/Nosek collaboration revealed circular telomeric DNA (t-circles) derived from the linear mitochondrial chromosomes of nonconventional yeast, which spurred discovery of t-circles in ALT-positive human cells. Collaborative work between the Griffith and McEachern labs demonstrated t-loops and t-circles in a series of yeast species. The de Lange and Zhuang laboratories then applied super-resolution light microscopy to demonstrate a genetic role for TRF2 in loop formation. Recent work from the Griffith laboratory linked telomere transcription with t-loop formation, providing a new model of the t-loop junction. A recent collaboration between the Cesare and Gaus laboratories utilized super-resolution light microscopy to provide details about t-loops as protective elements, followed by the Boulton and Cesare laboratories showing how cell cycle regulation of TRF2 and RTEL enables t-loop opening and reformation to promote telomere replication. Twenty years after the discovery of t-loops, we reflect on the collective history of their research as a case study in collaborative molecular biology.
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Affiliation(s)
- Ľubomír Tomáška
- Department of Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW, 2145, Australia
| | - Taghreed M AlTurki
- Lineberger Comprehensive Cancer Center and Departments of Microbiology and Immunology, and Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center and Departments of Microbiology and Immunology, and Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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5
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Tomáška Ľ, Nosek J. Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends. J Mol Evol 2020; 88:293-318. [PMID: 32157325 DOI: 10.1007/s00239-020-09935-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
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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6
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Peska V, Garcia S. Origin, Diversity, and Evolution of Telomere Sequences in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:117. [PMID: 32153618 PMCID: PMC7046594 DOI: 10.3389/fpls.2020.00117] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 05/18/2023]
Abstract
Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (TxAyGz)n. Although they are well conserved across large groups of organisms, recent findings in plants imply that their diversity has been underestimated. Changes in telomeres are of enormous evolutionary importance as they can affect whole-genome stability. Even a small change in the telomere motif of each repeat unit represents an important interference in the system of sequence-specific telomere binding proteins. Here, we provide an overview of telomere sequences, considering the latest phylogenomic evolutionary framework of plants in the broad sense (Archaeplastida), in which new telomeric sequences have recently been found in diverse and economically important families such as Solanaceae and Amaryllidaceae. In the family Lentibulariaceae and in many groups of green algae, deviations from the typical plant telomeric sequence have also been detected recently. Ancestry and possible homoplasy in telomeric motifs, as well as extant gaps in knowledge are discussed. With the increasing availability of genomic approaches, it is likely that more telomeric diversity will be uncovered in the future. We also discuss basic methods used for telomere identification and we explain the implications of the recent discovery of plant telomerase RNA on further research about the role of telomerase in eukaryogenesis or on the molecular causes and consequences of telomere variability.
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Affiliation(s)
- Vratislav Peska
- Department of Cell Biology and Radiobiology, The Czech Academy of Sciences, Institute of Biophysics, Brno, Czechia
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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7
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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] [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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8
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Abstract
The telomere regulator and transcription factor Rap1 is the only telomere protein conserved in yeasts and mammals. Its functional repertoire in budding yeasts is a particularly interesting field for investigation, given the high evolutionary diversity of this group of unicellular organisms. In the methylotrophic thermotolerant species Hansenula polymorpha DL-1 the RAP1 gene is duplicated (HpRAP1A and HpRAP1B). Here, we report the functional characterization of the two paralogues from H. polymorpha DL-1. We uncover distinct (but overlapping) DNA binding preferences of HpRap1A and HpRap1B proteins. We show that only HpRap1B is able to recognize telomeric DNA directly and to protect it from excessive recombination, whereas HpRap1A is associated with subtelomere regions. Furthermore, we identify specific binding sites for both HpRap1A and HpRap1B within promoters of a large number of ribosomal protein genes (RPGs), implicating Rap1 in the control of the RP regulon in H. polymorpha. Our bioinformatic analysis suggests that RAP1 was duplicated early in the evolution of the “methylotrophs” clade, and the two genes evolved independently. Therefore, our characterization of Rap1 paralogues in H. polymorpha may be relevant to other “methylotrophs”, yielding valuable insights into the evolution of budding yeasts.
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9
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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] [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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10
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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] [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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11
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Červenák F, Juríková K, Sepšiová R, Neboháčová M, Nosek J, Tomáška L. Double-stranded telomeric DNA binding proteins: Diversity matters. Cell Cycle 2017; 16:1568-1577. [PMID: 28749196 DOI: 10.1080/15384101.2017.1356511] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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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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] [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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13
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Casas-Vila N, Scheibe M, Freiwald A, Kappei D, Butter F. Identification of TTAGGG-binding proteins in Neurospora crassa, a fungus with vertebrate-like telomere repeats. BMC Genomics 2015; 16:965. [PMID: 26577093 PMCID: PMC4650311 DOI: 10.1186/s12864-015-2158-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/27/2015] [Indexed: 11/23/2022] Open
Abstract
Background To date, telomere research in fungi has mainly focused on Saccharomyces cerevisiae and Schizosaccharomyces pombe, despite the fact that both yeasts have degenerated telomeric repeats in contrast to the canonical TTAGGG motif found in vertebrates and also several other fungi. Results Using label-free quantitative proteomics, we here investigate the telosome of Neurospora crassa, a fungus with canonical telomeric repeats. We show that at least six of the candidates detected in our screen are direct TTAGGG-repeat binding proteins. While three of the direct interactors (NCU03416 [ncTbf1], NCU01991 [ncTbf2] and NCU02182 [ncTay1]) feature the known myb/homeobox DNA interaction domain also found in the vertebrate telomeric factors, we additionally show that a zinc-finger protein (NCU07846) and two proteins without any annotated DNA-binding domain (NCU02644 and NCU05718) are also direct double-strand TTAGGG binders. We further find two single-strand binders (NCU02404 [ncGbp2] and NCU07735 [ncTcg1]). Conclusion By quantitative label-free interactomics we identify TTAGGG-binding proteins in Neurospora crassa, suggesting candidates for telomeric factors that are supported by phylogenomic comparison with yeast species. Intriguingly, homologs in yeast species with degenerated telomeric repeats are also TTAGGG-binding proteins, e.g. in S. cerevisiae Tbf1 recognizes the TTAGGG motif found in its subtelomeres. However, there is also a subset of proteins that is not conserved. While a rudimentary core TTAGGG-recognition machinery may be conserved across yeast species, our data suggests Neurospora as an emerging model organism with unique features. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2158-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Núria Casas-Vila
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Marion Scheibe
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Anja Freiwald
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, 117599, Singapore, Singapore
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB) gGmbH, Ackermannweg 4, 55128, Mainz, Germany.
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Janoušková E, Nečasová I, Pavloušková J, Zimmermann M, Hluchý M, Marini V, Nováková M, Hofr C. Human Rap1 modulates TRF2 attraction to telomeric DNA. Nucleic Acids Res 2015; 43:2691-700. [PMID: 25675958 PMCID: PMC4357705 DOI: 10.1093/nar/gkv097] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
More than two decades of genetic research have identified and assigned main biological functions of shelterin proteins that safeguard telomeres. However, a molecular mechanism of how each protein subunit contributes to the protecting function of the whole shelterin complex remains elusive. Human Repressor activator protein 1 (Rap1) forms a multifunctional complex with Telomeric Repeat binding Factor 2 (TRF2). Rap1–TRF2 complex is a critical part of shelterin as it suppresses homology-directed repair in Ku 70/80 heterodimer absence. To understand how Rap1 affects key functions of TRF2, we investigated full-length Rap1 binding to TRF2 and Rap1–TRF2 complex interactions with double-stranded DNA by quantitative biochemical approaches. We observed that Rap1 reduces the overall DNA duplex binding affinity of TRF2 but increases the selectivity of TRF2 to telomeric DNA. Additionally, we observed that Rap1 induces a partial release of TRF2 from DNA duplex. The improved TRF2 selectivity to telomeric DNA is caused by less pronounced electrostatic attractions between TRF2 and DNA in Rap1 presence. Thus, Rap1 prompts more accurate and selective TRF2 recognition of telomeric DNA and TRF2 localization on single/double-strand DNA junctions. These quantitative functional studies contribute to the understanding of the selective recognition of telomeric DNA by the whole shelterin complex.
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Affiliation(s)
- Eliška Janoušková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ivona Nečasová
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Jana Pavloušková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Michal Zimmermann
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Milan Hluchý
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Victoria Marini
- Department of Biology, Faculty of Medicine, Masaryk University, Brno CZ-62500, Czech Republic
| | - Monika Nováková
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ctirad Hofr
- Chromatin Molecular Complexes, CEITEC and Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
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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] [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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Malyavko AN, Parfenova YY, Zvereva MI, Dontsova OA. Telomere length regulation in budding yeasts. FEBS Lett 2014; 588:2530-6. [PMID: 24914478 DOI: 10.1016/j.febslet.2014.05.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/23/2014] [Accepted: 05/23/2014] [Indexed: 11/19/2022]
Abstract
Telomeres are the nucleoprotein caps of chromosomes. Their length must be tightly regulated in order to maintain the stability of the genome. This is achieved by the intricate network of interactions between different proteins and protein-RNA complexes. Different organisms use various mechanisms for telomere length homeostasis. However, details of these mechanisms are not yet completely understood. In this review we have summarized our latest achievements in the understanding of telomere length regulation in budding yeasts.
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Affiliation(s)
- Alexander N Malyavko
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia; Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Yuliya Y Parfenova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia; Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia; Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia; Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia.
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