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Artikel ; Online: Uniparental silencing of 5S rRNA genes in plant allopolyploids - insights from Cardamine (Brassicaceae).

Mandáková, Terezie / Krumpolcová, Alice / Matyášek, Roman / Volkov, Roman / Lysak, Martin A / Kovařík, Ales

The Plant journal : for cell and molecular biology

2024

Abstract: While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address ... ...

Abstract	While the phenomenon of uniparental silencing of 35S rDNA in interspecific hybrids and allopolyploids is well documented, there is a notable absence of information regarding whether such silencing extends to the 5S RNA component of ribosomes. To address this gap in knowledge, we analyzed the 5S and 35S rDNA expression in Cardamine (Brassicaceae) allopolyploids, namely C. × insueta (2n = 3x = 24, genome composition RRA), C. flexuosa (2n = 4x = 32, AAHH), and C. scutata (2n = 4x = 32, PPAA) which share a common diploid ancestor (AA). We employed high-throughput sequencing of transcriptomes and genomes and phylogenetic analyses of 5S rRNA variants. The genomic organization of rDNA was further scrutinized through clustering and fluorescence in situ hybridization. In the C. × insueta allotriploid, we observed uniparental dominant expression of 5S and 35S rDNA loci. In the C. flexuosa and C. scutata allotetraploids, the expression pattern differed, with the 35S rDNA being expressed from the A subgenome, whereas the 5S rDNA was expressed from the partner subgenome. Both C. flexuosa and C. scutata but not C. × insueta showed copy and locus number changes. We conclude that in stabilized allopolyploids, transcription of ribosomal RNA components occurs from different subgenomes. This phenomenon appears to result in the formation of chimeric ribosomes comprising rRNA molecules derived from distinct parental origins. We speculate that the interplay of epigenetic silencing and rDNA rearrangements introduces an additional layer of variation in multimolecule ribosomal complexes, potentially contributing to the evolutionary success of allopolyploids.
Sprache	Englisch
Erscheinungsdatum	2024-06-05
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	1088037-9
ISSN	1365-313X ; 0960-7412
ISSN (online)	1365-313X
ISSN	0960-7412
DOI	10.1111/tpj.16850
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts.

Matyášek, Roman / Kovařík, Aleš

Genes

2020 Band 11, Heft 7

Abstract: The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated ... ...

Abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from
Mesh-Begriff(e)	Animals ; Base Sequence ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; Chiroptera/virology ; CpG Islands ; Cytosine/metabolism ; Evolution, Molecular ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide ; Severe acute respiratory syndrome-related coronavirus/classification ; Severe acute respiratory syndrome-related coronavirus/genetics ; Severe acute respiratory syndrome-related coronavirus/isolation & purification ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics ; Uracil/metabolism
Chemische Substanzen	Spike Glycoprotein, Coronavirus ; Uracil (56HH86ZVCT) ; Cytosine (8J337D1HZY)
Schlagwörter	covid19
Sprache	Englisch
Erscheinungsdatum	2020-07-07
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11070761
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts

Matyásek, Roman / Kovarík, Ales

Abstract	The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An accumulation of C>U mutations was also observed in SARS-CoV2 variants that arose within the human population. Globally, the C>U substitutions increased the frequency of codons for hydrophobic amino acids in SARS-CoV-2 peptides, while U>C substitutions decreased it. In contrast to most other coronaviruses, both SARS-CoV-2 and RaTG13 exhibited CpG depletion in their genomes. The data suggest that C-to-U conversion mediated by C deamination played a significant role in the evolution of the SARS-CoV-2 coronavirus. We hypothesize that the high frequency C>U transitions reflect virus adaptation processes in their hosts, and that SARS-CoV-2 could have been evolving for a relatively long period in humans following the transfer from animals before spreading worldwide.
Schlagwörter	covid19
Verlag	WHO
Dokumenttyp	Artikel
Anmerkung	WHO #Covidence: #639723
Datenquelle	COVID19

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Artikel ; Online: Analyses of the Updated "Animal rDNA Loci Database" with an Emphasis on Its New Features.

Sochorová, Jana / Gálvez, Francisco / Matyášek, Roman / Garcia, Sònia / Kovařík, Aleš

International journal of molecular sciences

2021 Band 22, Heft 21

Abstract: We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S ... ...

Abstract	We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively.The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extremely high number of loci were rare, and medians generally converged to two 5S sites and two 45S rDNA sites per diploid genome. No relationship was observed between the number of 5S and 45S loci. (ii) The position of 45S rDNA on sex chromosomes was relatively frequent in some groups, particularly in arthropods (14% of karyotypes). Furthermore, 45S rDNA was almost exclusively located in microchromosomes when these were present (in birds and reptiles). (iii) The proportion of active NORs (positively stained with silver staining methods) progressively decreased with an increasing number of 45S rDNA loci, and karyotypes with more than 12 loci showed, on average, less than 40% of active loci. In conclusion, the updated version of the database provides some new insights into the organization of rRNA genes in chromosomes. We expect that its updated content will be useful for taxonomists, comparative cytogeneticists, and evolutionary biologists. .
Mesh-Begriff(e)	Animals ; DNA, Ribosomal/genetics ; Databases, Genetic ; Evolution, Molecular ; Karyotype ; Karyotyping ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 5S/genetics ; Species Specificity
Chemische Substanzen	DNA, Ribosomal ; RNA, Ribosomal ; RNA, Ribosomal, 5S ; RNA, ribosomal, 45S
Sprache	Englisch
Erscheinungsdatum	2021-10-22
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222111403
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins.

Matyášek, Roman / Řehůřková, Kateřina / Berta Marošiová, Kristýna / Kovařík, Aleš

Genes

2021 Band 12, Heft 6

Abstract: The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 ... ...

Abstract	The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein-protein interactions, fusion of viral and cellular membranes, and virion assembly.
Mesh-Begriff(e)	APOBEC Deaminases ; Alleles ; Amino Acid Substitution ; Amino Acids/chemistry ; Amino Acids/genetics ; COVID-19/virology ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Genotype ; Host-Pathogen Interactions ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Protein Binding ; Protein Interaction Domains and Motifs ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Viral Proteins/chemistry ; Viral Proteins/genetics
Chemische Substanzen	Amino Acids ; Spike Glycoprotein, Coronavirus ; Viral Proteins ; APOBEC Deaminases (EC 3.5.4.5)
Sprache	Englisch
Erscheinungsdatum	2021-05-27
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060826
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context.

Šponer, Judit E / Šponer, Jiří / Výravský, Jakub / Matyášek, Roman / Kovařík, Aleš / Dudziak, Wojciech / Ślepokura, Katarzyna

iScience

2023 Band 26, Heft 9, Seite(n) 107600

Abstract: Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon ...

Abstract	Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
Sprache	Englisch
Erscheinungsdatum	2023-08-09
Erscheinungsland	United States
Dokumenttyp	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107600
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: Mutational Asymmetries in the SARS-CoV-2 Genome May Lead to Increased Hydrophobicity of Virus Proteins

Matyášek, Roman / Řehůřková, Kateřina / Berta Marošiová, Kristýna / Kovařík, Aleš

Genes. 2021 May 27, v. 12, no. 6

2021

Abstract	The genomic diversity of SARS-CoV-2 has been a focus during the ongoing COVID-19 pandemic. Here, we analyzed the distribution and character of emerging mutations in a data set comprising more than 95,000 virus genomes covering eight major SARS-CoV-2 lineages in the GISAID database, including genotypes arising during COVID-19 therapy. Globally, the C>U transitions and G>U transversions were the most represented mutations, accounting for the majority of single-nucleotide variations. Mutational spectra were not influenced by the time the virus had been circulating in its host or medical treatment. At the amino acid level, we observed about a 2-fold excess of substitutions in favor of hydrophobic amino acids over the reverse. However, most mutations constituting variants of interests of the S-protein (spike) lead to hydrophilic amino acids, counteracting the global trend. The C>U and G>U substitutions altered codons towards increased amino acid hydrophobicity values in more than 80% of cases. The bias is explained by the existing differences in the codon composition for amino acids bearing contrasting biochemical properties. Mutation asymmetries apparently influence the biochemical features of SARS CoV-2 proteins, which may impact protein–protein interactions, fusion of viral and cellular membranes, and virion assembly.
Schlagwörter	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; codons ; data collection ; databases ; genetic variation ; hydrophilicity ; hydrophobicity ; medical treatment ; mutation ; virion ; viruses
Sprache	Englisch
Erscheinungsverlauf	2021-0527
Erscheinungsort	Multidisciplinary Digital Publishing Institute
Dokumenttyp	Artikel
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060826
Datenquelle	NAL Katalog (AGRICOLA)

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Artikel ; Online: The origin of exon 3 skipping of paternal GLOBOSA pre-mRNA in some Nicotiana tabacum lines correlates with a point mutation of the very last nucleotide of the exon.

Fulneček, Jaroslav / Matyášek, Roman

Molecular genetics and genomics : MGG

2015 Band 291, Heft 2, Seite(n) 801–818

Abstract: In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after ... ...

Abstract	In plants, genome duplication followed by genome diversification and selection is recognized as a major evolutionary process. Rapid epigenetic and genetic changes that affect the transcription of parental genes are frequently observed after polyploidization. The pattern of alternative splicing is also frequently altered, yet the related molecular processes remain largely unresolved. Here, we study the inheritance and expression of parental variants of three floral organ identity genes in allotetraploid tobacco. DEFICIENS and GLOBOSA are B-class genes, and AGAMOUS is a C-class gene. Parental variants of these genes were found to be maintained in the tobacco genome, and the respective mRNAs were present in flower buds in comparable amounts. However, among five tobacco cultivars, we identified two in which the majority of paternal GLOBOSA pre-mRNA transcripts undergo exon 3 skipping, producing an mRNA with a premature termination codon. At the DNA level, we identified a G-A transition at the very last position of exon 3 in both cultivars. Although alternative splicing resulted in a dramatic decrease in full-length paternal GLOBOSA mRNA, no phenotypic effect was observed. Our finding likely serves as an example of the initiation of homoeolog diversification in a relatively young polyploid genome.
Mesh-Begriff(e)	Alternative Splicing/genetics ; Exons/genetics ; Gene Expression Regulation, Plant ; Homeodomain Proteins/biosynthesis ; Homeodomain Proteins/genetics ; Nucleotides/genetics ; Plant Proteins/biosynthesis ; Plant Proteins/genetics ; Point Mutation/genetics ; Polyploidy ; RNA Precursors/genetics ; Nicotiana/genetics ; Transcription, Genetic
Chemische Substanzen	GLOBOSA protein, plant ; Homeodomain Proteins ; Nucleotides ; Plant Proteins ; RNA Precursors
Sprache	Englisch
Erscheinungsdatum	2015-11-25
Erscheinungsland	Germany
Dokumenttyp	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2044817-X
ISSN	1617-4623 ; 1617-4615
ISSN (online)	1617-4623
ISSN	1617-4615
DOI	10.1007/s00438-015-1149-9
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations.

Matyášek, Roman / Kuderová, Alena / Kutílková, Eva / Kučera, Marek / Kovařík, Aleš

DNA research : an international journal for rapid publication of reports on genes and genomes

2019 Band 26, Heft 3, Seite(n) 273–286

Abstract: The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies ... ...

Abstract	The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300-1250 bp) and R2 (290-643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
Mesh-Begriff(e)	Cucurbita/genetics ; DNA, Ribosomal Spacer/chemistry ; DNA, Ribosomal Spacer/genetics ; DNA, Ribosomal Spacer/metabolism ; Genetic Variation ; Minisatellite Repeats ; Nucleic Acid Conformation ; Sequence Analysis, DNA
Chemische Substanzen	DNA, Ribosomal Spacer
Sprache	Englisch
Erscheinungsdatum	2019-06-23
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	1212508-8
ISSN	1756-1663 ; 1340-2838
ISSN (online)	1756-1663
ISSN	1340-2838
DOI	10.1093/dnares/dsz008
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP.

Wunnava, Sreekar / Dirscherl, Christina F / Výravský, Jakub / Kovařík, Aleš / Matyášek, Roman / Šponer, Jiří / Braun, Dieter / Šponer, Judit E

Chemistry (Weinheim an der Bergstrasse, Germany)

2021 Band 27, Heft 70, Seite(n) 17581–17585

Abstract: The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3',5'-cyclic guanosine monophosphate (3',5'-cGMP) has been proposed as ... ...

Abstract	The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3',5'-cyclic guanosine monophosphate (3',5'-cGMP) has been proposed as a candidate to create oligonucleotides of 15-20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.
Mesh-Begriff(e)	Catalysis ; Cyclic GMP ; Oligonucleotides ; Polymerization ; RNA
Chemische Substanzen	Oligonucleotides ; RNA (63231-63-0) ; Cyclic GMP (H2D2X058MU)
Sprache	Englisch
Erscheinungsdatum	2021-11-23
Erscheinungsland	Germany
Dokumenttyp	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202103672
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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