scholarly journals Organization of 5S ribosomal DNA of Litchi chinensis Sonn.

2021 ◽  
Vol 18 (1-2) ◽  
pp. 3-8
Author(s):  
O. O. Ishchenko ◽  
V. V. Kozub ◽  
I. I. Panchuk
Keyword(s):  
Ribosomal Dna ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Molecular Organization ◽  
Cloning And Sequencing ◽  
Litchi Chinensis ◽  
The Family ◽  
Repeated Unit ◽  
Eukaryotic Organisms

Aim. 5S ribosomal DNA (5S rDNA) represents a universal model for studying the evolution of repeated sequences in eukaryotic organisms. Taking into account that this region of the genome still remains almost undescribed in species of the family Sapindaceae, we investigated the molecular organization of a repeated unit of 5S rDNA in a member of this family, Litchi chinensis. Methods. PCR amplification, cloning and sequencing of 5S rDNA. Results. It was found that the length of the repeated unit of the 5S rDNA of L. chinensis is 321 -323 bp. The level of intragenomic similarity of 5S rDNA repeats is 87.1 %. Potential external elements of the RNA polymerase III promoter, which are localized in IGS, differ from those described for members of other families of angiosperms. Conclusions. In the genome of L. chinensis, at least two classes of 5S rDNA repeats are present, which differ in the sequence of external promoter elements. Keywords: 5S rDNA, molecular evolution, Litchi chinensis, Sapindaceae.

scholarly journals Molecular structure of 5S rDNA of Mandragora autumnalis Bertol.

2020 ◽  
Vol 17 (2) ◽  
pp. 187-195
Author(s):  
A. Y. Shelyfist ◽  
D. V. Yakobyshen ◽  
R. A. Volkov
Keyword(s):  
Molecular Structure ◽  
Molecular Evolution ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Coding Region ◽  
Eukaryotic Organisms

Aim. The region encoding 5S rRNA (5S rDNA) is present in the genome of all eukaryotic organisms. The 5S rDNA represents a universal model for studying the molecular evolution of the tandemly arranged repeated sequences. However, in the family Solanaceae, the molecular organization of 5S rDNA has been investigated only for few genera. In this regard, we decided to characterize the molecular structure of the 5S rDNA of Mandragora autumnalis, a representative of the Mandragoreae tribe, which occupies an isolated position in the nightshade family. Methods. PCR amplification, cloning and sequencing. Results. Two 5S rDNA clones of M. autumnalis were sequenced. It was found that in the genome of this species only one class of the 5S rDNA repeats possessing the 103 bp-long intergenic spacer (IGS) is present. This is the smallest size of IGS known to date for the Solanaceae family. The 5S rDNA IGS of M. autumnalis demonstrates a moderate level of sequence-similarity with the IGS of other representatives of the subfamily Solanoideae. Conclusions. The results support the current opinion about the isolated taxonomic position of the genus Mandragora within the subfamily Solanoideae. The increased level of similarity was found in the IGS regions, which contain potential external elements of the RNA polymerase III promoter and terminator. The mutations occurred in the part of the IGS up-stream of the coding region had a compensatory nature, which ensured that the external elements of the promoter were preserved during the evolution. Keywords: 5S rDNA, intergeneric spacer, molecular evolution, Mandragora autumnalis, Solanaceae.

Organization of 5S ribosomal DNA of Poa pratensis L.

2020 ◽  
Vol 12 (2) ◽  
pp. 135-140
Author(s):  
Olha Ishchenko ◽  
Roman Volkov
Keyword(s):  
Poa Pratensis ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Transcription Terminator ◽  
Coding Regions ◽  
Poaceae Family ◽  
Rdna Igs

5S rDNA, which belongs to the class of repeated sequences, represents a convenient model for studying the molecular evolution of plants. The 5S rDNA repeated unit consists of a conserved region encoding 5S rRNA and variable intergenic spacer (IGS) that contains the motifs required for initiation and termination of transcription. The IGS sequences can be used as a molecular marker for elucidation of the phylogenetic relationships of low-ranking taxa. Today, the molecular organization of 5S rDNA in species of the Poaceae family, which includes many economically important crops, is still poorly understood. Therefore, the aim of the study was to investigate the organization and polymorphism of 5S rDNA IGS in the genome of Poa pratensis L., a member of one of the largest genera of the Poaceae family. Using PCR amplification, cloning, sequencing and analysis of the SRA database, two variants of the 5S rDNA repeated units were found in the genome of P. pratensis. The two variants possess 119 bp-long coding regions, whereas the length of IGS ranges from 169 to 185 bp. At the beginning of IGS, the oligo-T sequence of the RNA polymerase III transcription terminator is present. In members of the Poaceae family, the putative external elements of the 5S rDNA promoter differ from those in previously studied groups of plants.

scholarly journals Subrepeats in 5s rDNAs as a molecular marker in Acer platanoides L. populations

2019 ◽  
Vol 25 ◽  
pp. 80-85 ◽  
Author(s):  
I. I. Panchuk ◽  
R. M. Kasianchuk ◽  
R. A. Volkov
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Molecular Organization ◽  
Acer Platanoides ◽  
Rdna Transcription ◽  
Rdna Sequences ◽  
Rdna Igs

Aim. To study the genetic diversity of tree species it is necessary to use only those regions of genome, which evolve at the highest rate, such as 5S rDNA. To estimate the potential of 5S rDNA to be used as a molecular marker for genogeographic studies, the molecular organization of this genomic region was compared between samples from two geogra-phically remote Bulgarian and Ukrainian populations of Norway maple, Acer platanoides. Methods. PCR amplification, cloning and sequencing. Results. It was shown that in the genome of A. platanoides the 5S rDNA sequences are highly similar. However, in the 5S rDNA intergenic spacer (IGS) of A. platanoides from the Bulgarian population three copies of GTCCGTT subrepeats are present, whereas only one copy of this sequence occurs in plants from the Ukrainian population. Except for different number of subrepeats, the 5S rDNA sequences of the Bulgarian and Ukrainian samples of A. platanoides are identical. In two taxonomically distant species, A. platanoides and A. pseudoplatanus, the region of 5S rDNA IGS, which contains the potential external elements of the promoter of RNA polymerase III, shows no difference, and therefore evolves at a lower rate than other parts of the IGS. Conclusions. The identity of the potential external promoter elements within the genus Acer supports the idea that this part of the IGS could be involved in the initiation of 5S rDNA transcription. The presence of different numbers of sub-repeats in the 5S rDNA IGS in various populations of A. platanoides makes them suitable for identification of intraspecific forms and for evaluation of the intraspecific genetic diversity of A. platanoides. Keywords: 5S rDNA, molecular evolution, sub-repetitions, intraspecific variability, Acer.

scholarly journals Molecular organization of 5S rDNA of perennial ryegrass Lolium perenne L.

2019 ◽  
Vol 16 (2) ◽  
pp. 166-173 ◽  
Author(s):  
O. O. Ishchenko ◽  
I. I. Panchuk
Keyword(s):  
Lolium Perenne ◽  
Sequence Similarity ◽  
Molecular Taxonomy ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Important Species ◽  
Convenient Model

Aim. Ribosomal DNA (rDNA) is an important tool for molecular taxonomy and represents a convenient model for studying the evolution of repeated sequences. However, for many groups of angiosperms, 5S rDNA remains poorly studied, in particular for such a large group as the Poaceae (Gramineae) family. Accordingly, it was decided to analyze the molecular organization of 5S rDNA in the widespread and economically important species Lolium perenne. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. Two clones of L. perenne 5S rDNA were sequenced. It was shown that only one variant of 5S rDNA repeats with a 188–189 bp-long intergenic spacer (IGS) is present in the genome of L. perenne. Putative RNA polymerase III promoter elements were detected in the IGS. The level of IGS sequence similarity between representatives of different genera of the tribe Poeae ranges from 46 to 63 %. Conclusions. Comparison of IGS can be used to clarify the phylogenetic relationship between taxa of low ranks, in particular, between species and genera of the tribe Poeae. Keywords: 5S rDNA, intergenic spacer, molecular evolution, Lolium, Poaceae.

scholarly journals Molecular organization of 5S rDNA of Brunfelsia uniflora (Pohl.) D. Don

2018 ◽  
Vol 16 (1) ◽  
pp. 61-68 ◽  
Author(s):  
A. Y. Shelyfist ◽  
Y. O. Tynkevich ◽  
R. A. Volkov
Keyword(s):  
Molecular Evolution ◽  
Transcription Initiation ◽  
Rna Polymerase Iii ◽  
Pcr Amplification ◽  
5S Rdna ◽  
Genomic Region ◽  
High Rate ◽  
Molecular Organization ◽  
Low Rank ◽  
Solanaceae Family

Aim. The 5S rDNA represents a convenient model for studying of the molecular evolution of tandemly arranged repeated sequences. However, in many groups of angiosperms this genomic region still remains poorly studied. So far, in the family Solanaceae the 5S rDNA was described only for five genera. In order to elucidate the 5S rDNA organization in representatives of other genera of Solanaceae, we decided to explore organization of this region in Brunfelsia uniflora (tribe Petunieae). Methods. PCR amplification, cloning and sequencing of 5S rDNA. Results. Three clones of 5S rDNA of Brunfelsia uniflora were sequenced. It was found that only one class of repeats ranging in length from 343 to 347 bp is present in the genome of B. uniflora. The level of intragenomic similarity for the 5S rDNA intergeneric spacer regions (IGS) ranges from 86.7 to 96.4 %. The IGSs of B. uniflora and of other members of Solanaceae family differ significantly: the sequence homology was detected only for sequence motives required for RNA polymerase III transcription initiation and termination. Conclusions. The molecular evolution of the 5S rDNA IGS occurs at a high rate in the Solanaceae family. Accordingly, the comparison of the IGS should be used to clarify the phylogenetic relationship between taxa of low rank, in particular between species and genera of the tribe Petunieae. Keywords: 5S rDNA, intergeneric spacer, molecular evolution, Brunfelsia, Solanaceae.

Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 723-730 ◽  
Author(s):  
María Úbeda-Manzanaro ◽  
Manuel Alejandro Merlo ◽  
José Luis Palazón ◽  
Carmen Sarasquete ◽  
Laureana Rebordinos
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
5S Rdna ◽  
Purifying Selection ◽  
The Other ◽  
Fish Family ◽  
Sequence Characterization ◽  
Rdna Sequences ◽  
The Family ◽  
Clear Differentiation

5S ribosomal DNA (rDNA) sequences were analyzed in four species belonging to different genera of the fish family Batrachoididae. Several 5S rDNA variants differing in their non-transcribed spacers (NTSs) were found and were grouped into two main types. Two species showed both types of 5S rDNA, whereas the other two species showed only one type. One type of NTS of Amphichthys cryptocentrus showed a high polymorphism due to several deletions and insertions, and phylogenetic analysis showed a between-species clustering of this type of NTS in Amphichthys cryptocentrus. These results suggest a clear differentiation in the model of 5S rDNA evolution of these four species of Batrachoididae, which appear to have been subject to processes of concerted evolution and birth-and-death evolution with purifying selection.

scholarly journals Organization of 5S rDNA repeated unit of Quercus imbricaria Michx.

2020 ◽  
Vol 17 (2) ◽  
pp. 179-186 ◽  
Author(s):  
A. S. Stratiichuk ◽  
T. O. Derevenko ◽  
Y. O. Tynkevych
Keyword(s):  
Molecular Evolution ◽  
Secondary Structure ◽  
Pcr Amplification ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Sequence Elements ◽  
Related Plant

Aim. The 5S rDNA repeats represent a universal model for the investigation of molecular evolution of repeated sequences. Also, comparison of 5S rDNA was successfully applied for the elucidation of phylogenetic relationships between the closely related plant species. However, there is practically no data regarding the molecular organization of 5S rDNA repeats in members of the section Lobatae, one of the largest groups of the genus Quercus. Accordingly, our aim was to investigate the 5S rDNA organization for Q. imbricaria, a species that belongs to this section. Methods. DNA extraction, PCR amplification, cloning and sequencing. Results. A complete 5S rDNA repeat of Q. imbricaria was cloned and sequenced. It has been found that in the oak genome, the 5S rDNA coding region contains five nucleotide substitutions as compared to that in Arabidopsis. Nevertheless, the predicted secondary structure of the transcript retains all typical features of 5S rRNA. Presumptive sequence elements of the external promoter were identified in the IGS. Conclusions. The nucleotide substitutions that occur in the 5S rRNA during evolution appear to be compensatory, resulting in conservation of its secondary structure. Due to considerable differences among the species of different sections, the 5S rDNA IGS can be applied for the taxonomic studies in the genus Quercus. Keywords: 5S rDNA, molecular evolution, Quercus, Lobatae.

Organization of 5S rDNA of field maple (Acer campestre L.)

2019 ◽  
Vol 11 (1) ◽  
pp. 40-45
Author(s):  
Olha Іshchenko ◽  
Irina Panchuk ◽  
Roman Volkov
Keyword(s):  
Related Species ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Molecular Organization ◽  
Coding Region ◽  
Closely Related Species ◽  
Acer Campestre ◽  
Convenient Model

In recent decades, molecular methods have been widely used to study plant speciation and taxonomy. The 5S rDNA, which belongs to the class of repeated sequences present in the genomes of all eukaryotes, represents a convenient model for studying the patterns of molecular evolution in plants. Each of 5S rDNA repeated units consist of a coding region and an intergenic spacer (IGS). The coding sequence is highly conserved in evolution, whereas the IGS can differ between related species and even between populations of the same species. The molecular organization of the 5S rDNA in representatives of genus Acer is still poorly explored. Accordingly, the aim of the study was to investigate the organization and variability of the 5S rDNA of the European species Acer campestre. Analysis of the obtained sequences showed, that the 5S rDNA clones of A. campestre are identical. The level of IGS sequence similarity between A. сampestre and A. platanoides amounts to 96.1%, whereas the similarity between these species and A. pseudoplatanus is lower, namely – 81,9–82,4%. Therefore, A. campestre and A. platanoides can be considered as closely related species. Only one class of 5S rDNA repeats is present in the genome of A. сampestre. The potential external elements of the RNA polymerase III promoter localized in the IGS differ from those described early for representatives of other families of angiosperms.

scholarly journals Molecular organization of 5S rDNA in two ukrainian populations of sycamore (Acer pseudoplatanus)

2016 ◽  
Vol 14 (2) ◽  
pp. 216-220 ◽  
Author(s):  
O. O. Rusak ◽  
V. I. Petrashchuk ◽  
I. I. Panchuk ◽  
R. A. Volkov
Keyword(s):  
Molecular Evolution ◽  
Molecular Marker ◽  
Tree Species ◽  
Sequence Similarity ◽  
Rna Polymerase Iii ◽  
5S Rdna ◽  
Molecular Organization ◽  
Acer Pseudoplatanus ◽  
Rate Of Molecular Evolution ◽  
Rdna Igs

Aim. The genetic variability of tree species has still not been studied enough at the molecular level. Considering the relatively low rate of molecular evolution in perennial tree species, it is necessary to use only those regions of genome, which demonstrate a high level of variability, such as 5S rDNA. Accordingly, to estimate the potential of 5S rDNA as a molecular marker for tree species, the organization of this genomic region was compared between samples from two geographically remote Ukrainian populations of sycamore, Acer pseudoplatanus. Methods. PCR amplification, cloning and sequencing of the 5S rDNA IGS of A.pseudoplatanus. Results. It was shown that only one variant of 5S rDNA repeat with a length of 475 bp is present in the genome of A. pseudoplatanus.  Also, it was found that the elements typical for the angiosperm RNA polymerase III promoter, which are localized in IGS, appear to be different from those previously described for species of other families. The level of IGS sequence similarity within the populations exceeds 99%, while the level of IGS sequence similarity between various populations is only 93,3-94,3%. Conclusions. High rate of molecular evolution of the 5S rDNA IGS makes them a convenient molecular marker for evaluation of intraspecific variation in populations of A. pseudoplatanus.Key words: 5S rDNA, molecular markers, intraspecific variability, Acer

scholarly journals Amino acid residues modulating the activities of staphylococcal glutamyl endopeptidases

2010 ◽  
Vol 391 (10) ◽  
Author(s):  
Toshio Ono ◽  
Yuko Ohara-Nemoto ◽  
Yu Shimoyama ◽  
Hisami Okawara ◽  
Takeshi Kobayakawa ◽  
...  
Keyword(s):  
Family Members ◽  
Glutamyl Endopeptidase ◽  
Peptidase Activity ◽  
Amino Acid Residues ◽  
Virulence Determinants ◽  
Cloning And Sequencing ◽  
New Family ◽  
The Family ◽  
N Terminus ◽  
Staphylococcus Epidermis

AbstractThe glutamyl endopeptidase family of enzymes from staphylococci has been shown to be important virulence determinants of pathogenic family members, such asStaphylococcus aureus. Previous studies have identified the N-terminus and residues from positions 185–195 as potentially important regions that determine the activity of three members of the family. Cloning and sequencing of the new family members fromStaphylococcus caprae(GluScpr) andStaphylococcus cohnii(GluScoh) revealed that the N-terminal Val residue is maintained in all family members. Mutants of the GluV8 enzyme fromS. aureuswith altered N-terminal residues, including amino acids with similar properties, were inactive, indicating that the Val residue is specifically required at the N-terminus of this enzyme family in order for them to function correctly. Recombinant GluScpr was found to have peptidase activity intermediate between GluV8 and GluSE fromStaphylococcus epidermisand to be somewhat less specific in its substrate requirements than other family members. The 185–195 region was found to contribute to the activity of GluScpr, although other regions of the enzyme must also play a role in defining the activity. Our results strongly indicate the importance of the N-terminal and the 185–195 region in the activity of the glutamyl endopeptidases of staphylococci.

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