sequence specificity
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Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readouts.
- MeSH
- arginin chemie MeSH
- bakteriální proteiny chemie MeSH
- biokatalýza MeSH
- DNA bakterií chemie metabolismus MeSH
- křížová struktura DNA chemie MeSH
- párování bází MeSH
- sekvence nukleotidů MeSH
- simulace molekulární dynamiky MeSH
- Thermus thermophilus metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Class IIa histone deacetylases (HDACs) play critical roles in vertebrate development and physiology, yet direct evidence of their intrinsic deacetylase activity and on substrate specificity regarding the peptide sequence is still missing. In this study, we designed and synthesized a combinatorial peptide library allowing us to profile class IIa HDACs sequence specificity at positions +3 through -3 from the central lysine modified by the well-accepted trifluoroacetyl function. Our data revealed a strong preference for bulky aromatic acids directly flanking the central trifluoroacetyllysine, while all class IIa HDACs disfavor positively charged residues and proline at the +1/-1 positions. The chemical nature of amino acid residues N-terminally to the central trifluoroacetyllysine has a more profound effect on substrate recognition as compared to residues located C-terminally. These findings were validated by designing selected favored and disfavored peptide sequences, with the favored ones are accepted with catalytic efficacy of 75 000 and 525 000 M-1 s-1 for HDAC7 and HDAC5, respectively. Results reported here could help in developing class IIa HDACs inhibitors and also in the search for new natural class IIa HDACs substrates.
Súčasná klasifikácia zaraďuje sclerosis multiplex ( SM ) medzi orgánovo špecifické autoimúnne ochorenia, v ktorých je imunitná odpoveď namierená proti myelínovým antigénom. Pretože SM je častou príčinou invalidity už v produktívnom veku a skutočnosť , že Slovenská republika patrí medzi krajiny s tzv. vysokým rizikom výskytu SM ( incidencia 50-100 / 100 000 obyvateľov ), je toto ochorenie veľmi závažné aj zo socioekonomického hľadiska. Koncepcia terapeutického prístupu k pacientovi s diagnózou SM by mala obsahovať optimálnu medikamentóznu liečbu a vo všetkých štádiách ochorenia nepostrádateľnú rehabilita č nú lie č bu. Cie- ľ om práce bola sumarizácia poznatkov z dostupnej literatúry o SM a snaha tieto poznatky vhodne zaradiť pri koncipovaní metodického postupu.
In the present classification a multiple sclerosis is included among specific auto-immune diseases, where the immune response is directed against myelin antigenes. One of the main medical problems is caused by relatively high prevalence of autoimmune diseases in the population (5-7%) of present civilized and industrial societes. Because of disability in productive age caused by multiple sclerosis and the fact, that Slovak republic belongs to countries with high risk of MS occurence (incidence 50-100/100 000 inhabitants) this disease represents serious problem from the socio-economic point of view. Optimal drug treatment should be included into the concept of therapeutic attitude to patient with diagnosis MS and in all disease stages an indispensable rehabilitation treatment too. A summation of contemporary literary knowledges about MS and an effort to assign this knowledges into the concept of methodological attitude to the treatment was the goal of this interdisciplinary study.
All grass species evolved from an ancestor that underwent a whole-genome duplication (WGD) approximately 70 million years ago. Interestingly, the short arms of rice chromosomes 11 and 12 (and independently their homologs in sorghum) were found to be much more similar to each other than other homeologous regions within the duplicated genome. Based on detailed analysis of rice chromosomes 11 and 12 and their homologs in seven grass species, we propose a mechanism that explains the apparently 'younger' age of the duplication in this region of the genome, assuming a small number of reciprocal translocations at the chromosome termini. In each case the translocations were followed by unbalanced transmission and subsequent lineage sorting of the involved chromosomes to offspring. Molecular dating of these translocation events also allowed us to date major chromosome 'fusions' in the evolutionary lineages that led to Brachypodium and Triticeae. Furthermore, we provide evidence that rice is exceptional regarding the evolution of chromosomes 11 and 12, inasmuch as in other species the process of sequence exchange between homeologous chromosomes ceased much earlier than in rice. We presume that random events rather than selective forces are responsible for the observed high similarity between the short arm ends of rice chromosomes 11 and 12.
- MeSH
- časové faktory MeSH
- chromozomy rostlin genetika MeSH
- druhová specificita MeSH
- duplikace genu MeSH
- fylogeneze MeSH
- genetická variace MeSH
- genom rostlinný genetika MeSH
- lipnicovité klasifikace genetika MeSH
- molekulární evoluce * MeSH
- molekulární sekvence - údaje MeSH
- rekombinace genetická MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční homologie nukleových kyselin MeSH
- selekce (genetika) MeSH
- syntenie MeSH
- translokace genetická MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises significant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell specificity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3.net and https://github.com/antigenomics/vdjdb-db.
- MeSH
- analýza jednotlivých buněk MeSH
- anotace sekvence * MeSH
- antigeny chemie imunologie metabolismus MeSH
- databáze proteinů * MeSH
- hlavní histokompatibilní komplex genetika imunologie MeSH
- interakční proteinové domény a motivy MeSH
- internet MeSH
- lidé MeSH
- Macaca mulatta MeSH
- molekulární modely MeSH
- myši MeSH
- receptory antigenů T-buněk chemie imunologie metabolismus MeSH
- sekundární struktura proteinů MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie aminokyselin MeSH
- sekvenční seřazení MeSH
- software * MeSH
- T-lymfocyty cytologie imunologie MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ascochyta blight of chickpea is caused by Ascochyta rabiei (Pass.) Labr. which is primarily seedborne. For rapid detection and precise identification of A. rabiei, a sequence-characterized amplified region (SCAR) marker was developed for detection of genomic DNA and infected plant DNA. An SSR primer amplified monomorphic band was cloned in pGEM®-T easy vector and sequenced. The best primer pair was selected and validated on A. rabiei. The specificity and sensitivity of the SCAR-based marker designated as MBAR was evaluated using conventional PCR and real-time PCR. The marker produced consistently an amplicon size of 196 bp in all A. rabiei isolates tested. The sensitivity of the marker was 0.1 ng of genomic fungal DNA and 0.5 ng of plant DNA by conventional PCR and 0.5 pg of A. rabiei DNA and 1.0 pg of plant DNA by real-time PCR. This is the first SCAR marker having high specificity and sensitivity towards A. rabiei. The marker may be useful in detecting the pathogen before the disease appearance and in plant quarantine program to detect the pathogen in seed lots.
Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.
- MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- fyzikální mapování chromozomů MeSH
- genom * MeSH
- genová dávka * MeSH
- křeček rodu Peromyscus genetika MeSH
- molekulární evoluce * MeSH
- molekulární sekvence - údaje MeSH
- počítačová simulace MeSH
- restrikční mapování MeSH
- satelitní DNA genetika izolace a purifikace MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- sekvenční seřazení MeSH
- Southernův blotting MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
