• MeSH
• adenosindifosfát ribosa metabolismus   MeSH
• aminoacyl-tRNA-synthetasy metabolismus   MeSH
• centrifugace - gradient hustoty MeSH
• fosforylace MeSH
• iniciační faktory metabolismus   MeSH
• messenger RNA metabolismus   MeSH
• molekulová hmotnost MeSH
• polyribozomy metabolismus   MeSH
• posttranslační úpravy proteinů MeSH
• proteiny vázající RNA MeSH
• proteosyntéza MeSH
• ribonukleoproteiny metabolismus   MeSH
• RNA malá jaderná MeSH
• RNA metabolismus   MeSH
• transportní proteiny fyziologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• adenosindifosfát ribosa MeSH
• aminoacyl-tRNA-synthetasy MeSH
• iniciační faktory MeSH
• messenger RNA MeSH
• proteiny vázající RNA MeSH
• ribonukleoproteiny MeSH
• RNA malá jaderná MeSH
• RNA MeSH
• transportní proteiny MeSH

MRP1/2 is a heteromeric protein complex that functions in the trypanosomatid mitochondrion as part of the RNA editing machinery, which facilitates multiple targeted insertions and deletions of uridines. MRP1/2 was shown to interact with MRB8170, which initiates RNA editing by marking pre-edited mRNAs, while TbRGG2 is required for its efficient progression on pan-edited mRNAs. Both MRP1/2 and TbRGG2 are capable of modulating RNA-RNA interactions in vitro. As determined by using iCLIP and RIP-qPCR, RNAs bound to MRP1/2 are characterized and compared with those associated with MRB8170 and TbRGG2. We provide evidence that MRP1 and MRB8170 have correlated binding and similar RNA crosslinking peak profiles over minimally and never-edited mRNAs. Our results suggest that MRP1 assists MRB8170 in RNA editing on minimally edited mRNAs.

• Klíčová slova
• RNA binding proteins, RNA editing, iCLIP, mitochondrion, ribonuclear protein, trypanosome,
• MeSH
• editace RNA MeSH
• messenger RNA genetika   metabolismus   MeSH
• mitochondrie genetika   metabolismus   MeSH
• proteiny vázající RNA metabolismus   MeSH
• protozoální proteiny genetika   metabolismus   MeSH
• RNA mitochondriální genetika   metabolismus   MeSH
• Trypanosoma genetika   metabolismus   MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• gBP21 protein, Trypanosoma brucei MeSH Prohlížeč
• messenger RNA MeSH
• mitochondrial messenger RNA MeSH Prohlížeč
• proteiny vázající RNA MeSH
• protozoální proteiny MeSH
• RNA mitochondriální MeSH

Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.

• Klíčová slova
• Bioconjugations, Cross-Linking, Modified RNA, Proteins, RNA Polymerases,
• MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• DNA metabolismus   MeSH
• nukleotidy * metabolismus   MeSH
• proteiny vázající RNA MeSH
• reagencia zkříženě vázaná MeSH
• RNA sondy MeSH
• RNA * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chloroacetamide MeSH Prohlížeč
• DNA řízené RNA-polymerasy MeSH
• DNA MeSH
• nukleotidy * MeSH
• proteiny vázající RNA MeSH
• reagencia zkříženě vázaná MeSH
• RNA sondy MeSH
• RNA * MeSH

DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.

• Klíčová slova
• DNA/RNA binding protein, biomarkers, cancer, mutation, targeted treatment,
• MeSH
• DNA vazebné proteiny metabolismus   MeSH
• DNA MeSH
• lidé MeSH
• nádory * genetika   metabolismus   MeSH
• proteiny vázající RNA * metabolismus   MeSH
• RNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• DNA MeSH
• proteiny vázající RNA * MeSH
• RNA MeSH

RNA-binding proteins (RBPs) are critical to posttranscriptional gene regulation. Therefore, characterization of the RNA molecules bound by RBPs in vivo represent a key step in elucidating their function. The recently developed iCLIP technique allows single nucleotide resolution of the RNA binding footprints of RBPs. We present the iCLIP technique modified for its application to Trypanosoma brucei and most likely other kinetoplastid flagellates. By using the immuno- or affinity purification approach, it was successfully applied to the analysis of several RBPs. Furthermore, we also provide a detailed description of the iCLIP/iCLAP protocol that shall be particularly suitable for the studies of trypanosome RBPs.

• Klíčová slova
• Posttranscriptional gene regulation, RNA-binding proteins (RBPs), iCLAP, iCLIP,
• MeSH
• imunoprecipitace metody   MeSH
• nukleotidy genetika   metabolismus   MeSH
• parazitologie metody   MeSH
• proteiny vázající RNA analýza   genetika   metabolismus   MeSH
• protozoální proteiny analýza   genetika   metabolismus   MeSH
• RNA protozoální genetika   metabolismus   MeSH
• RNA genetika   metabolismus   MeSH
• Trypanosoma brucei brucei genetika   MeSH
• ultrafialové záření MeSH
• vazba proteinů genetika   účinky záření   MeSH
• vazebná místa genetika   MeSH
• zobrazení jednotlivé molekuly metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nukleotidy MeSH
• proteiny vázající RNA MeSH
• protozoální proteiny MeSH
• RNA protozoální MeSH
• RNA MeSH

Binding of the major avian retroviral nucleocapsid protein ASLV NC(p12) to the MAV-1 (myeloblastosis-associated virus) proviral dsDNA and viral ssRNA was analysed using electron microscopy. Specificity of the binding was estimated by special computer programs. The NC(p12) protein bound to MAV-1 proviral dsDNA (clone pAT153--MAV-1), but specificity of this binding was not found by computer evaluation. NC(p12) also bound to nondenatured 70S viral RNA at a rate of 25 +/- 3 molecules per RNA molecule. When this RNA was denatured either before or after the complexing, it showed no binding affinity for the protein. This result implies that preserved secondary structure of the viral RNA was required for the binding.

• MeSH
• DNA vazebné proteiny metabolismus   MeSH
• DNA virů metabolismus   ultrastruktura   MeSH
• DNA metabolismus   MeSH
• kapsida metabolismus   MeSH
• kur domácí MeSH
• proteiny vázající RNA MeSH
• proteiny virového jádra metabolismus   MeSH
• proviry genetika   metabolismus   MeSH
• Retroviridae - proteiny * MeSH
• RNA virová metabolismus   ultrastruktura   MeSH
• transportní proteiny metabolismus   MeSH
• vazebná místa MeSH
• virové plášťové proteiny * MeSH
• virus ptačí leukózy genetika   MeSH
• virus ptačí myeloblastózy genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• DNA virů MeSH
• DNA MeSH
• nucleocapsid protein, Avian retrovirus MeSH Prohlížeč
• proteiny vázající RNA MeSH
• proteiny virového jádra MeSH
• Retroviridae - proteiny * MeSH
• RNA virová MeSH
• transportní proteiny MeSH
• virové plášťové proteiny * MeSH

The RNA editing core complex (RECC) catalyzes mitochondrial U-insertion/deletion mRNA editing in trypanosomatid flagellates. Some naphthalene-based sulfonated compounds, such as C35 and MrB, competitively inhibit the auto-adenylylation activity of an essential RECC enzyme, kinetoplastid RNA editing ligase 1 (KREL1), required for the final step in editing. Previous studies revealed the ability of these compounds to interfere with the interaction between the editosome and its RNA substrates, consequently affecting all catalytic activities that comprise RNA editing. This observation implicates a critical function for the affected RNA binding proteins in RNA editing. In this study, using the inhibitory compounds, we analyzed the composition and editing activities of functional editosomes and identified the mitochondrial RNA binding proteins 1 and 2 (MRP1/2) as their preferred targets. While the MRP1/2 heterotetramer complex is known to bind guide RNA and promote annealing to its cognate pre-edited mRNA, its role in RNA editing remained enigmatic. We show that the compounds affect the association between the RECC and MRP1/2 heterotetramer. Furthermore, RECC purified post-treatment with these compounds exhibit compromised in vitro RNA editing activity that, remarkably, recovers upon the addition of recombinant MRP1/2 proteins. This work provides experimental evidence that the MRP1/2 heterotetramer is required for in vitro RNA editing activity and substantiates the hypothesized role of these proteins in presenting the RNA duplex to the catalytic complex in the initial steps of RNA editing.

• Klíčová slova
• MRP1/2, RNA editing, RNA editing initiation, RNA-binding protein, inhibitor, trypanosome,
• MeSH
• editace RNA účinky léků   genetika   MeSH
• guide RNA, Kinetoplastida účinky léků   MeSH
• ligasy antagonisté a inhibitory   MeSH
• messenger RNA genetika   MeSH
• mitochondriální proteiny genetika   MeSH
• mitochondrie účinky léků   genetika   MeSH
• proteiny vázající RNA genetika   MeSH
• protozoální proteiny genetika   MeSH
• rekombinantní proteiny genetika   MeSH
• RNA mitochondriální genetika   MeSH
• RNA protozoální genetika   MeSH
• Trypanosoma brucei brucei účinky léků   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• gBP21 protein, Trypanosoma brucei MeSH Prohlížeč
• gBP25 protein, Trypanosoma brucei MeSH Prohlížeč
• guide RNA, Kinetoplastida MeSH
• ligasy MeSH
• messenger RNA MeSH
• mitochondriální proteiny MeSH
• proteiny vázající RNA MeSH
• protozoální proteiny MeSH
• rekombinantní proteiny MeSH
• RNA mitochondriální MeSH
• RNA protozoální MeSH

Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.

• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• DNA chemie   metabolismus   MeSH
• G-kvadruplexy * MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• promotorové oblasti (genetika) MeSH
• RNA chemie   metabolismus   MeSH
• stárnutí MeSH
• telomery MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• DNA MeSH
• RNA MeSH

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.

• Klíčová slova
• Z-DNA, Z-RNA, Zα domain, bioinformatics, protein binding,
• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• interakční proteinové domény a motivy * MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely * MeSH
• proteiny vázající RNA chemie   metabolismus   MeSH
• RNA chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Z-DNA chemie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• proteiny vázající RNA MeSH
• RNA MeSH
• Z-DNA MeSH

The binding of the avian retroviral matrix protein ASLV MA(p19) to homologous viral ssRNA and proviral dsDNA was analysed using electron microscopic methods combined with a special computer evaluation. No binding affinity of MA(p19) to homologous nondenatured or denatured viral RNA was found. In contrast, ASLV MA(p19) was shown to have one specific binding site on MAV-1 proviral dsDNA at position 6795 +/- 345 bp from the 5' end of the molecule. A second specific binding site was found in a cellular sequence.

• MeSH
• DNA vazebné proteiny metabolismus   MeSH
• DNA virů metabolismus   ultrastruktura   MeSH
• klonování DNA MeSH
• kur domácí MeSH
• proteiny virové matrix metabolismus   ultrastruktura   MeSH
• proviry genetika   metabolismus   MeSH
• Retroviridae - proteiny metabolismus   ultrastruktura   MeSH
• RNA virová metabolismus   ultrastruktura   MeSH
• vazebná místa MeSH
• virus ptačí leukózy genetika   MeSH
• virus ptačí myeloblastózy genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• avian retrovirus proteins MeSH Prohlížeč
• DNA vazebné proteiny MeSH
• DNA virů MeSH
• proteiny virové matrix MeSH
• Retroviridae - proteiny MeSH
• RNA virová MeSH