G-quadruplexes (G4s) formed within RNA are emerging as promising targets for therapeutic intervention in cancer, neurodegenerative disorders and infectious diseases. Sequences containing a succession of short GG blocks, or uneven G-tract lengths unable to form three-tetrad G4s (GG motifs), are overwhelmingly more frequent than canonical motifs involving multiple GGG blocks. We recently showed that DNA is not able to form stable two-tetrad intramolecular parallel G4s. Whether RNA GG motifs can form intramolecular G4s under physiological conditions and play regulatory roles remains a burning question. In this study, we performed a systematic analysis and experimental evaluation of a number of biologically important RNA regions involving RNA GG motifs. We show that most of these motifs do not form stable intramolecular G4s but need to dimerize to form stable G4 structures. The strong tendency of RNA GG motif G4s to associate may participate in RNA-based aggregation under conditions of cellular stress.

• MeSH
• dimerizace MeSH
• G-kvadruplexy * MeSH
• genetická transkripce MeSH
• lidé MeSH
• nukleotidové motivy * MeSH
• RNA * chemie   metabolismus   genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 °C. Our findings show that iMFPS displaying pHT < 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pHT > 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.

• MeSH
• azidy * MeSH
• benzazepiny * MeSH
• DNA MeSH
• HeLa buňky MeSH
• lidé MeSH
• magnetická rezonanční tomografie * MeSH
• protilátky MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Cytosine-rich DNA regions can form four-stranded structures based on hemi-protonated C.C+ pairs, called i-motifs (iMs). Using CD, UV absorption, NMR spectroscopy, and DSC calorimetry, we show that model (CnT3)3Cn (Cn) sequences adopt iM under neutral or slightly alkaline conditions for n > 3. However, the iMs are formed with long-lasting kinetics under these conditions and melt with significant hysteresis. Sequences with n > 6 melt in two or more separate steps, indicating the presence of different iM species, the proportion of which is dependent on temperature and incubation time. At ambient temperature, kinetically favored iMs of low stability are formed, most likely consisting of short C.C+ blocks. These species act as kinetic traps and prevent the assembly of thermodynamically favored, fully C.C+ paired iMs. A higher temperature is necessary to unfold the kinetic forms and enable their substitution by a slowly developing thermodynamic structure. This complicated kinetic partitioning process considerably slows down iM folding, making it much slower than the timeframes of biological reactions and, therefore, unlikely to have any biological relevance. Our data suggest kinetically driven iM species as more likely to be biologically relevant than thermodynamically most stable iM forms.

• MeSH
• DNA * genetika   chemie   MeSH
• kinetika MeSH
• koncentrace vodíkových iontů MeSH
• konformace nukleové kyseliny MeSH
• nukleotidové motivy MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Many patients with chronic myeloid leukemia in deep remission experience return of clinical disease after withdrawal of tyrosine kinase inhibitors (TKIs). This suggests signaling of inactive BCR-ABL, which allows the survival of cancer cells, and relapse. We show that TKI treatment inhibits catalytic activity of BCR-ABL, but does not dissolve BCR-ABL core signaling complex, consisting of CRKL, SHC1, GRB2, SOS1, cCBL, p85a-PI3K, STS1 and SHIP2. Peptide microarray and co-immunoprecipitation results demonstrate that CRKL binds to proline-rich regions located in C-terminal, intrinsically disordered region of BCR-ABL, that SHC1 requires pleckstrin homology, src homology and tyrosine kinase domains of BCR-ABL for binding, and that BCR-ABL sequence motif located in disordered region around phosphorylated tyrosine 177 mediates binding of three core complex members, i.e., GRB2, SOS1, and cCBL. Further, SHIP2 binds to the src homology and tyrosine kinase domains of BCR-ABL and its inositol phosphatase activity contributes to BCR-ABL-mediated phosphorylation of SHC1. Together, this study characterizes protein-protein interactions within the BCR-ABL core complex and determines the contribution of particular BCR-ABL domains to downstream signaling. Understanding the structure and dynamics of BCR-ABL interactome is critical for the development of drugs targeting integrity of the BCR-ABL core complex.

• MeSH
• adaptorové proteiny signální transdukční metabolismus   MeSH
• aminokyselinové motivy MeSH
• bcr-abl fúzní proteiny chemie   genetika   metabolismus   MeSH
• chronická myeloidní leukemie metabolismus   patologie   MeSH
• čipová analýza proteinů MeSH
• fosfatidylinositol-3,4,5-trisfosfát-5-fosfatasy metabolismus   MeSH
• fosforylace MeSH
• HEK293 buňky MeSH
• inhibitory proteinkinas farmakologie   MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• pyrimidiny farmakologie   MeSH
• signální transdukce účinky léků   MeSH
• vazba proteinů účinky léků   MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH

This article suggests a new mechanistic scheme of the catalytic 8-oxoguanine excision with the hOGG1 base excision repair protein. The energy-efficient and substratespecific scheme employs enforced pyramidalization of the glycosidic nitrogen in the nucleobase within the hOGG1 catalytic pocket.

• Klíčová slova
• human 8-oxoguanine glycosylase1 protein,
• MeSH
• chemické jevy MeSH
• deoxyguanosin chemie   MeSH
• DNA-glykosylasy * chemie   MeSH
• enzymy opravy DNA * chemie   MeSH
• lidé MeSH
• molekulární modely MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH

• Publikační typ
• abstrakt z konference MeSH

The mitochondrial RNA-binding proteins (MRP) 1 and 2 play a regulatory role in RNA editing and putative role(s) in RNA processing in Trypanosoma brucei. Here, we report the purification of a high molecular weight protein complex consisting solely of the MRP1 and MRP2 proteins from the mitochondrion of T. brucei. The MRP1/MRP2 complex natively purified from T. brucei and the one reconstituted in Escherichia coli in vivo bind guide (g) RNAs and pre-mRNAs with dissociation constants in the nanomolar range, and efficiently promote annealing of pre-mRNAs with their cognate gRNAs. In addition, the MRP1/MRP2 complex stimulates annealing between two non-cognate RNA molecules suggesting that along with the cognate duplexes, spuriously mismatched RNA hybrids may be formed at some rate in vivo. A mechanism of catalysed annealing of gRNA/pre-mRNA by the MRP1/MRP2 complex is proposed.

• MeSH
• chromatografie MeSH
• editace RNA MeSH
• elektronová mikroskopie MeSH
• financování organizované MeSH
• guide RNA, Kinetoplastida metabolismus   ultrastruktura   MeSH
• lidé MeSH
• mitochondriální proteiny fyziologie   metabolismus   ultrastruktura   MeSH
• prekurzory RNA metabolismus   ultrastruktura   MeSH
• proteiny spojené s mnohočetnou rezistencí k lékům fyziologie   chemie   MeSH
• proteiny vázající RNA metabolismus   ultrastruktura   MeSH
• rekombinantní proteiny farmakologie   MeSH
• RNA protozoální genetika   MeSH
• Trypanosoma brucei brucei genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH

Tetrahymena telomerase RNA (TER) contains several regions in addition to the template that are important for function. Central among these is the stem-loop IV domain, which is involved in both catalysis and RNP assembly, and includes binding sites for both the holoenzyme assembly protein p65 and telomerase reverse transcriptase (TERT). Stem-loop IV contains two regions with high evolutionary sequence conservation: a central GA bulge between helices, and a terminal loop. We solved the solution structure of loop IV and modeled the structure of the helical region containing the GA bulge, using NMR and residual dipolar couplings. The central GA bulge with flanking C-G base pairs induces a approximately 50 degrees semi-rigid bend in the helix. Loop IV is highly structured, and contains a conserved C-U base pair at the top of the helical stem. Analysis of new and previous biochemical data in light of the structure provides a rationale for some of the sequence conservation in this region of TER. The results suggest that during holoenzyme assembly the protein p65 recognizes a bend in stem IV, and this binding to central stem IV helps to position the structured loop IV for interaction with TERT and other region(s) of TER.

• MeSH
• genetické matrice MeSH
• holoenzymy metabolismus   MeSH
• katalýza MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely MeSH
• molekulární sekvence - údaje MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• párování bází MeSH
• protozoální proteiny fyziologie   chemie   metabolismus   MeSH
• RNA protozoální metabolismus   MeSH
• RNA genetika   metabolismus   MeSH
• sekundární struktura proteinů MeSH
• sekvence nukleotidů MeSH
• telomerasa genetika   metabolismus   MeSH
• terciární struktura proteinů MeSH
• Tetrahymena thermophila enzymologie   genetika   metabolismus   MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH