Dinucleoside polyphosphates (NpnNs) were discovered 50 years ago in all cells. They are often called alarmones, even though the molecular target of the alarm has not yet been identified. Recently, we showed that they serve as noncanonical initiating nucleotides (NCINs) and fulfill the role of 5' RNA caps in Escherichia coli. Here, we present molecular insight into their ability to be used as NCINs by T7 RNA polymerase in the initiation phase of transcription. In general, we observed NpnNs to be equally good substrates as canonical nucleotides for T7 RNA polymerase. Surprisingly, the incorporation of ApnGs boosts the production of RNA 10-fold. This behavior is due to the pairing ability of both purine moieties with the -1 and +1 positions of the antisense DNA strand. Molecular dynamic simulations revealed noncanonical pairing of adenosine with the thymine of the DNA.
- MeSH
- bakteriofág T7 enzymologie MeSH
- dinukleosidfosfáty genetika metabolismus MeSH
- DNA řízené RNA-polymerasy genetika metabolismus MeSH
- DNA metabolismus MeSH
- iniciace genetické transkripce * MeSH
- párování bází MeSH
- RNA čepičky genetika MeSH
- RNA genetika metabolismus MeSH
- simulace molekulární dynamiky MeSH
- vazba proteinů MeSH
- virové proteiny genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS: To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS: Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
- MeSH
- DNA-polymerasa II metabolismus MeSH
- iniciace genetické transkripce * MeSH
- modely genetické MeSH
- počátek transkripce * MeSH
- promotorové oblasti (genetika) MeSH
- Saccharomyces cerevisiae enzymologie genetika MeSH
- transkripční faktory hlavní metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
The first described small non-coding RNA was microRNA lin-4 from Caenorhabditis elegans in 1993. This miRNA has begun a new age of research leading to the discovery of previously unknown, endogenous, single stranded, 22–25 nucleotides long molecules regulating nearly 30 % of genes. Recently, it was demonstrated that a number of organic substances presented in the diet induces the formation of various miRNAs. Besides this, plant and animal miRNA may enter the host organisms as food. In host organism, they can resist degradation and can enter the bloodstream. Although lacking sufficient experimental support, the discussion whether such dietary miRNAs can participate in post-transcriptional regulation of host genes is an actual topic. Either of these mechanisms could also explain some of the biological activities of medicinal plants. Non-coding RNAs have also significance as diagnostic biomarkers of some diseases or as targets for complex disease therapies.
- MeSH
- biologické markery metabolismus MeSH
- genetická transkripce genetika imunologie MeSH
- iniciace genetické transkripce MeSH
- lidé MeSH
- mikro RNA izolace a purifikace metabolismus MeSH
- nekódující RNA * genetika izolace a purifikace metabolismus MeSH
- potraviny MeSH
- regulace genové exprese u nádorů genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
RNA polymerase (RNAP) is the central enzyme of transcription of the genetic information from DNA into RNA. RNAP recognizes four main substrates: ATP, CTP, GTP and UTP. Experimental evidence from the past several years suggests that, besides these four NTPs, other molecules can be used to initiate transcription: (i) ribooligonucleotides (nanoRNAs) and (ii) coenzymes such as NAD+, NADH, dephospho-CoA and FAD. The presence of these molecules at the 5΄ ends of RNAs affects the properties of the RNA. Here, we discuss the expanding portfolio of molecules that can initiate transcription, their mechanism of incorporation, effects on RNA and cellular processes, and we present an outlook toward other possible initiation substrates.
Lipoxygenázy (LOX, linoleate: oxygen oxidoreductases, EC 1.13.11.12) tvoria rodinu dioxygenáz, ktoré obsahujú nehémové, nesulfidové železo. Vyskytujú sa nielen u živočíchov, ale aj u rastlín. Ich prítomnosť bola dokázaná aj v koraloch, machu, hubách a v niektorých baktériách. LOX katalyzujú polohovo- a stereo- špecifickú inzerciu molekulového kyslíka do molekuly nenasýtenej mastnej kyseliny s cis,cis-1,4-pentadiénovým systémom za vzniku príslušných hydroperoxidových derivátov. Tento krok dioxygenácie vyúsťuje do kaskády reakcií, ktoré sa označujú ako lipoxygenázová (oktadekánová) cesta. Koncové produkty tejto cesty (nazývané oxylipíny) zohrávajú u rastlín významnú úlohu ako signálne molekuly pri hojení rán a pri obranných procesoch. V živočíšnych organizmoch sú zase zapojené do procesov zápalových reakcií, astmy a ochorení srdca.
Lipoxygenases (LOX, linoleate: oxygen oxidoreductases, EC 1.13.11.12) constitute a family of dioxygenases, which contain non-heme, non-sulfide iron. These enzymes occur not only in animals, but in plants as well. They have been detected in coral, moss, fungi and also in some bacteria. LOXs catalyse the regiospecific and stereospecific insertion of molecular oxygen into the molecule of polyunsaturated fatty acid with the cis,cis- -1,4-pentadiene system to yield the corresponding hydroperoxides. This step of dioxygenation leads to a cascade of reactions called the lipoxygenase (octadecanoid) pathway. The products of this pathway (called oxylipins) play an important role as signal molecules in wound healing and defence processes in plants. In animals they are involved in inflammation, asthma and heart diseases.
- MeSH
- biochemické jevy * MeSH
- buněčná diferenciace MeSH
- iniciace genetické transkripce MeSH
- lipoxygenasy * fyziologie MeSH
- membránové potenciály MeSH
- membránové transportní proteiny MeSH
- nenasycené mastné kyseliny chemie MeSH
- oxylipiny * chemie MeSH
- rostliny MeSH
- signální transdukce MeSH
- transkripční faktory MeSH
- Publikační typ
- přehledy MeSH
