Bioinformatyk.eu nowy serwis o bioinformatyce i programowaniu » Biochemia

Modified bases in RNA

dr Krystian Rother — Fri, 14 Jan 2011 12:56:27 +0000

Many RNA molecules are posttranscriptionally modified. This means that specific positions in the RNA chain are chemically changed by enzymes, mostly adding extra chemical groups.

RNA modifications are most abundant in tRNA, where about 20% of the residues are modified. They stabilize the tRNA tertiary structure, increase the accuracy of recognition by proteins from the aaRS families that aminoacylate the tRNA, and they allow one anticodon to recognize more than one codon. Some modified positions like the dihydrouridine in the D-loop and pseudouridine in the P-loop are highly conserved. Modifications also occur in rRNA. Some methylations of specific positions of the active site of bacterial ribosomes have been shown to confer resistance to antibiotics targeting translation. Other types of RNA (group I introns, mRNA, snRNA) also are modified occasionally.

About half of the known modified nucleotides are methylated. Especially, methylation of the 2′OH-position is common, because it provides some protection against hydrolysis. Many other chemical types of modifications are known: aminoacylation, glycosylation, thiolation, and sometimes a nucleotide is even modified more than once (hypermodified nucleotides). To date, about 119 different nucleotide modifications are known, all of which are listed in the Modomics database (http://iimcb.genesilico.pl/modomics).

The enzymes that introduce modifications belong to a wide variety of families. Generally, each enzyme is specifically modifying only one or just a few positions in its RNA target. Therefore, it is not surprising that many different enzymes are required. It has been estimated, that up to 10% of the proteins in E.coli are methyltransferases – a part of which methylates DNA, not RNA, though.

Experimental determination of nucleotide modifications is difficult, because they cannot be detected by standard sequencing or in vitro transcription techniques. One method especially useful for identifying modified nucleotides is mass spectrometry.

RNA Base pairs

dr Krystian Rother — Fri, 14 Jan 2011 12:49:45 +0000

Base pairs are the most important interaction found in folded RNA. Formed by hydrogen bonding, both classical Watson-Crick pairs (A-U, G-C) and wobble base pairs (G-U) can be found frequently – the bases then are oriented in the same way as in DNA. These are termed canonical base pairs (70%). Less frequently (30%), the nucleotide bases can also form hydrogen bonds in different ways, forming noncanonical base pairs. These noncanonical pairs can be formed on all sides of the purine and pyrimidine rings.

One can distinguish three edges on each base: The Watson-Crick edge (W), the Hoogsteen edge (H), and the Sugar edge (S). Any two of these can be combined. In addition, base pairs can be dividied into cis (c) and trans (t), depending on the orientation of the riboses. Together, there are twelve combinations possible (3 edges on one base * 3 edges on the second base * 2 cis/trans). Each combination of edges can occur with different combinations of bases.

Examples for names of base pair types are „trans-Watson-Watson (A-U)”, or „cis-Watson-Hoogsteen (A-G)”. For all twelve classes of base pairs, some exemplars have been found in nature. A comprehensive catalog of base pairs can be found on the FR3D website: http://rna.bgsu.edu/FR3D/basepairs).

In the hydrogen bonds in these base pairs, basically all possible hydrogen donor and acceptor atoms in the bases participate. When the sugar edge is involved, the 2′OH-group acts as a hydrogen donor as well. What makes visual and computational identification of these hydrogen bonds challenging is that sometimes a water molecule mediates the contact between both bases (water-mediated hydrogen bonds), and sometimes a hydrogen donor can have two acceptors or vice versa (bifurcated hydrogen bonds). The FR3D software can calculate base pairs with these properties as well from a 3D structure.

Szlaki biochemiczne dla wytrwałych

Justi — Tue, 02 Mar 2010 22:33:30 +0000

Ostatnio, w celach edukacyjnych (sesja) przeszukiwałam internet. Oto co znalazłam o cyklach i szlakach biochemicznych i metabolicznych (Biochemical Pathways, Metabolic Pathways):

Cyfrowa wersja planszy, wyprodukowanej przez firmę Roche. W pierwszym momencie może przyprawić o zawrót głowy uzupełniona o milszą już dla oka wyszukiwarkę. Całość jest na tyle intuicyjna, że nie wymaga instrukcji obsługi, umieszczona na serwerze ExPASy Molecular Biology Server, który daje również dostęp do informacji o poszczególnych procesach zachodzących w danym szlaku. W podglądzie powiększonego kwadratu można skorzystać z odnośników, którymi są teksty wydrukowane niebieską czcionką.

Baza BioCyc, w której cała mapa szlaków metabolicznych została rozdzielona na poszczególne składowe. Każdy kluczowy związek został oznaczony symbolem (legenda z prawej), który jednocześnie jest odnośnikiem do bardziej szczegółowych informacji. Zamieszczono również instrukcję obsługi w formie screencast’ów. Całość jako plakat można ściągnąć stąd.
Baza MouseCyc, oparta częściowo na BioCyc, przedstawia szlaki metaboliczne zbadane u myszy laboratoryjnych. Przykładowy cykl: cykl kwasu cytrynowego, daje nam wiele możliwości podglądu, możemy pomniejszyć bądź powiększyć dany fragment, co ukaże nam więcej szczegółów. Dodatkowo poznamy miejsca w gnomie myszy, w którym ulokowane są geny kodujące enzymy niezbędne do przeprowadzania tego cyklu.