Friday, September 23, 2011

Weekly RNA News - Week XXXVI - September 2011

Not One but Two!, Recent Reviews on RNA Structure, Interactions, and Folding Principles.


Two reviews have just come out from the Mondragón group at Northwestern and from the Pyle group at Yale.


Emerging Structural Themes in Large RNA Molecules
Nicholas J. Reiter, Clarence W. Chan and Alfonso Mondragón
Current Opinion in Structural Biology 21, 319-326 (2011)

In line with their previous research (i.e. the RNase P X-Ray structure, PDB_ID:3Q1Q) the authors stick to reviewing what has been learned from intermediate size RNA molecules, that is, RNA molecules larger than a hundred nucleotides, but smaller than say a thousand nucleotides.

The main points argued in this review are:

- RNA's of this size are relatively flat due to tertiary interactions, namely, "extensive" coaxial stacking, loop-loop interactions, and not mentioned in the review side by side helical arrangements.
- The structures of the functional cores of intermediate size RNA's are conserved, not necessarily the sequences.
- The functional cores don't need large conformational arrangements, they are said to be preassembled and usually this happens around a metal ion.
- Molecular recognition of "targets" is accomplished by shape-complementarity and specific atomic interactions (base-pairing, base-stacking, base-sugar, base-backbone). This is a general principle in molecular recognition.
- Adenine's are statistically more abundant than any other base in tertiary interacting regions, they are also the most conserved in all RNase P's.
- Proteins extend the functionality of RNA's and can be essential as in the case of the ribosome and the spliceosome, or non-essential, as in the case of RNase P and Group I and II Introns.

They conclude that the best is yet to come concerning RNA's in line with the promise, highly encouraged by Breaker's Lab. research, that many more RNA structures are to come and then this few empirical facts we've come to know will expand or change accordingly.



For the Group II Intron one can have an image like the above one, showing the helical regions as blue cylinders and the phosphates colored grey connected with a string in red, to illustrate the "flatness" of intermediate sized RNA's.


The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks
Samuel E. Butcher and Anna Marie Pyle
Accounts of Chemical Research X, xxx-xxx (2011)

Interestingly enough the previous paper (the one of Reiter) comes from a whole issue devoted to nucleic acids and edited by Anna Pyle.

In this review Butcher and Pyle take a look at the main interactions and structural elements found in RNA's today.
These seem to be split into:

- Coaxial Stacking of Helical Regions.
- Geometric Organization of Helical Junctions.
- Long-Range Interactions of Watson-Crick Base-Pairs.
    * Kissing-Loops.
    * Pseudoknots.
- Minor Groove Triples and A-Minor Motifs.
- Kink Turns and Other Turn Motifs.
- Tetraloop-Receptor Motifs.
- Intercalation Motifs (T-Loops).
- Triple-stranded RNA's (more like RNA triplets)
- RNA Quadruplexes.

The final remarks on the review concern the nature of the ribose, the 2'-OH interactions (e.g. Ribose Zippers), metal ions (the description of new crystallographic results in accordance to Draper's seminal paper reviewed in this here blog) and non-canonical base-pairs.

In Figure 2 of the article an image of a kissing-loop interaction is shown. The following image reproduces such image with helical regions identified by 3DNA represented as blue cylinders.

Tuesday, September 13, 2011

Weekly RNA News - Week XXXV - September 2011

RNAase P: At Last, the Key Finds its Lock
Benoit Masquida and Eric Westhof
RNA 7, 1615-1618 (2011)

Masquida and Westhof who are both at Strasbourg, France, review the X-ray structure obtained with a resolution of 4.2 Angstroms of RNase P, a ribozyme like the ribosome which has the ability to work as a "multiple turnover" enzyme. The structure of RNase P has PDB_ID's: 3Q1Q and 3Q1R, the difference is that the second one contains the 5'-leader whereas the first comes without, and at 3.8 Angstrom resolution.
The structure was determined by a group of researchers at Northwestern University and the University of Chicago and the main author is Nicolas Reiter who is a post-doctoral researcher at Alfonso Mondragon's Lab at Northwestern. The reason for the review is mainly that Tsai, Masquida, Westhof and others proposed a structure for RNase P in 2003 from secondary structure maps enriched with hydroxyl-radical footprinting data and it's quite close to the final crystal structure. A pymol generated figure showing the full holoenzyme is drawn below:

Notice the 5'-leader is rendered as spheres with carbons in grey color and just in top of the protein part (drawn in black) of the holoenzyme (holoenzyme=enzyme+cofactors). The surface in blue is just given the name P-RNA, and the part rendered as sticks is  pre-tRNAphe. The whole structure has a total of 423 bases coming from the P-RNA and the pre-tRNAphe.

Thursday, September 8, 2011

Weekly RNA News - Week XXXIV - September 2011

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs
Jan Gorodkin and Ivo L. Hofacker
PLOS Comp. Bio. 7, e1002100 (2011)

This is one of those cases where an article defies the traditional classification. By this I mean that although this article is clearly a review, it is not being published in a review journal, or maybe it's more likely that I don't understand the format of how PLoS works, for example their dislike for the traditional page-numbering scheme.
OK, stop ranting about irrelevancies and stick to the article.
Ohh, well, I can't stop with the "irrelevancies".
I guess it's the model of PLoS which makes articles hard to read, yes, an unfair judgement based on one article which you were expecting to be great (due to the authors) and then you're thoroughly deceived by the many errors and the lack of depth of the content, specially when compared with their much nicer article "De novo prediction of structured RNAs from genomic sequences" published in Trends in Biotechnology, a "regular" type of journal without the PLoS hype.

The article main topic is that of "de novo" discovery of non-coding RNA's. To this end the authors highlight two main strategies.

1) Sequence based alignments.
2) Synteny/Orthology with structure realignment.

Strategy one doesn't need much explanation, just that databases of know RNA sequences are necessary to make comparisons across organisms, for example the Rfam (RNA-families) database.
The second case brings up jargon, and it's not clear what they might mean if one sticks to the wikipedia definition of the term synteny. It would be nice if there was an example of what they mean in practice. What I understand is that perhaps in the second strategy secondary structure alignments are taken into account in the context of distant regions in the same chromosome which might refer to the "same" gene.


BlastR—fast and accurate database searches for non-coding RNAs
Giovanni Bussotti and Emanuele Raineri and Ionas Erb and Matthias Zytnicki and Andreas Wilm and Emmanuel Beaudoing and Philipp Bucher and Cedric Notredame
Nucleic Acids Research, 39, 6886-6895 (2011)

The main idea of this article is to use the already existing techniques for alignments of proteins to the alignment of RNA's. To test the perl script they have implemented to interact with the already existing ncbi-blast package I downloaded the full long-non-coding RNA database from :
http://www.lncrnadb.org/
And then I used it as database to compare, say, one of the sequences existing in such database.
Not surprisingly the result is a 100% score in their similarity measure, and it took a couple of hours to get it all done. Here's a snapshot of the results of running the command:

blastallR.pl -p blastr -i NR_003141.3 -d database/ncbi_blastR_format/db -m 8


Not surprisingly the first score matches as indicated by the 100% score.