Transcription and Translation

RNA Export Diagram

Earlier today I gave our weekly journal club. As usual there is some large scheme/model/godzilla image associated with the intro/summary. Here’s mine … mRNA nuclear export in yeast:

i-17efedc4a3a3041a30d4ee256a8541c8-RNAscheme.jpg

Highlighted are 3 major systems. Many proteins are listed, many more are not.

Nucleoplasm is on the bottom, cytosol on the top. The bilayered nuclear membrane is represented by the two black lines. The big red/blue thing with the purple basket is the nuclear pore complex (NPC).

In purple hue is the Mpl1/2 system. These proteins are the orthologues of TPR in mammalian cells and form the basket of the NPC. Mpl1p and Mlp2p scan the Ribonuclear protein complexes (RNPs = mRNA + associated proteins) and act as a quality control checkpoint. If mRNA is not spliced or the RNP is not properly formed then export is blocked. The RES (the Retention and Splicing) complex, which associates with the splicing machinery, may play a role in this process. Unlike the next two systems, the role of these proteins is to block the export of improperly formed RNPs.

In green is the Sub2/Yra1/Mex67 system. As oppose to the Mlp1/2 system, these proteins are pro-export. They are loaded sequentially but may also bind to transcripts independently. Many RNA processing events can stimulate their association to the RNA. Mex67 can associate with the FG repeats, a mesh work found inside the NPC and thus allows passage across this barrier. Thus the function of these proteins is to get across the FG repeat region of the pore.

In reddish hues is the Gle1/Dbp5/Nup82complex system. Dbp5p is a helicase that may help to pull the mRNA out of the nucleus and/or strip off proteins (helicase=protein that can unwind/separate in this case RNA). It is thought to be loaded onto the RNP during translation and it’s activity is stimulated at the outer edge of the NPC by Gle1p. For some odd reason, Gle1p’s activity is stimulated by Inositol hexakisphosphate (IP6). Enzymes on the IP6 biosynthetic pathway genetically interact with the Gle1/Dbp5/Nup82complex system. The function of this complex may be to drive the whole mRNA export mechanism.

Now there are MANY other proteins that affect the distribution of poly-A transcripts in yeast. Some are being place in one of these “systems”, most haven’t. Another important note: many transcripts are unaffected by the disabling of the three “systems” presented above and so it is likely that other systems do exit. In fact, I did not add info here on the Exon Junction Complex … although the EJC, as it is known, is involved in nonsense mediated decay and barely affects export.

Another point is that the NPC is divided into 3 parts. The basket and cytoplasmic protrusions (the purple and red parts) are primarily involved in RNA export and seem dispensable for protein export/import. The interior (blue part) is a barrier that all nuclear transport must contend with.

And with that I’m off for the weekend. (I guess it’s time for my export!)

Comments

  1. #1 Sandra Porter
    December 1, 2006

    I think your RNA should be folded up – for some reason, I think that enzymes involved in RNA processing interact with both the 5′ and 3′ ends, too.

  2. #2 apalazzo
    December 2, 2006

    So this idea that the 5′ and 3′ ends interact comes from the fact that proteins that bind to the poly-A tail also bind to the cap binding proteins. It’s thought that this occurs in the cytoplasm, although some (like Marilyn Kozak) think that this isn’t really true. It is clear that this cytoplasmic 5′-3′ interaction (if it’s true) is not universal. For example it’s clear that mRNAs translated on the surface of the ER form spirals where one end is in the center of the spiral the other end is on the outside. There is no evidence that the 5′-3′ interaction occurs in the nucleus.

    As for my diagram and RNA binding proteins, the diagram is limited to a subset of RNA binding proteins in yeast that play a role in mRNA export. There are many many many more proteins that bind mRNA to form RNPs. Most of the mRNA molecule is coated with RNA binding proteins. The RNP is also a compact structure as viewed by electron microscopy, and this is due mainly by protein binding although the secondary structure of the RNA could also play a role. Some have claimed that the RNP elongates when it goes through the pore and that the 5′ end goes in first, the 3′ end goes in last.

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