9.18.2006

An mRNA Nuclear Export Factor Regulates Itself

Biology is filled with feedback loops and other natural buffers to promote homeostasis. In the latest Nature, there is a ... cute ... paper about how the RNA export factor Tap (aka NXF1) mediates the nuclear export of an alternatively spliced form of it's own mRNA transcript. (For more background on the mechanism of nuclear export of mRNA, click here).

Viruses like the Mason-Pfizer monkey virus can exploit our mRNA export pathway by having their transcripts bind directly to export factors such as Tap. The RNA elements that bind Tap are called constitutive export elements (CTEs). In a hunt for CTEs in transcripts endogenous to the mammalian genome, the authors came up with a CTE in Tap's own transcript. Turns out that this CTE is only present in an alternatively spliced (and shorter) form of Tap. This small Tap has a RNA binding domain but lacks a domain that interacts with the nuclear pore complex thus disabling the protein's nuclear export capability.

This feedback loop may regulate Tap activity -- the more Tap activity one has, the more mRNA that encodes inactivated Tap is exported. Once synthesized, inactivated Tap may suppress Tap activity, however the exact mechanism remains unclear. One problem is that the small Tap remains cytosolic. Any ideas? From the paper:

... Although the function of the small Tap protein is unclear, it retains the RNA-binding domain but lacks the nucleoporin and NXT1-binding domains, and locates mainly to the cytoplasm. Thus, it may regulate the function of Tap at the translational level.


We'll have to see how the loose ends get tied up in this story.

Ref:
Ying Li, Yeou-cherng Bor, Yukiko Misawa, Yuming Xue, David Rekosh and Marie-Louise Hammarskjöld
An intron with a constitutive transport element is retained in a Tap messenger RNA
Nature (2006) 443:234-237

9.08.2006

Physics versus Signaling

This is a very simple paper that attempts to answer a simple question – does physics play any role in regulating cell siganling. As cell biologists we generally like to think of signaling cascades as regulating cellular processes. We consider that an extracellular ligand binds a receptor triggering a cascade that results in some cellular behavior. The Odde lab however takes a different approach and proposes that physics, specifically cell size and shape play an important role in regulating cell signaling. Using mathematical models they show that if two signals are spatially segregated, there will be a sharp drop off in activity. In the theoretical portion of the paper they use the example of a protein that is phosphorylated by a membrane bound kinase and dephosphorylated by a cytosolic phosphatase under a variety of situations (a migrating cell is depicted to the left). While it seems obvious that if you bring the membrane close together you will increase the local kinase concentration/activity and decrease the local phosphatase concentration/activity, I don’t remember it being said before. Finally they use their model to recapitulate Cdc42 activity as was experimentally shown by Nalbant et al. (right), but unfortunately this is the only experimental evidence they site.

This is certainly an interesting take on signaling however, it raises a chicken or the egg type of question. Do we know as a matter of fact that Cdc42 does not contribute to cell “flattening” where it is active? Similarly they use a migrating cell in their models as an example of a situation where one would have spatially segregated signaling but as far as I can tell it is difficult to ascertain whether cellular physics lead to signaling or if signaling precedes the physics.

9.01.2006

IP6 and mRNA Export

See this entry for background on inositols. Inositol-6-phosphate (aka Inositol hexaphosphate, phytic acid, phytate) is a strange compound.

Apparently plants make loads of it, and it is thought that they use this molecule to store phosphate. Also it would seem that lots of cancer researchers have been throwing this compound onto oncogenic cell lines. Apparently IP6 works to inhibit cell growth ... but as to it's effectiveness in vivo, I don't know. Phytate is also sold as a dietary supplement. But lets talk about its known cellular functions. Now it turns out that IP6 is a co-factor required for mRNA export.

mRNA export is a strange field. Some background ... mRNA is synthesized in the nucleus and then exported to the cytoplasm where it is translated into protein. It was originally thought that mRNA utilized karyopherins and the Ran cycle to get exported from the nucleus (click here for more on nuclear transport), but it turned out that mRNA used its very own transport machinery. In vertebrates, UAP56 is recruited to the mRNA during transcription. Then during splicing, a second factor Aly associates with UAP56. Finally Aly recruits a heterodimer of TAP and NXT1 which have to ability to interact with components of the Nuclear Pore Complex (NPC)and thus facilitate nuclear export. Now obviously mRNA export must be powered by an energy utilizing process. Enter Dbp5, an RNA helicase that is situated in the NPC. Helicases are enzymes that use ATP derived energy to walk along DNA or RNA chains (conceptually similar to a myosin motor using ATP to walk along an actin filament). As the helicase move along the DNA/RNA it acts to either separate double stranded nucleic acid chains or strip off proteins that are bound to the single stranded RNA. OK a simple story. Dbp5 is a motor that drags mRNA out of the nucleus and strips off all these factors that got it to the NPC in the first place.

Now some weird stuff. In yeast, Inositol kinases mutants had mRNA export defects. As I explained a couple of days ago, many Inositol derivatives act as signalling molecules. So what gives? Well it turns out that Dbp5 requires IP6 as a co-factor. This small molecule stimulates Dbp5's helicase activity and it's ability to bind to NPC components such as Gle1. This is illuatrated in this diagram from a recent review:

nuclearexport.jpg

Now why would IP6 be involved in mRNA export? There must be something big behind this. And I'm sure we will get more information soon. But it sounds like IP6 could act as a regulatory molecule ... want to bump up mRNA export? Make IP6. Want to turn it off? Degrade IP6. Now when and why global mRNA export should be regulated is completely unknown, but that's also true of 90% of cellular behavior ...

ref:
Cole CN, Scarcelli JJ. Related Articles, Links
Transport of messenger RNA from the nucleus to the cytoplasm.
Curr Opin Cell Biol. (2006) 18:299-306.

Weirich CS, Erzberger JP, Flick JS, Berger JM, Thorner J, Weis K.
Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export.
Nat Cell Biol. (2006) 8:668-76


Alcazar-Roman AR, Tran EJ, Guo S, Wente SR
Inositol hexakisphosphate and Gle1 activate the DEAD-box protein Dbp5 for nuclear mRNA export.
Nat Cell Biol. (2006) 8:711-6.