BMCB625:Exon Jxn Complex

From OpenWetWare
Revision as of 16:27, 31 May 2007 by Jonfay (talk | contribs) (Jon)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
BMCB625 Advanced Topics in Molecular Biology

RainbowLong.jpg

Home        People        Materials        Schedule        Help        Discussion       

Papers

  1. Bono F, Ebert J, Lorentzen E, and Conti E. The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell. 2006 Aug 25;126(4):713-25. DOI:10.1016/j.cell.2006.08.006 | PubMed ID:16923391 | HubMed [Bono]

Bonus Materials

Ranking:

  • Critical Read/of Outstanding Interest (oo)
  • Importand Read (o)
  • of Interest (no label)
  • (o)(Ref 3, LeHir, et al) A good overview on how introns may influence gene expression, and why the EJC (Exon Junction Complex) is such an important player in the "mRNA to translation steps" in the control of gene expression.
  • (o)(Ref4, Tange, et al)) Great Review on EJC, and a relatively quick read (five to ten minutes).
  1. Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Séraphin B, Le Hir H, and Andersen GR. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science. 2006 Sep 29;313(5795):1968-72. DOI:10.1126/science.1131981 | PubMed ID:16931718 | HubMed [Andersen]
  2. Le Hir H, Nott A, and Moore MJ. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci. 2003 Apr;28(4):215-20. DOI:10.1016/S0968-0004(03)00052-5 | PubMed ID:12713906 | HubMed [LeHir]
  3. Tange TØ, Nott A, and Moore MJ. The ever-increasing complexities of the exon junction complex. Curr Opin Cell Biol. 2004 Jun;16(3):279-84. DOI:10.1016/j.ceb.2004.03.012 | PubMed ID:15145352 | HubMed [GREAT-EJC-REVIEW]
  4. Stroupe ME, Tange TØ, Thomas DR, Moore MJ, and Grigorieff N. The three-dimensional arcitecture of the EJC core. J Mol Biol. 2006 Jul 21;360(4):743-9. DOI:10.1016/j.jmb.2006.05.049 | PubMed ID:16797590 | HubMed [3D-EJC]
  5. Shibuya T, Tange TØ, Sonenberg N, and Moore MJ. eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat Struct Mol Biol. 2004 Apr;11(4):346-51. DOI:10.1038/nsmb750 | PubMed ID:15034551 | HubMed [eIF4AIII]
  6. Ballut L, Marchadier B, Baguet A, Tomasetto C, Séraphin B, and Le Hir H. The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity. Nat Struct Mol Biol. 2005 Oct;12(10):861-9. DOI:10.1038/nsmb990 | PubMed ID:16170325 | HubMed [EJC-eIF4AIII]
  7. Shi H and Xu RM. Crystal structure of the Drosophila Mago nashi-Y14 complex. Genes Dev. 2003 Apr 15;17(8):971-6. DOI:10.1101/gad.260403 | PubMed ID:12704080 | HubMed [Mago-Y14]
  8. Cordin O, Banroques J, Tanner NK, and Linder P. The DEAD-box protein family of RNA helicases. Gene. 2006 Feb 15;367:17-37. DOI:10.1016/j.gene.2005.10.019 | PubMed ID:16337753 | HubMed [DEADbox]
  9. of the Breast Cancer Protein MLN51 with the Exon Junction Complex via Its Speckle Localizer and RNA Binding Module

    [[1]]

    [Association]
All Medline abstracts: PubMed | HubMed

Unresolved Questions for Followup


(Homework) Discussion Topics /Questions

Paper for additional Discussion (2 figures presented in EJC presentation on Thurs. 31 May 2007):

  • Noble CG, Song H (2007) MLN51 Stimulates the RNA-Helicase Activity of eIF4AIII. PLoS ONE 2(3): e303. doi:10.1371/journal.pone.0000303[[1]]
  • Can post a comment on PLos (Public Library of Science) for everyone in the world to discuss the positive aspects, as well as limitations of this paper.

Larry


Chayne


Jon

  1. Assuming that Y14 and Magoh inhibit ATP hydrolysis and in the ATP bound form eIF4AIII binds the mRNA tightly, why might such a fragile system be favorable?

Perhaps the inhibition of ATP hydrolysis by Magoh and Y14 lends the complex to be primed to uncouple from the mRNA in the pioneering translation round.

  1. If MLN51 (Btz) stimulates ATP hydrolysis, and Y14/Magoh inhibits would you expect an ordered binding of these subunits to eIF4AIII?

This is pure speculation but since there are competing forces (activators and inhibitors )perhaps there is some interplay and one might go so far to say that there MAY even an sequential binding.

  1. Why didn't the authors further verify their "large conformational change" with an additional in vitro experiment (rhetorical)?





Jeremy

Q1. The authors down play the observation that the RNA is in a bent conformation. Why might this actually be important?

A1. The bent conformation observed for the bound polyU RNA may help explain why the EJC complex binds specifically at exon junctions. The spliceosome bends RNA through out the splicing cycle. The EJC complex may therefore bind at particular bends imposed by the spliceosome - this would lower the entropic cost of binding for the EJC complex.


Q2. Suggest some possible experiments to test the observed protein-protein interaction network and it's effect on assembly on RNA?

A2. As for all x-ray crystal structures, the crystallographers or collaborators should make an attempt to support their structure using experiments in solution. This is particularly important when characterizing protein-protein interactions, where point mutations should be made at sites thought to be important from the crystal structure and tested in a solution based assay. This helps to rule out crystal packing artifacts, a somewhat common artifact of shoving proteins together to form a crystal lattice. The authors unfortunately did not do this for the EJC crystal structure. GST pull down assay and native PAGE using radiolabeled RNA could be used to test important contacts, and investigate potential cooperativity between protomers in the EJC complex as it forms on RNA.

Faculty Questions and Comments