LEGO June 1, 2015

From GO Wiki
Jump to: navigation, search


Agenda

LEGO Curation

GTPase Signaling Pathways

  • Annotating GTPases to reflect their role in a signaling pathway
    • Annotate entity as GTP-bound form (via PRO ID, for example)?
    • We have a term, GO:0030742, GTP-dependent protein binding; what is the intended use of this term?
      • Definition: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP.

Annotation Issues

  • Neuron Migration in C. elegans
  • GTPase activities
  • Q cell migration model
  • MIG-2 (C. elegans RhoG) has low affinity for GTP (similar to GTP binding-defective negative control) but GTPase activity similar to other Rho GTPases, so evidence for GTP binding is weak
  • Paper uses an engineered GTP-bound mimic to assess binding to downstream effector, ANI-1
  • What's the correct annotation for the binding?
    • ANI-1: GTP-Rho binding? Rho GTPase binding?
  • What's the correct MF annotation for MIG-2 for this signaling pathway?
  • Wrt linking annotons, clarify what experimental evidence supports use of:
    • causally_upstream_of : p is upstream of q if and only if p precedes q and p and q are linked in a causal chain
      • To test this, we introduced GFP::ANI-1 into mig-2(mu28)-null mutants, and we showed that GFP::ANI-1 left the plasma membrane and became evenly distributed in the cytoplasm in mig-2(mu28) animals (Figures 6 A–6E for QR.ap;Movie S2).
    • directly_activates : p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
      • To test this, we introduced GFP::ANI-1 into mig-2(mu28)-null mutants, and we showed that GFP::ANI-1 left the plasma membrane and became evenly distributed in the cytoplasm in mig-2(mu28) animals (Figures 6 A–6E for QR.ap;Movie S2).
      • We further showed that GFP::moesinABD was largely reduced at the leading edge (Figures 3B, 3D, and 3E): the fluorescence intensity ratio between the green F-actin and the red plasma membrane was decreased from 4.2- to 0.3-fold during Q cell migration and from 4.0- to 0.2-fold during neurite growth in ani-1 conditional knockouts (Figures 3F and S3). Thus, Anillin regulates neuronal migration and neurite growth by stabilizing the actin cytoskeleton in the leading edge.
      • Under a low centrifugation force (see the Supplemental Experimental Procedures), we showed that the presence of Anillin or its MBD-ABD domain increased the amount of preassembled actin filaments in the pellet(Figure4E;Plastin 3 as the positive control), suggesting that Anillin may organize actin filaments into higher-order structures. This bundling activity was further confirmed by directly visualizing the effects of these Anillin constructs on preassembled actin filaments under a fluorescence microscope (Figure 4F).
    • positively_regulates : x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y
      • We showed that 20% of A/PQR neurons reduced their migration distance in ani-1 conditional mutants (Figures 2C and 2E).