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Mining the TRAF6/p62 interactome for a selective ubiquitination motif.

Jadhav TS, Wooten MW, Wooten MC - BMC Proc (2011)

Bottom Line: NRIF (K19), TrkA (K485), TrkB (K811), TrkC (K602 and K815), NTRK2 (K828), NTRK3 (K829) and MBP (K169) were found to possess a perfect match for the amino acid consensus motif for TRAF6/p62 ubiquitination.Collectively, our results reveal an unappreciated role for the scaffold protein in targeting ubiquitination.The findings described herein could be used to aid in identification of other E3/scaffold ubiquitination sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Cellular and Molecular Biosciences, Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL, 36849, USA. wootemc@auburn.edu.

ABSTRACT
A new approach is described here to predict ubiquitinated substrates of the E3 ubiquitin ligase, TRAF6, which takes into account its interaction with the scaffold protein SQSTM1/p62. A novel TRAF6 ubiquitination motif defined as [-(hydrophobic)-k-(hydrophobic)-x-x-(hydrophobic)- (polar)-(hydrophobic)-(polar)-(hydrophobic)] was identified and used to screen the TRAF6/p62 interactome composed of 155 proteins, that were either TRAF6 or p62 interactors, or a negative dataset, composed of 54 proteins with no known association to either TRAF6 or p62. NRIF (K19), TrkA (K485), TrkB (K811), TrkC (K602 and K815), NTRK2 (K828), NTRK3 (K829) and MBP (K169) were found to possess a perfect match for the amino acid consensus motif for TRAF6/p62 ubiquitination. Subsequent analyses revealed that this motif was biased to the C-terminal regions of the protein (nearly 50% the sites), and had preference for loops (~50%) and helices (~37%) over beta-strands (15% or less). In addition, the motif was observed to be in regions that were highly solvent accessible (nearly 90%). Our findings suggest that specific Lysines may be selected for ubiquitination based upon an embedded code defined by a specific amino acid motif with structural determinants. Collectively, our results reveal an unappreciated role for the scaffold protein in targeting ubiquitination. The findings described herein could be used to aid in identification of other E3/scaffold ubiquitination sites.

No MeSH data available.


Sub-cellular localization of TRAF6/p62 substrates. Comparisons presented for each database showing the total proportion of proteins in each category versus the proportion predicted among the perfect and near perfect motif match proteins.
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Figure 6: Sub-cellular localization of TRAF6/p62 substrates. Comparisons presented for each database showing the total proportion of proteins in each category versus the proportion predicted among the perfect and near perfect motif match proteins.

Mentions: To study the subcellular distribution of the predicted TRAF6/p62 substrates, compartmentalization of the proteins in both the datasets was examined (Table 2, Figure 6). Proteins were assigned to cellular compartments based on the literature, curated information in protein databases and GO ontology for protein subcellular localization [36].


Mining the TRAF6/p62 interactome for a selective ubiquitination motif.

Jadhav TS, Wooten MW, Wooten MC - BMC Proc (2011)

Sub-cellular localization of TRAF6/p62 substrates. Comparisons presented for each database showing the total proportion of proteins in each category versus the proportion predicted among the perfect and near perfect motif match proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3090762&req=5

Figure 6: Sub-cellular localization of TRAF6/p62 substrates. Comparisons presented for each database showing the total proportion of proteins in each category versus the proportion predicted among the perfect and near perfect motif match proteins.
Mentions: To study the subcellular distribution of the predicted TRAF6/p62 substrates, compartmentalization of the proteins in both the datasets was examined (Table 2, Figure 6). Proteins were assigned to cellular compartments based on the literature, curated information in protein databases and GO ontology for protein subcellular localization [36].

Bottom Line: NRIF (K19), TrkA (K485), TrkB (K811), TrkC (K602 and K815), NTRK2 (K828), NTRK3 (K829) and MBP (K169) were found to possess a perfect match for the amino acid consensus motif for TRAF6/p62 ubiquitination.Collectively, our results reveal an unappreciated role for the scaffold protein in targeting ubiquitination.The findings described herein could be used to aid in identification of other E3/scaffold ubiquitination sites.

View Article: PubMed Central - HTML - PubMed

Affiliation: Program in Cellular and Molecular Biosciences, Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL, 36849, USA. wootemc@auburn.edu.

ABSTRACT
A new approach is described here to predict ubiquitinated substrates of the E3 ubiquitin ligase, TRAF6, which takes into account its interaction with the scaffold protein SQSTM1/p62. A novel TRAF6 ubiquitination motif defined as [-(hydrophobic)-k-(hydrophobic)-x-x-(hydrophobic)- (polar)-(hydrophobic)-(polar)-(hydrophobic)] was identified and used to screen the TRAF6/p62 interactome composed of 155 proteins, that were either TRAF6 or p62 interactors, or a negative dataset, composed of 54 proteins with no known association to either TRAF6 or p62. NRIF (K19), TrkA (K485), TrkB (K811), TrkC (K602 and K815), NTRK2 (K828), NTRK3 (K829) and MBP (K169) were found to possess a perfect match for the amino acid consensus motif for TRAF6/p62 ubiquitination. Subsequent analyses revealed that this motif was biased to the C-terminal regions of the protein (nearly 50% the sites), and had preference for loops (~50%) and helices (~37%) over beta-strands (15% or less). In addition, the motif was observed to be in regions that were highly solvent accessible (nearly 90%). Our findings suggest that specific Lysines may be selected for ubiquitination based upon an embedded code defined by a specific amino acid motif with structural determinants. Collectively, our results reveal an unappreciated role for the scaffold protein in targeting ubiquitination. The findings described herein could be used to aid in identification of other E3/scaffold ubiquitination sites.

No MeSH data available.