Figure 1.
The TRAPPII interactome. The data are derived from an analysis of IP-MS from inflorescences with the TRAPPII-specific subunit CLUB:GFP as bait (see Fig. 1 B; Kalde et al., 2019). Each protein was present in all three biological replicates. The soluble GFP empty vector was used as a negative control. (A) Gene ontology (GO) term enrichment analysis of the TRAPPII interactome. Depicted are highly enriched (fold enrichment ≥4) and significant (FDR-adjusted P value ≤0.003) GO term associations of biological processes of level 0 as bar plots. The length of each bar depicts the fold enrichment of GO terms associated with detected proteins, while the color intensity indicates the significance given as the P value adjusted for the false discovery rate (FDR). Interactors of intermediate intensity (>5 and <8) were used (see Fig. S1 A for an analysis of high-confidence interactors). In addition to the expected ontologies describing traffic, transport, cell division, and microtubule organization, significantly enriched GO categories describe responses to stimuli such as light and metal ions. (B and C) Volcano plots are presented. On the X axis: The ratio (or fold change) was calculated for each protein as the average intensity of the signal in the experiment divided by its average intensity in the control. On the Y axis the P values of the signal in the experiment versus the control, depicted along a negative log10 scale, are shown. Dotted gray lines represent cutoffs: P value ≤0.02 in B and C and ratio >8 for high fold change or >5 for intermediate fold change in B. (B) Note that TRAPPII subunits (light blue for core TRAPP; dark blue for TRAPPII-specific subunits; the CLUB/AtTRS130:GFP TRAPPII-specific bait is depicted as an open circle) are in the upper right field, indicating high abundance and good reproducibility. AtSKs (magenta), MAP65-1 (orange) and RAB-A2a GTPase (green) are all in the upper middle field; these may be transient interactors of TRAPPII. Note that AtSKs (AtSK11/12/32) are more significant than validated interactors such as MAP65 and RAB-A2a (Kalde et al., 2019; Steiner et al., 2016). (C) Highlighted in magenta are members of the brassinosteroid signaling pathway that were differentially enriched over light- versus dark-grown seedlings in a different IP-MS experiment. Note that BSK8, and ROC1 did not meet the significance cutoffs. The most significant interactors were GSK3/AtSK shaggy-like kinases and TOR. Related to Fig. S1 and Table S1.

The TRAPPII interactome. The data are derived from an analysis of IP-MS from inflorescences with the TRAPPII-specific subunit CLUB:GFP as bait (see Fig. 1 B; Kalde et al., 2019). Each protein was present in all three biological replicates. The soluble GFP empty vector was used as a negative control. (A) Gene ontology (GO) term enrichment analysis of the TRAPPII interactome. Depicted are highly enriched (fold enrichment ≥4) and significant (FDR-adjusted P value ≤0.003) GO term associations of biological processes of level 0 as bar plots. The length of each bar depicts the fold enrichment of GO terms associated with detected proteins, while the color intensity indicates the significance given as the P value adjusted for the false discovery rate (FDR). Interactors of intermediate intensity (>5 and <8) were used (see Fig. S1 A for an analysis of high-confidence interactors). In addition to the expected ontologies describing traffic, transport, cell division, and microtubule organization, significantly enriched GO categories describe responses to stimuli such as light and metal ions. (B and C) Volcano plots are presented. On the X axis: The ratio (or fold change) was calculated for each protein as the average intensity of the signal in the experiment divided by its average intensity in the control. On the Y axis the P values of the signal in the experiment versus the control, depicted along a negative log10 scale, are shown. Dotted gray lines represent cutoffs: P value ≤0.02 in B and C and ratio >8 for high fold change or >5 for intermediate fold change in B. (B) Note that TRAPPII subunits (light blue for core TRAPP; dark blue for TRAPPII-specific subunits; the CLUB/AtTRS130:GFP TRAPPII-specific bait is depicted as an open circle) are in the upper right field, indicating high abundance and good reproducibility. AtSKs (magenta), MAP65-1 (orange) and RAB-A2a GTPase (green) are all in the upper middle field; these may be transient interactors of TRAPPII. Note that AtSKs (AtSK11/12/32) are more significant than validated interactors such as MAP65 and RAB-A2a (Kalde et al., 2019; Steiner et al., 2016). (C) Highlighted in magenta are members of the brassinosteroid signaling pathway that were differentially enriched over light- versus dark-grown seedlings in a different IP-MS experiment. Note that BSK8, and ROC1 did not meet the significance cutoffs. The most significant interactors were GSK3/AtSK shaggy-like kinases and TOR. Related to Fig. S1 and Table S1.

This Feature Is Available To Subscribers Only

or Create an Account

Close Modal
Close Modal