Figure 4.

Depletion of Nop53 also affects the Rrp43 interactome. To analyze how Nop53 modulates the interaction of Rrp43 with other factors, a coimmunoprecipitation assay was performed both in the presence (−doxycycline) and upon depletion (+doxycycline) of Nop53 using the conditional strain Δnop53/tetOff::GFP-NOP53 containing RRP43-TAP fusion in a plasmid. As a negative control, the same strain carrying only the TAP tag was used. For each condition, the elution of biological triplicates was subjected to label-free quantitative analysis. Using the PatternLab software, the identified proteins in at least two biological replicates were grouped in a Venn diagram, showing that among a total of 417 proteins, six were exclusively identified in the presence of Nop53, and 64 uniquely upon depletion of Nop53. The exclusively identified proteins in each condition are listed in boxes, highlighting the over-representation of pre-60S (red) and pre-90S/pre-40S (blue) assembly factors.