Proteomics Analysis of the Nucleolus in Adenovirus-infected Cells

Lam, Yun W.; Evans, Vanessa C.; Heesom, Kate J.; Lamond, Angus I.; Matthews, David A.

This table lists all the proteins identified as having a 2-fold enrichment or depletion in the infected cell nucleoli compared with the uninfected cell nucleoli. Each protein is listed with the gi number, the number of peptides identified, percent coverage a brief description of its function (if known), and a ratio of depletion (shown as a negative ratio) or enrichment (shown as a positive ratio Nopp140 protein showed some co-localization with viral DBP but also significant enrichment in centers adjacent to DBP, reminiscent of our previously published findings that UBF is sequestered into regions adjacent to DBP (11) . We therefore compared UBF with Nopp140 to confirm that some Nopp140 is apparently sequestered in a manner similar to that of UBF (Fig. 3B, bottom row) . The next group of proteins, hnRNPU isoform a, SFPQ, U2AF 65 , hnRNPA2/B1, histone H1c, and exportin 5 were not detectable in the nucleolus by immunofluorescence ( Fig. 1, C, D, E, and F, top rows) . However, they were consistently detected in the nucleolus using proteomics methods and are considered components of the nucleolar proteome (51) . In adenovirus-infected cells, they all showed a pattern of exclusion from the DBP-rich replication centers apart from hnRNPA2/B1, which did not show any striking change in its distribution. However, we noted that hnRNPU, SFPQ, and U2AF65 were localized adjacent to DBP-rich centers, whereas histone H1c was clearly distinct and separated from the DBP-rich centers (Fig. 3G) . Exportin 5 was also readily detectable in the cytoplasm of infected cells but not in uninfected cells (Fig. 3H) .