Changes in the association of LSU biogenesis factors with early LSU precursors after <i>in vivo</i> depletion of LSU r-proteins required for early LSU pre-rRNA processing.

<p>Conditional r-protein expression mutants or wild type cells were cultivated as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143768#pone.0143768.g002" target="_blank">Fig 2</a>. Noc2-TAP and associated pre-ribosomal particles were then affinity purified from corresponding cellular extracts (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143768#sec008" target="_blank">Materials and Methods</a>). Proteins in Noc2-TAP fractions were identified and quantified by mass spectrometry. Isobaric labeling of peptides (iTRAQ, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143768#sec008" target="_blank">Materials and Methods</a>) was used to directly compare levels of individual proteins in Noc2-TAP fractions from wild type cells with the respective levels in Noc2-TAP fractions from conditional r-protein expression mutants. In <b>A)</b> is shown the average proteome composition of nine Noc2-TAP fractions analyzed in this study by mass spectrometry. In <b>B)</b> the changes in levels of individual LSU biogenesis factors in Noc2-TAP fractions from mutant versus wild type cells as determined by iTRAQ analyzes are summarized. Each pair wise comparison (“mutant <i>versus</i> wild type”) was performed at least twice starting from independent cell cultures. Data from 17 pairwise comparisons were used to detect co-behaving groups of LSU biogenesis factors by a clustering algorithm (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143768#sec008" target="_blank">Materials and Methods</a>). Similar behaving proteins are grouped in the same branch of the dendrogram depicted on the left. The iTRAQ ratios of LSU biogenesis factors for each individual pairwise comparison are shown as heat map using the color code depicted on the upper right. Only LSU biogenesis factors were included in these analyses, which were identified in at least 70% of the 17 pairwise comparisons. Groups of LSU biogenesis factors mentioned in the text are highlighted by bars on the right.