Proteomic Analysis of the Plant Nucleolus

The nucleolus is a prominent sub-nuclear structure found in all eukaryotes. It is where the ribosomal RNA genes are transcribed and ribosomes are synthesised. However, much evidence has now accumulated that the nucleolus is involved in many other nuclear processes. Nucleoli are of moderate protein complexity, comprising a few hundred proteins, and can be isolated for proteomic analysis. In this chapter we describe the purification and analysis of plant nucleoli by proteomic methods and summarise the current results. We also discuss more specific tagging methods that have been used to analyse individual protein complexes, as well as methods for analysing post-translational modifications of nucleolar proteins. Finally we discuss the assessment of the reliability of such proteomic data, and the presentation and curation of this type of data.