Target selection

625 candidate proteins were sampled from a list compiled from the human, bovine and plant nucleolar proteomes [1,2,3,4], supplemented with selected entries from the Gene Ontology database: proteins referenced as ribosome biogenesis (GO 0042254) and/or rRNA processing (GO 0006364) [5] were included. A compilation of the yeast ribosome processing factors was generated mainly from references: [6,7,8]. The human homologs were retrieved using a BLASTP search (expected p value below 10-15). From this assembled list of 847 human proteins with putative functions in pre-rRNA processing, we excluded all the ribosomal proteins, as they were already described [9], or are currently studied elsewhere, some histones and other proteins with conflicting subcellular localization (e.g. mitochondria, the ER, etc ). The list of the 625 genes analyzed is available here.

 

References

  1. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M, Lamond AI (2002) Directed proteomic analysis of the human nucleolus. Curr Biol 12: 1-11.
  2. Scherl A, Coute Y, Deon C, Calle A, Kindbeiter K, Sanchez JC, Greco A, Hochstrasser D, Diaz JJ (2002) Functional proteomic analysis of human nucleolus. Mol Biol Cell 13: 4100-4109.
  3. Pendle AF, Clark GP, Boon R, Lewandowska D, Lam YW, Andersen J, Mann M, Lamond AI, Brown JW, Shaw PJ (2005) Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol Biol Cell 16: 260-269.
  4. Patel AK, Olson D, Tikoo SK (2010) Proteomic analysis of bovine nucleolus. Genomics Proteomics Bioinformatics 8: 145-158.
  5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
  6. Fromont-Racine M, Senger B, Saveanu C, Fasiolo F (2003) Ribosome assembly in eukaryotes. Gene 313: 17-42.
  7. Kressler D, Linder P, de La Cruz J (1999) Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 19: 7897-7912.
  8. Strunk BS, Karbstein K (2009) Powering through ribosome assembly. RNA 15: 2083-2104.
  9. O’Donohue MF, Choesmel V, Faubladier M, Fichant G, Gleizes PE (2010) Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. J Cell Biol 190: 853-866.