Gene ontology analysis of the centrosome proteomes of Drosophila and human

Abstract

The centrosome is a complex cell organelle in higher eukaryotic cells that functions in microtubule organization and is integrated into major cellular signaling pathways.^1-3 For example a tight link exists between cell cycle regulation and centrosome duplication, as centrosome number must be precisely controlled to ensure high fidelity of chromosome segregation.⁴ The analysis of the centrosome's protein composition provides the opportunity for a better understanding of centrosome function and to identify possible links to cellular signaling pathways.^5,6 Our proteomics study of the Drosophila centrosome recently identified 251 centrosome candidate proteins that we subsequently characterized by RNAi in Drosophila SL2 cells and classified according to their function in centrosome duplication/segregation, structure maintenance and cell cycle regulation.⁷ Interestingly, functional characterization of their human orthologue proteins revealed the highest functional conservation in the process of centrosome duplication and separation. To analyze functional and biochemical interdependencies further, we carried out an analysis of the gene ontology (GO) annotation of the identified Drosophila centrosome proteins, as well as of the human centrosome proteome.⁵ The GO analysis of the group of proteins that did not show a centrosome, chromosome segregation or cell cycle related phenotype in our RNAi assays suggests that these molecules may constitute linker proteins to other cellular signaling pathways. Furthermore, the results of our GO analysis of components of the human and of the Drosophila centrosome reflect the somatic and embryonic origin, respectively, of the isolated centrosomes, implicating the Drosophila centrosome proteins in developmental signaling and cell differentiation. 

This article refers to:

Acknowledgements

This work was supported by (a) B.L. laboratory: Berliner Senat für Kultur, Wissenschaft und Forschung, EFRE; NGFN Plus, IG Mutanom; EU. (b) A.P. laboratory: Leibniz Society, Pakt für Forschung und Innovation. (c) R.H. laboratory: German Science Foundation grant No. HE4607/3-1.

Figures and Tables

Figure 1 (A) The enrichment of GO annotation terms (biological process level 3) in the phenotypic classes “centrosome duplication/separation.” “Centrosome structure” and “no phenotype” were analyzed using DAVID Functional Annotation Tool with the 251 MS-identified centrosomal candidate proteins as background. Bars indicate the fold enrichment of the respective GO terms in the phenotypic classes. (B) Semantic similarity scores (i) within and (ii) between the three protein sets. Scores were calculated with the Bioconductor package ‘GOSemSim’ (Version 1.8.2). N gives the total number of proteins, N effective gives the number of proteins with GO annotation sufficient for score calculation. p values for score differences were calculated using the Mann-Whitney U test.

Figure 2 Comparative GO term enrichment analysis reveals functional homology between the Drosophila and human centrosome proteome. GO term enrichment in the category biological process level 3 was analyzed for all proteins classified as human centrosomal, centrosome candidate and centrosome novel5 using the DAVID bioinformatics tool and the whole human genome as the background. The Drosophila centrosome proteome was analyzed accordingly and statistically significantly enriched terms (p value < 0.01) were compared between the two datasets. Less informative terms not directly related to centrosome structure or function were merged and labeled with the term of the next higher level of the GO hierarchy (italic).

Addendum to: