Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins

Shiri Freilich¹ , Tim Massingham¹ , Sumit Bhattacharyya² , Hannes Ponstingl¹ , Paul A Lyons² , Tom C Freeman¹ and Janet M Thornton¹

¹EMBL-EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SB, UK

²Rosalind Franklin Centre Genomics Research, Wellcome Trust Genome Campus, Cambridge, CB10 1SB, UK

author email corresponding author email

Genome Biology 2005, 6:R56doi:10.1186/gb-2005-6-7-r56


Published:	29 June 2005

Subject areas: Evolution

Abstract

Background

The combination of complete genome sequence information with expression data enables us to characterize the relationship between a protein's evolutionary origin or functional category and its expression pattern. In this study, mouse proteins were assigned into functional and phyletic groups and the gene expression patterns of the different protein groupings were examined by microarray analysis in various mouse tissues.

Results

Our results suggest that the proteins that are universally distributed in all tissues are predominantly enzymes and transporters. In contrast, the tissue-specific set is dominated by regulatory proteins (signal transduction and transcription factors). An increased tendency to tissue-specificity is observed for metazoan-specific proteins. As the composition of the phyletic groups highly correlates with that of the functional groups, the data were tested in order to determine which of the two factors - function or phyletic age - is dominant in shaping the expression profile of a protein. The observed differences in expression patterns of genes between functional groups were found mainly to reflect their different phyletic origin. The connection between tissue specificity and phyletic age cannot be explained by the recent rate of evolution. Finally, although metazoan-specific proteins tend to be tissue-specific compared with phyletically conserved proteins present in all domains of life, many such 'universal' proteins are also tissue-specific.

Conclusion

The minimal cellular transcriptome of the metazoan cell differs from that of the ancestral unicellular eukaryote: new functions were added (metazoan-specific proteins), whilst other functions became specialized and no longer took place in all cells (tissue-specific pre-metazoan proteins).