What makes species unique? The contribution of proteins with obscure features

Martin Gollery¹ , Jeff Harper¹ , John Cushman¹ , Taliah Mittler¹ , Thomas Girke² , Jian-Kang Zhu² , Julia Bailey-Serres² and Ron Mittler¹

¹Department of Biochemistry and Molecular Biology, University Of Nevada, Reno, NV 89557, USA

²Center for Plant Cell Biology, University Of California, Riverside, CA 92521, USA

author email corresponding author email

Genome Biology 2006, 7:R57doi:10.1186/gb-2006-7-7-r57


Published:	19 July 2006

Subject areas: Genome studies, Evolution, Biochemistry and structural biology

Abstract

Background

Proteins with obscure features (POFs), which lack currently defined motifs or domains, represent between 18% and 38% of a typical eukaryotic proteome. To evaluate the contribution of this class of proteins to the diversity of eukaryotes, we performed a comparative analysis of the predicted proteomes derived from 10 different sequenced genomes, including budding and fission yeast, worm, fly, mosquito, Arabidopsis, rice, mouse, rat, and human.

Results

Only 1,650 protein groups were found to be conserved among these proteomes (BLAST E-value threshold of 10^-6). Of these, only three were designated as POFs. Surprisingly, we found that, on average, 60% of the POFs identified in these 10 proteomes (44,236 in total) were species specific. In contrast, only 7.5% of the proteins with defined features (PDFs) were species specific (17,554 in total). As a group, POFs appear similar to PDFs in their relative contribution to biological functions, as indicated by their expression, participation in protein-protein interactions and association with mutant phenotypes. However, POF have more predicted disordered structure than PDFs, implying that they may exhibit preferential involvement in species-specific regulatory and signaling networks.

Conclusion

Because the majority of eukaryotic POFs are not well conserved, and by definition do not have defined domains or motifs upon which to formulate a functional working hypothesis, understanding their biochemical and biological functions will require species-specific investigations.