The functional make up of proteomes is remarkably conserved

• Published in: 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) pp. 1023 - 1025
• Main Authors: Nasir, A., Naeem, A., Khan, M. J., Lopez-Nicora, H. D., Caetano-Anolles, G.
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01-11-2011
• Subjects: Bioinformatics; fold superfamily; functional annotation; Genomics; Microorganisms; molecular function; protein domain; Protein engineering; Proteins; SCOP; structure; superkingdom
• ISBN: 9781457716126; 1457716127
• DOI: 10.1109/BIBMW.2011.6112546

Here we analyze the functional annotation of protein domains in almost a thousand sequenced genomes. Our results yield fundamental insights into the structural and functional diversity of proteomes. We find that the functional makeup of proteomes is remarkably conserved across cellular superkingdoms. In general, most of the proteome repertoire is spent for functions related to metabolic processes but there are significant differences in the usage of protein domains both between and within superkingdoms. Our results provide support to the hypotheses that the proteomes of the eukaryal superkingdom evolved via genome expansion mechanisms while those of microbial superkingdoms evolved by reductive evolutionary processes. We also identify few genomic outlier groups in each superkingdom that deviate significantly from the conserved functional design. These genomes are reduced and belong to parasitic organisms.