Bacterial protein meta-interactomes predict cross-species interactions and protein function.

Background: Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactome studies while several more have had substantial segments of their proteomes screened for interactions. The protein interactomes of several bacterial species have been completed, including several from prominent human pathogens.

Protein complexes in bacteria.

Large-scale analyses of protein complexes have recently become available for Escherichia coli and Mycoplasma pneumoniae, yielding 443 and 116 heteromultimeric soluble protein complexes, respectively. We have coupled the results of these mass spectrometry-characterized protein complexes with the 285 "gold standard" protein complexes identified by EcoCyc. A comparison with databases of gene orthology, conservation, and essentiality identified proteins conserved or lost in complexes of other species.

Applications to aging networks.

This chapter will introduce a few additional network concepts, and then it will focus on the application of the material in the previous chapter to the study of systems biology of aging. In particular, we will examine how the material can be used to study aging networks in two sample species: Caenorhabditis elegans and Saccharomyces cerevisiae.