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Abstract
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. For instance, of 285 “gold standard” protein complexes in E. coli, less than 10% are fully conserved among a set of 7 distantly-related bacterial “model” species. Complex conservation follows one of three models: well-conserved complexes, complexes with a conserved core, and complexes with partial conservation but no conserved core. Expanding the comparison to 894 distinct bacterial genomes illustrates fractional conservation and the limits of co-conservation among components of protein complexes: just 14 out of 285 model protein complexes are perfectly conserved across 95% of the genomes used, yet we predict more than 180 may be partially conserved across at least half of the genomes. No clear relationship between gene essentiality and protein complex conservation is observed, as even poorly conserved complexes contain a significant number of essential proteins. Finally, we identify 183 complexes containing well-conserved components and uncharacterized proteins which will be interesting targets for future experimental studies.
Highlights
Abundant genome sequencing revealed an astounding diversity among bacterial genomes
We investigate the protein complements across bacterial genomes, how proteins are combined into protein complexes across species, and whether these complexes have been conserved across diverse branches on the prokaryotic tree of life
The list of binary protein-protein interactomes is clearly larger but has not been considered in this study. Based on this limited dataset, we investigated whether the complexes found in a few model organisms are sufficient to reconstruct homologous protein complexes in other species
Summary
Even species that inhabit the same environment may only share a fraction of their genes. This raises the question how these organisms have adapted to their environments using only a limited number of genes. We investigate the protein complements across bacterial genomes, how proteins are combined into protein complexes across species, and whether these complexes have been conserved across diverse branches on the prokaryotic tree of life. Studies comparing baker’s yeast and fission yeast found that essentiality varies between species [3]. This might be explained by functional redundancy and the importance of mechanism over structure. The extent of the differences might be unexpected but make sense when seen in the light of evolutionary flexibility [1]
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