My paper about protein complexes in bacteria is officially published - check it out in PLoS Computational Biology.
Essentially a picture of how many species are not E. coli (except those at the bottom - many of them are E. coli). Click to zoom in or get more context in the linked paper.
The one-sentence summary is as follows: bacteria are different from each other. OK, so that isn't really a mind-blowing observation. Microbiologists tend to think of conserved features in a monolithic way when they're working with multiple species, though, to the point that a ribosome from E. coli is considered more or less equivalent to a ribosome from a Bacillus species or even something exotic like Thermus thermophilus.
Our point here was to show that E. coli protein complexes, on average, don't appear to provide a solid model of those complexes present in other bacterial species. The really well conserved protein complexes tend to be those critical to Life As We Know It (i.e., RNA polymerases), but even among some complexes crucial to one species' existence, a closely-related species may lack one piece of the larger complex.* There's a broader biocomplexity issue here, too: we can't work under the assumption that protein complex components will be consistently co-conserved. Two species may appear to contain a complex of similar function, but one species may put the complex together in a different way than the other.
In some cases, complex parts may even be replaced with those more appropriate to the needs of the species. That's a broader discussion than we attempt in this manuscript but it's an ongoing course of study.
*Lack is a strong word here. If a strain or species doesn't need a certain protein (that is, it's not essential) and it doesn't have any obvious inability to maintain growth in its own environmental niche, does it really lack the protein?