By overexpressing an eukaryotic mitochondrial membrane protein in E.coli, I was wondering if I can assume the same subcellular localization in bacteria cells. Otherwise, any advice about how to assess the localization, for instance by means of bioinformatic tools?
There are two membranes in E. coli, the inner/cytoplasmic and outer membrane. There are methods available for isolating each of these membranes using sucrose gradient ultracentrifugation, allowing the presence of the protein to be assessed by SDS-PAGE or Western blot. A third, highly probable location for an integral membrane protein expressed in E. coli is as an insoluble pellet or inclusion bodies within the cytoplasm. This can be assessed by a low-speed centrifugation after cell breakage.
Unless your protein has an export signal there is no reason to think that the protein will be anywhere but in the inclusion bodies.
If you get the protein sequence you can try different programs or software , found
http://bioinformatics.ysu.edu/tools/subcell.html
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