I want to add a subcellular localization filter on my predicted host-pathogen interactome. Could someone please tell me what should be the localization of protein interaction if one partner is from bacterial host and other partner is from eukaryotic organism.
Dear Ashmit,
This is really a good and challenging question. The location of such interactions is case dependent and can take place in different subcellular locations.
For example, proteins of Gram negative bacteria are localized in cytoplasm, inner membrane, periplasmic space, outer membrane or extra-cellular space. Some outer membrane proteins of extra-cellular bacteria can interact with host membrane proteins on the surface of the plasma membrane. However, if the case is for an intracellular bacteria the interaction may take place in different compartments of the infected host cell, such as cytoplasm or lysosome, mitochondria and that is dependent on the life cycle of the bacteria.
Another interesting scenario can occur when bacterial effector proteins, which help pathogenic bacteria to invade host tissues, are injected into the host cell usually using type 3 secretion system (TTSS). In this case, the effector proteins might use the host post-transnational machinery to get some necessary PT modification to enable them to be co-localized with the host target proteins. You can have a look at this interesting review "http://www.ncbi.nlm.nih.gov/pubmed/23588250".
So in conclusion, the location of the interaction is different from case to case and there is no tool to predict such location!
Good luck
Yaqoub
Dear Ashmit,
This is really a good and challenging question. The location of such interactions is case dependent and can take place in different subcellular locations.
For example, proteins of Gram negative bacteria are localized in cytoplasm, inner membrane, periplasmic space, outer membrane or extra-cellular space. Some outer membrane proteins of extra-cellular bacteria can interact with host membrane proteins on the surface of the plasma membrane. However, if the case is for an intracellular bacteria the interaction may take place in different compartments of the infected host cell, such as cytoplasm or lysosome, mitochondria and that is dependent on the life cycle of the bacteria.
Another interesting scenario can occur when bacterial effector proteins, which help pathogenic bacteria to invade host tissues, are injected into the host cell usually using type 3 secretion system (TTSS). In this case, the effector proteins might use the host post-transnational machinery to get some necessary PT modification to enable them to be co-localized with the host target proteins. You can have a look at this interesting review "http://www.ncbi.nlm.nih.gov/pubmed/23588250".
So in conclusion, the location of the interaction is different from case to case and there is no tool to predict such location!
Good luck
Yaqoub
From the bacterial side I guess it would make sense to put a filter for secreted or outer membrane proteins, particularly emphasizing substrates for any of the dedicated secretion system involved in pathogenicity such as the TTSS mentionned above, but also the T4SS and T6SS.
As for the site of the interaction complex between an eukaryotic and a prokaryotic protein, I agree with the previous answer; there is no way for the moment to limit the search to a specific organelle or location within the host cell.
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