I am constructing an interolog based host-pathogen protein-protein interaction network. As per I know the secretory, extracellular and membrane proteins of gram negative bacteria can interact with host. In my network there are several cytoplasmic proteins of bacteria. Such interactions are reported by high throughput methods also (I know now very accurate). Some of the cytoplasmic proteins of bacteria in my network was predicted to interact with immune proteins of insect host. Can such interactions be 'True Positive'?
Ashmit, perhaps if the bacterial cells become internalized within the eukaryotic cell, then when walls and membranes breakdown the cytoplasmic proteins may interact for some time. We are examining this phenomenon in plants. In the roots of some plants bacterial cells become internalized and eventually appear to breakdown. There could be some protein-protein interactions after the bacterial membranes breakdown.
Ashmit, perhaps if the bacterial cells become internalized within the eukaryotic cell, then when walls and membranes breakdown the cytoplasmic proteins may interact for some time. We are examining this phenomenon in plants. In the roots of some plants bacterial cells become internalized and eventually appear to breakdown. There could be some protein-protein interactions after the bacterial membranes breakdown.
During your process cytoplasmic proteins of bacteria will interact with proteins but it's temporary. but in final stage it will be breakdown. not possible to record this information as a proof., but in your case you have some interesting finding, it may be some increasing concentration. it's good only know. so you can able to report this in your research findings.
Hopeful work
While it is rather likely that many of the interactions are false-positives, some "cytoplasmatic" proteins might be able to get into a host. For example, Xanthomonas uses a Type III secretion system. Below a few links that might point in the right direction.
Not sure if proteins addressed by this system are detected as secreted.
http://www.ncbi.nlm.nih.gov/m/pubmed/16386329/
http://www.sciencedirect.com/science/article/pii/S017616170500458X
http://www.ncbi.nlm.nih.gov/m/pubmed/10430949/
are you sure that these proteins are cytoplasmic?
If you have specific antibodies, You can check this with western blot or through chemiluminescence to see whether these proteins can translocate to the membrane
Hello
agree with researchers also , Although the predicted PPIs may contain some false positives, the computational methods provide reasonable amount of interactions which can be further validated by high throughput experiments.
Good Luck
Of course it can e.g. toxins and enzymes involving in pathophysiology.
if the bacterial cells internalized within the eukaryotic cell, when walls and membranes breakdown the proteins may interact almost. same way some plants bacterial cells become internalized and eventually try to breakdown. This because of some protein-protein interactions after the bacterial membranes breakdown.
Its interesting way, so if it's possible to record means it make some sense, so you keep try in this area..,
Good Luck & Regards
R.Selva..........
You may find it useful to review how Shigella and Salmonella, among others, infect vertebrates. Murray et al's textbook of Medical Microbiology (Mosby-Elsevier) can shed light on this for you.
The interaction of microbial proteins are very complex. I think you must set up experiments in following different conditions: (If you don't Mind)
1. Study the expression of proteins while maintaining pure culture of particular bacterial strain.
1.1 Identify the expression level of extra cellular protein
1.2 Identification of membrane proteins.
1.3 Then lyse the pure culture to identify intracellular protein expression.
After identifying three different protein expression levels , you will easily able to differentiate the cytoplasmic proteins.
Now you can study total match the proteome of the infected insect and proteome of the non infected insect under investigation.
Well as far as microbial proteins are concerned whether extracellular, membrane bound and Intracellular all are found to interact with the host especially in case of plants.
There may be couple of ways how the proteins, which appear to have a cytoplasmic localization may interact with host proteins. 1. After the bacteria is phagocytosed or before the phagocytosis, few of the bacterial cells may lysed (mechanical sheering etc) and the bacterial cytoplasmic proteins may be exposed and interact with host proteins. 2. Another possibility is the bacterial proteins which are appeared to have cytoplasmic localization because of absence of any known secretory signal peptide sequence in them, may not be cytoplasmic proteins and they may use any novel and unknown secretory mechanism for their extracellular export.
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