How do plasmids protect themselves from restriction enzymes released by bacteria (i.e., against bacteriophages)?
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The strains that we use in the lab have defective restriction machinery.
In the case of DH5α it is mostly because of the endA1 and hsdR17 mutation. The former mutation eliminates an endonuclease that can degrade plasmids and the latter one eliminates the restriction system.
Check this.
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$\begingroup$ What about the plasmids naturally present in bacteria ? $\endgroup$– biogirlCommented Aug 20, 2013 at 9:46
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$\begingroup$ usually they are compatible and have undergone methylation at these restriction sites. since you compared it with immune response i'll give you an analogy. The proteins that are already present in the system are not considered antigens because the immune system actively tries to not launch a response against them. Similarly the natural plasmids are marked to be treated as endogenous. You may ask how they acquired the plasmids in the first place which is something like a chicken-egg question; the likely explanation is that they acquired it during the time of stress (nutrient deprivation etc) $\endgroup$– WYSIWYGCommented Aug 21, 2013 at 3:08