Microbial recognition is mediated by pattern recognition receptors (PRRs). These germline-encoded receptors recognizing highly conserved microbial structures are essential for survival and are therefore not subjective to high frequent mutations. The recognition of these so-called pathogen-associated molecular patterns (PAMPs) enables the immune system to distinguish between self and non-self and induce the appropriate immune responses upon infection. PRRs are located on extracellular surfaces, on intracellular membranes or in the cytosol. However, there will be specifically focused on receptors enabling intracellular recognition of microbes. Furthermore, a newly identified intracellular killing mechanism by autophagy will be discussed. This process is important in the metabolic homeostasis of cells, and it was recently found to be important in the clearance of bacteria as well. Interestingly, PRRs are able to influence autophagy, contributing to the newly established link between innate immunity and the evolutionary highly conserved process of autophagy
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