Pathogen Associated Molecular Patterns (PAMPs)
Generally speaking PAMPs are structures that are found in microbes but not mammalian cells. For example, many PAMPs have a sugar, or carbohydrate part. This is because many microbes, especially bacteria, can make sugars that mammalian cells are unable to make. These unique carbohydrates, or glycans, are therefore recognised as different or 'foreign' by the innate immune system. Although most PAMPs are glycolipids (part sugar, part fat), some are also proteins, like porin that makes a pore in the bacterial cell wall for uptake of nutrients, and flagellin, a structural protein of the tail, or flagella, that some bacteria use to move around. In the graphic (click link to activate zoom) roll over the magnify symbols to view some common bacterial PAMPs (drawn in red). Think about where they are found. What do you think would happen to the bacteria if these PAMPs had to change their structure to escape recognition by PRRs?
Nucleotides are also recognised PAMPs partly due to their chemical differences. For example, viral single stranded (ss) RNA is chemically different to mammalian ssRNA as it contains something called a triphosphate. This difference is very important as it helps the PRRs to distinguish viral from host ssRNA that coexist within the cell in the cytosol. Microbial DNA is also chemically different as it has many more sites where the nucleotide cytosine (C) is directly followed by guanine (G) with only a phosphate (p) separating them. These motifs are referred to CpG motifs. When present in mammalian DNA, CpGs carry a methyl group, hence are methylated. This is not the case with microbial CpGs which are unmethylated and therefore well recognised PAMPs.
But despite these chemical differences our PRRs recognise all DNA as foreign. How do you think our cells have adapted themselves so not to get activated by our own DNA? Find out on the next page.