Nucleoid-associated proteins (NAPs) are essential to organise and condense bacterial DNA, enabling relatively large genomes to be compressed into small bacterial cells.
NAPs are analogous to histone proteins in eukaryotic cells, condensing and coiling DNA to control gene expression. These proteins (NAPs) also stabilise supercoiling (where the DNA is twisted to condense it further), as well as controlling access to promoters, modulating RNA polymerase binding.
Bacterial genes are regulated by regulatory domains. These include promoters, operator regions, as well as sigma factors (which bind to the RNA polymerase to form a holoenzyme). Promoters are, normally, formed of two sequences, at –35 and –10 nucleotide positions from the start codon. ‘Perfect’ promoters have 17 base pairs between the two sites. Different promoters can be used to allow different sigma factors to induce RNA polymerase to interact. NAPs could change these interactions by condensing promoter sequences, thus preventing RNA polymerase from interacting. This would suppress gene expression.
Where there is a risk of DNA damage, such as due to a mutagen being present, the DNA can be coiled more tightly. Using CbpA or Dps, tight coils can be formed to prevent the damaging molecules from accessing the DNA and subsequently reducing the likelihood of mutations occurring.
H-NS acts as a global repressor, predominantly of horizontal gene transfer, and also of transcription generally.
Fis can be used to bend promoters into stable conformations, activating transcription.