3.3) How does Hfq compare to other NAPs?
The amount of Hfq in the bacterial cell is comparable to that of other
NAPs such as HU or H-NS (Table 1 ). However, only 20% of the
Hfq content is localised in the nucleoid, corresponding to approximately
2000 hexamers. Therefore, a rough estimate suggests that Hfq hexamers
represent around 5% of the total NAPs, compared to 20 and 40% for Fis
and HU, respectively, during the exponential phase of growth,
respectively (Talukder and Ishihama, 2015). Furthermore, Hfq appears to
have a heterogeneous localisation in the nucleoid, in contrast to the
more uniform distribution of other NAPs (Azam, Hiraga and Ishihama,
2000). This heterogeneous distribution may be due to the preferred
AT-rich Hfq-binding motif, whose consensus is (A/T)T(A/G)TGCCG
(Updegrove et al. , 2010), or to the polyphosphate molecule, which
was suspected to have a role in the site-specific DNA binding properties
of Hfq in bacteria (Beaufay et al. , 2021). Recently, Hfq and Fis
have also been reported to be highly concentrated on EPODs (Extended
protein occupancy domains) in the E. coli genome to ensure the
silencing of prophage acquired DNA (Amemiya, Schroeder and Freddolino,
2021). The distribution of Hfq in EPODs would be consistent with the
observation that the fibre-like pattern generated by Hfq can cover large
regions of DNA.