3.2) Hfq, a nucleoid-associated protein
Hfq has also been described as one of the NAP that shape the bacterial
chromosome (Azam and Ishihama, 1999). Hfq is capable of binding
double-stranded and single-stranded DNA but with less affinity than RNA
(Updegrove et al. , 2010; Geinguenaud et al. , 2011; Kubiaket al. , 2022). The majority of studies examining Hfq as a NAP
have been conducted in E. coli . Fluorescence microscopy imaging
of single DNA molecules and atomic force microscopy experiments have
demonstrated the formation of a nucleoprotein complex between Hfq and
double-stranded DNA (Jiang et al. , 2015). The nucleoprotein
complex between Hfq and DNA remains flexible with a moderate increase in
bending persistence length, compared to the rigid filaments observed
after H-NS binding (Boudreau et al. , 2018). However, as observed
for H-NS, the nucleoprotein complex with DNA compacts the DNA into a
condensed form by bridging DNA segments (Jiang et al. , 2015). The
DNA binding involves the CTR domain (Updegrove et al. , 2010), a
sequence of 35 amino acids that has been predicted to be unstructured,
but whose crystal structure remains unknown (Vogel and Luisi, 2011).
Upon interaction with DNA, these domains self-assemble and form
amyloid-like fibrillar structures in vitro (Arluison et
al. , 2006; Fortas et al. , 2015). These structures have been
shown to be responsible for the self-assembly with DNA, the DNA bridging
and compaction (Figure 1 ) (Malabirade et al. , 2018a).
Although the full-length Hfq binds to DNA via the interface of
its toroidal hexameric ring, the NTR by itself is not required for Hfq
to bind to DNA and only the presence of the CTR is necessary for DNA
compaction (Malabirade et al. , 2017). A model has been proposed
whereby Hfq can form a bridge by anchoring one or more of its other CTR
arms to another section of the same or another DNA molecule and/or by
CTR-mediated self-interactions among multiple proteins (Malabiradeet al. , 2017). Recently, it was confirmed that amyloid structures
are formed in vivo (Partouche et al. , 2019), indicating
that the CTR is responsible for the nucleoid remodelling in vivo through DNA binding, bridging and compaction (Figure 1 ) (Cossaet al. , 2022). In contrast to H-NS, the bridging formed by the
nucleoprotein complex doesn’t affect DNA topology (Malabirade et
al. , 2018a). It has therefore been suggested that the effect of Hfq on
DNA supercoiling observed in vivo (Tsui, Leung and Winkler, 1994)
may be indirect. Indeed, Hfq post-transcriptionally regulates the
expression of proteins that affect DNA topology (Figure 1 )
(Sledjeski, Whitman and Zhang, 2001). Finally, the CTR of Hfq has been
shown to bind to G-quadruplexes, a type of alternative DNA and RNA
structure. G-quadruplex structures consist of three or more guanine
quadruplex rings that are held together by Hoogsteen hydrogen bonds
(Gellert, Lipsett and Davies, 1962), forming highly stable four-stranded
structures. Hfq enhances the stability of G-quadruplex structures, which
can lead to the termination of DNA replication and a significant
increase in the mutation rate. Therefore, the stabilisation of
G-quadruplexes by Hfq may drive the evolution or alternation of
bacterial gene expression (Parekh et al. , 2019, 2020).