2.1) H-NS
H-NS (Histone-like Nucleoid Structuring protein), originally named
as histone-like protein H1, is a 15.5 kDa basic protein composed of two
regions: a DNA-binding domain at the C-terminal side of the protein
linked to the oligomerisation interfaces located at the N-terminal side
of the protein (Table 1 ) (Grainger, 2016). H-NS is widely
distributed in Gram-negative bacteria, and several H-NS-like proteins
are often present in a single species, with possible cross-talks between
these proteins (Leonard et al. , 2009). H-NS exhibits a binding
preference for AT-rich curved DNA regions. This process involves the
initial nucleation of H-NS at high affinity sites, followed by the
subsequent spreading along the neighbouring AT-rich DNA (Lang et
al. , 2007; Sette et al. , 2009). On binding DNA, H-NS can
oligomerise, leading to the formation of nucleoprotein filaments that
can alter DNA topology, i.e. the 3-D structure and spatial arrangement
of DNA (Dame, Wyman and Goosen, 2000). Both linear (or “stiffened”)
and cross-bridged filaments have been observed in vitro (Boudreauet al. , 2018). In addition, H-NS affects the interactions
between RNA polymerase (RNAP) and DNA, thereby repressing gene
expression through a variety of mechanisms. H-NS can interact directly
with RNAP, exclude RNAP from specific DNA localisation, or form
repressive loops that trap RNAP and prevent it from entering the
elongation phase of transcription (Grainger, 2016; Boudreau et
al. , 2018). All of these regulatory mechanisms have a major impact on
gene expression (Hommais et al. , 2001; Zghidi-Abouzid et
al. , 2016). H-NS can also inhibit elongation: the bridged filaments
strongly increase pausing by RNA polymerase at a subset of pausing sites
with high potential for backtracking (Kotlajich et al. , 2015).
Horizontally acquired genes, pathogenic operons, and antisense
transcripts, all of which tend to be AT-rich, are typical targets of
H-NS (Navarre et al. , 2006, 2007; Doyle et al. , 2007;
Singh et al. , 2014). In addition, H-NS can bind nascent
transcripts near translation initiation sites, which has been proposed
to facilitate correct ribosome positioning and enhance translation (Parket al. , 2010). H-NS was initially designated as a modulator of
environmentally regulated gene expression (Atlung and Ingmer, 1997) due
to its involvement in acclimation to stress-inducing conditions.
Environmental conditions, such as osmolarity and temperature, can
modulate DNA curvature and alter H-NS binding to DNA (Shahul Hameedet al. , 2019; Zhao et al. , 2021).
The activity of H-NS can also be modulated by proteins such as StpA,
YdgT, the Hha family of co-repressors, such as Hha, YmoA and Cnu. The
formation of heteromeric protein–protein complexes with H-NS results in
the modulation of H-NS activity (Stoebel, Free and Dorman, 2008; Uedaet al. , 2013; Hustmyer et al. , 2022; Lukose et al. ,
2024). Finally, other DNA-binding proteins, such as LeuO and SlyA can
act through anti-silencing mechanisms and prevent filament formation
with DNA (Stoebel, Free and Dorman, 2008).