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).