2.2) HU
HU (Heat Unstable) is a highly conserved small (9 kDa), basic
histone-like protein that is abundantly expressed (Table 1 )
(Rouvière-Yaniv and Gros, 1975; Ali Azam et al. , 1999). Its main
function is to control DNA topology by introducing bends into
double-stranded DNA, making it a critical component of the bacterial
nucleoid, e.g. a deficiency of HU protein results in a reduction
in nucleoid condensation (Bensaid et al. , 1996). Investigation of
the role of HU has shown that, like H-NS, it is involved in the global
modulation of gene transcription (Oberto et al. , 2009). HU is
composed of two homologous subunits, α and β, which are encoded by thehupA and hupB genes, respectively. It exists in three
dimeric forms: HUα2, HUβ2, and HUαβ. The levels of the α and β subunits
vary during the growth cycle, resulting in a different composition of HU
at different stages. HUα2 is predominant in the exponential phase,
whereas HUαβ is predominant in the stationary phase. HUβ2 is almost
undetectable in any growth phase (Claret and Rouviere-Yaniv, 1997). HU
exhibits two distinct modes of DNA binding, both of which are sequence
non-specific. The first is a non-specific binding mode characterised by
ionic bonds between positively charged amino acid residues and the DNA
phosphate backbone, while the second is a structure-specific binding
mode involving preferential binding of HU to contorted DNA, including
DNA with kinks, nicks, gaps, or cruciform structures, as well as bent
DNA within loops (Verma et al. , 2023). Bettridge et al., (2021)
showed that the non-specific binding interactions with the DNA
decondensed the DNA, while the specific structure-binding interactions
with the DNA compacted the nucleoid, demonstrating a dual role for HU in
maintaining a proper nucleoid volume. Accordingly, HU is known to play a
significant role in DNA repair and recombination (Kamashev and
Rouviere-Yaniv, 2000), but also in replication (Bahloul, Boubrik and
Rouviere-Yaniv, 2001). In 2002, Balandina and colleagues investigated
the general RNA binding properties of HU and showed that it has a
non-specific binding affinity for double-stranded RNA, DNA, and DNA-RNA
complexes. In addition, DsrA was identified as a specific RNA target for
HU (Balandina, Kamashev and Rouviere-Yaniv, 2002). Subsequent RNA
immunoprecipitation assays, followed by microarray analysis, revealed
additional RNA molecules that interact with HU, including tRNA, rRNA,
several mRNAs including rpoS , sRNAs and various REPs, which are repeated extragenic palindromic elements encoding RNAs
molecules (Macvanin et al. , 2012).