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).