Abstract
Bacterial histone-like HU proteins are critical to maintenance of the nucleoid structure. In addition, they participate in all DNA-dependent functions, including replication, repair, recombination and gene regulation. In these capacities, their function is typically architectural, inducing a specific DNA topology that promotes assembly of higher-order nucleo-protein structures. Although HU proteins are highly conserved, individual homologs have been shown to exhibit a wide range of different DNA binding specificities and affinities. The existence of such distinct specificities indicates functional evolution and predicts distinct in vivo roles. Emerging evidence suggests that HU proteins discriminate between DNA target sites based on intrinsic flexure, and that two primary features of protein binding contribute to target site selection: The extent to which protein-mediated DNA kinks are stabilized and a network of surface salt-bridges that modulate interaction between DNA flanking the kinks and the body of the protein. These features confer target site selection for a specific HU homolog, they suggest the ability of HU to induce different DNA structural deformations depending on substrate, and they explain the distinct binding properties characteristic of HU homologs. Further divergence is evidenced by the existence of HU homologs with an additional lysine-rich domain also found in eukaryotic histone H1.
Highlights
Integrity of the bacterial genome is essential to survival of the organism
A number of such nucleoid-associated proteins have been identified in Escherichia coli, including H-NS, Fis, Dps (DNA protection during starvation), HU, and IHF (Integration Host Factor), all of which are present at concentrations up to or even exceeding 10 mM, depending on growth conditions (Azam and Ishihama, 1999)
Analysis of HU from E. coli, B. subtilis, and H. pylori has shown that less binding energy is expended on bending more flexible DNA substrates, resulting in preferred binding and a greater bend angle that brings flanking DNA into contact with the sides of the protein; this results in a longer DNA site size in flexible DNA compared to perfect duplex (Pontiggia et al, 1993; Bonnefoy et al, 1994; Pinson et al, 1999; Wojtuszewski and Mukerji, 2003; Arthanari et al, 2004; Chen et al, 2004; Kamau et al, 2005)
Summary
Integrity of the bacterial genome is essential to survival of the organism. Further, the size of the bacterial cell necessitates significant compaction of the genomic DNA, yet availability to various cellular machineries is important for cell growth. Analysis of HU from E. coli, B. subtilis, and H. pylori has shown that less binding energy is expended on bending more flexible DNA substrates, resulting in preferred binding and a greater bend angle that brings flanking DNA into contact with the sides of the protein; this results in a longer DNA site size in flexible DNA compared to perfect duplex (Pontiggia et al, 1993; Bonnefoy et al, 1994; Pinson et al, 1999; Wojtuszewski and Mukerji, 2003; Arthanari et al, 2004; Chen et al, 2004; Kamau et al, 2005).
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