Histone-like proteins and bacterial chromosome structure.

Prokaryotic cells synthesize a set of small, usually basic proteins that bind DNA and are collectively called histonelike proteins because their biochemical properties resemble eukaryotic histones. Whereas the eukaryotic histones have a well defined function in packaging DNA through restraining left-handed toroidal DNA supercoils in nucleosomes, the functions of the prokaryotic histone-like proteins are not yet clear. However, recent studies of the interactions of certain histone-like proteins with DNA and genetic studies of cells that are mutated in genes coding for these proteins are beginning to suggest functions for some of the proteins. These findings and the relations to prokaryotic chromosome structure will be briefly reviewed here. At this time five different types of bacterial proteins are considered to be histone-like. These include: 1) the HU protein (for review see Drlica and Rouviere-Yaniv, 1987), which is a small dimeric protein that in Escherichia coli is composed of subunits of M, 9,535 and 9,225 named HU-a and HU-8, respectively, also called HU-2 and HU-1, respectively, and coded by the genes hupA and hupB, respectively (many other bacterial species have only a single gene and a single type of HU subunit); 2) integration host factor (IHF)' (Nash and Robertson, 1981), a basic protein having substantial amino acid sequence homology with HU, apparently composed of two subunits IHF-a and IHF-@, having M, 11,224 and 10,581, respectively, and coded by the E. coli genes himA and hip, respectively; 3) protein H1 (Spassky et al., 1984), a neutral protein existing in three different forms Hla, Hlb, and Hlc having different isoelectric points, but the same M , 15,500; 4) HLPl (Lathe et al., 1980), a protein of M, 17,000, which is apparently the product of the E. coli firA gene; 5) protein H (Hubscher et al., 1980) of M, 28,000, cross-reacting with antibodies specific for eukaryotic histone H2A. Also, bacteriophages can code for specific proteins having homology to HU protein (Greene et al., 1984) and can make proteins that couple to host cell HU and apparently modify it functionally.2 Each of these histone-like proteins has a relatively high intracellular concentration, which in E. coli ranges from that of H and HU which are the most abundant, roughly 120,000 and 60,000 monomers per cell, respectively, to the least abundant H1 and IHF estimated at about 14,000 to 20,000 copies or less per exponentially growing cell. It is important to recognize that some of the figures for abundance could be underestimated, since they are calculated from recoveries after purification. The HU proteins, which are the most thoroughly studied, are highly conserved in different prokaryotes and are found in eubacteria, archaebacteria, blue-green