Growth phase-dependent variation in protein composition of the Escherichiacoli nucleoid

The genome DNA of Escherichia coil is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, a nd transcription. Using a quantitative Western blot method, we have perform ed for the first time a systematic determination of the intracellular conce ntrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, a lso known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversio n stimulation), Hfq (host factor for phage Q(beta)), H-NS (histone-like nuc leoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhi bitor of chromosome initiation A), IHF (integration host factor), Lrp (leuc ine-responsive regulatory protein), and StpA (suppressor of td mutant pheno type A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and Stp A, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation , calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H -NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent th e stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob ), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis an d HU in the growing phase to Ups in the stationary phase. The curved UNA-bi nding protein, CbpA, appears only in the late stationary phase. These chang es in the composition of nucleoid-associated proteins in the stationary pha se are accompanied by compaction of the genome DNA and silencing of the gen ome functions.