H‐NS, IHF, and DnaA lead to changes in nucleoid organizations, replication initiation, and cell division

Abstract

Histone-like nucleoid-structuring protein (H-NS) and integration host factor (IHF) are major nucleoid-associated proteins, and DnaA, a replication initiator, may also be related with nucleoid compaction. It has been shown that proteindependent DNA compaction is related with many aspects of bacterial physiology, including transcription, DNA replication, and site-specific recombination. However, the mechanism of bacterial physiology resulting from nucleoid compaction remains unknown. Here, we show that H-NS is important for correct nucleoid compaction in a medium-independent manner. H-NSmediated nucleoid compaction is not required for correct cell division, but the latter is dependent on H-NS in rich medium. Further, it is found that the IHFαmediated nucleoid compaction is needed for correct cell division, and the effect is dependent on medium. Also, we show that the effects of H-NS and IHF on nucleoid compaction are cumulative. Interestingly, DnaA also plays an important role in nucleoid compaction, and the effect of DnaA on nucleoid compaction appears to be related to cell division in a medium-dependent manner. The results presented here suggest that scrambled initiation of replication, improper cell division, and slow growth is likely associated with disturbances in nucleoid organization directly or indirectly.

Negative feedback forDARS2–Fis complex by ATP–DnaA supports the cell cycle-coordinated regulation for chromosome replication

“…MG1655 and subDnaA box V cells were transformed with pOZihfBA3-1, a derivative of pBAD18 carrying the IHF coding genes ihfA and ihfB , downstream of an arabinose-inducible promoter ( 7 ), and the resulting strains were analyzed for cell size and DNA content as mentioned earlier. When IHF expression was induced in the wild-type DARS2 cells at 42°C, the four-chromosome peak was moderately increased compared with cells without induction (Figure 3B , 42°C), consistent with previous data ( 57 ). However, in subDnaA box V cells grown under the same conditions, IHF overexpression dramatically stimulated replication initiation, diminishing the two-chromosome peak while increasing the four-chromosome peak.…”

Genome and transcriptomic analysis of the adaptation of Escherichia coli to environmental stresses

“…Huang et al reported that histone-like proteins, H-Ns and IHF, in E. coli affected the higher-order DNA compaction while H-NS and IHF regulated the gene expression as transcription factors. Similarly, the transcription factor DnaA has also been shown to affect the compaction of nucleoid [68] , [69] and RNA structures [70] . Le Berre et al observed the link between gene expression and chromosomal spatial organization, which turned out to be essential for bacterial adaptation to changing environmental circumstances [71] .…”