Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli.

Aliazam Talukder,Akira Ishihama

doi:10.1007/s11427-015-4898-0

Abstract

The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/ DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase. In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Qβ (Hfq) and suppressor of td(-) phenotype A (StpA). Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, StpA and Hfq, while Dps occupies more than half of the stationary phase nucleoid. It has been known for a while that Dps is the main nucleoid-associated protein at stationary phase. From these results and the prevailing information, we propose a model for growth phase dependent changes in the structure and protein composition of nucleoid in E. coli.

Highlights

The chromosomes in the eukaryotic nucleus are compacted into the nucleosomes with histone proteins as the basic unit
In addition to factor for inversion stimulation (Fis), histone-like nucleoid structuring protein (H-NS), heat-unstable nucleoid protein (HU) and integration host factor (IHF) here we have identified, three new candidates of E. coli nucleoid, namely DNA-binding protein from starved cells (Dps), host factor for phage Q Hfq) and suppressor of td phenotype A (StpA)
Our results reveal that the major components of exponential phase nucleoid are Fis, HU, H-NS, suppressor of td phenotype A (StpA) and Hfq, while Dps occupies more than half of the stationary phase nucleoid

Summary

Introduction

The chromosomes in the eukaryotic nucleus are compacted into the nucleosomes with histone proteins as the basic unit. At present, a clear picture of how the E. coli nucleoid is organized is far from being complete This may be due to insufficient documentation of the molecular structure and composition of E. coli nucleoid and its growth phase dependent variations. No. comparison of the sequence recognition specificity and the DNA-binding affinities among twelve species of the nucleoid-associated proteins, including curved DNA-binding protein A (CbpA), curved DNA-binding protein B or right arm of the replication origin binding protein (CbpB or Rob), DNA-binding protein A (DnaA), DNA-binding protein from starved cells (Dps), Fis, host factor for phage Q (Hfq), H-NS, HU, inhibitor of chromosome initiation A (IciA), IHF, leucine-responsive regulatory protein (Lrp) and suppressor of td phenotype A (StpA) [26]. Cellular abundance and variation of these proteins might be involved in the growth phase dependent changes in the structure of E. coli nucleoids

Methods

Results

Conclusion