title: Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli.
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.
authors.affiliation: Department of Microbiology, Jahangirnagar University, Dhaka, 1342, Bangladesh. tunubj@yahoo.com.|Micro-Nano Technology Research Center, Hosei University, Tokyo, 184-0003, Japan. tunubj@yahoo.com.
authors.forename: AliAzam
authors.initials: A
authors.lastname: Talukder
authors.affiliation: Department of Molecular Genetics, National Institute of Genetics, Shizuoka, 411-8540, Japan.|Micro-Nano Technology Research Center, Hosei University, Tokyo, 184-0003, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Ishihama
mesh_terms: D000906:Antibodies / Q000737:chemistry; D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D002499:Centrifugation, Density Gradient; D004269:DNA, Bacterial / Q000235:genetics; D004268:DNA-Binding Proteins / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D035021:Factor For Inversion Stimulation Protein; D023281:Genomics; D035001:Host Factor 1 Protein / Q000378:metabolism; D008856:Microscopy, Fluorescence; D018832:Molecular Chaperones / Q000378:metabolism; D010641:Phenotype; D013395:Sucrose / Q000737:chemistry
chemical_list: D000906:Antibodies; D001425:Bacterial Outer Membrane Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D018832:Molecular Chaperones; C090104:StpA protein, E coli; C088010:dps protein, E coli; D013395:Sucrose
keywords: DNA binding protein; DNA compaction; bacterial nucleoid; growth phase; sucrose gradient