Organization of DNA in a bacterial nucleoid

BMC Microbiology

Research Article

Michael Y. Tolstorukov¹  Victor B. Zhurkin²  Konstantin Virnik³  Sankar Adhya⁴ 

[1] Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, 02114, Boston, MA, USA;Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA;Laboratory of Immunoregulation, Division of Viral Products, Office of Vaccines, Center for Biologics, FDA, 20993, Silver Spring, MD, USA;Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA;

关键词: Bacterial;    Nucleoid;    MNase;    Digestion;    Sequencing;    Genomic;    DNA;    Packaging;    Structural;    Organization;   

DOI  :  10.1186/s12866-016-0637-3

 received in 2015-04-09, accepted in 2016-02-04,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundIt is unclear how DNA is packaged in a bacterial cell in the absence of nucleosomes. To investigate the initial level of DNA condensation in bacterial nucleoid we used in vivo DNA digestion coupled with high-throughput sequencing of the digestion-resistant fragments. To this end, we transformed E. coli cells with a plasmid expressing micrococcal nuclease. The nuclease expression was under the control of AraC repressor, which enabled us to perform an inducible digestion of bacterial nucleoid inside a living cell.ResultsAnalysis of the genomic localization of the digestion-resistant fragments revealed their non-random distribution. The patterns observed in the distribution of the sequenced fragments indicate the presence of short DNA segments protected from the enzyme digestion, possibly because of interaction with DNA-binding proteins. The average length of such digestion-resistant segments is about 50 bp and the characteristic repeat in their distribution is about 90 bp. The gene starts are depleted of the digestion-resistant fragments, suggesting that these genomic regions are more exposed than genomic sequences on average. Sequence analysis of the digestion-resistant segments showed that while the GC-content of such sequences is close to the genome-wide value, they are depleted of A-tracts as compared to the bulk genomic DNA or to the randomized sequence of the same nucleotide composition.ConclusionsOur results suggest that DNA is packaged in the bacterial nucleoid in a non-random way that facilitates interaction of the DNA binding factors with regulatory regions of the genome.

【 授权许可】

CC BY   
© Tolstorukov et al. 2016