Abstract
Bacterial genomic DNA is packed within the nucleoid of the cell along with various proteins and RNAs. We previously showed that the nucleoid in log phase cells consist of fibrous structures with diameters ranging from 30 to 80 nm, and that these structures, upon RNase A treatment, are converted into homogeneous thinner fibers with diameter of 10 nm. In this study, we investigated the role of major DNA-binding proteins in nucleoid organization by analyzing the nucleoid of mutant Escherichia coli strains lacking HU, IHF, H–NS, StpA, Fis, or Hfq using atomic force microscopy. Deletion of particular DNA-binding protein genes altered the nucleoid structure in different ways, but did not release the naked DNA even after the treatment with RNase A. This suggests that major DNA-binding proteins are involved in the formation of higher order structure once 10-nm fiber structure is built up from naked DNA.
Highlights
Both prokaryotic and eukaryotic cells store large size genomic DNA with various proteins and RNAs
To determine whether major DNA-binding proteins are involved in formation of the nucleoid structure, we examined the nucleoid released from DNA-binding protein deletion mutants (Table 1)
We previously assumed that bacterial genomic DNA is folded step-wise to form the nucleoid as follows: DNA, 10-nm fiber, 30-nm fiber, 80-nm fibers/beads, condensed nucleoid [13,14,15,16,17]
Summary
Both prokaryotic and eukaryotic cells store large size genomic DNA with various proteins and RNAs. Genomic DNA exists in the form of chromatin and is packed into a well-defined nucleus [2]. In both cases, a set of distinct structural DNA-binding proteins (e.g., histones in eukaryotic cells) plays a major role in organizing DNA into higher-order structures. In the case of eukaryotic chromatin, particular proteins (i.e., histones and condensins) mediate the step-wise folding of genomic DNA into higher-order architectures such as the nucleosome, 30-nm chromatin, 300-nm chromatin, and metaphase chromosomes. How bacterial DNA-binding proteins participate in organizing genomic DNA within the cell remains largely unknown
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