Role of RNA polymerase and transcription in the organization of the bacterial nucleoid.

One of the major structural differences that provides a taxonomic distinction between eukaryotic and prokaryotic organisms is that prokaryotes lack the nuclear envelope, with exceptions such as planctomycetes 1, and genomic organization mechanisms found in eukaryotes. Instead, the prokaryotic genome is partitioned into a somewhat amorphous region of the cell known as the nucleoid 2–4. In both prokaryotes and eukaryotes, the genome must be compacted to fit into its allotted space while maintaining a level of organization that allows efficient functionality. In eukaryotes, this is accomplished by well-defined histone proteins that form nucleosomal and chromatin structures and yet can be remodeled to allow for the decondensation critical for gene expression 5–9. Although the bacterial genome must also be densely compacted, more than one-thousand-fold, and also organized for optimum functionality (chromosome replication/segregation, recombination and transcription) 10–14, the mechanisms by which this is accomplished remain unclear. The lack of “beads-on-a-string” morphology indicates different and/or multiple roles for nucleoid-associated proteins. Since transcription is a major cellular function and involves protein-DNA interaction and DNA topological domain structures, the transcription machinery themselves may play a role in nucleoid organization. Conversely, the nucleoid structure and organization may influence gene expression in a manner analogous to chromatin decondensation in eukaryotes. The interactions involved in nucleoid structure and gene expression continue to be challenging issues in the post-genomic era. Escherichia coli is a preferred model system for prokaryotic research due to the extensive studies into its genetic, physiology, biochemistry, and molecular biology mechanisms 15. The study of nucleoid organization is intrinsically difficult mainly due to the small size of bacteria in comparison to the limits of optical resolution of conventional instrumentation. Until very recently, images of the nucleoid have not changed much over the last four decades and reveal no structural details 16–18. Consequently, most of the earlier studies were focused on the biochemical properties and morphologies of isolated nucleoids and electron microscopic images after fixation 3–4,19–24. However, any preparation or fixation procedure will potentially introduce different organizations of the nucleoids or even artifacts. For example, different fixation procedures produced different nucleoid shapes of electron microscopic images 3. Additionally, growing evidence indicates that the organization of the nucleoid in the cell is plastic and sensitive to changes in growth and stress. The challenge of the research is to capture the “true” organization of the nucleoid reflecting the dynamic states of the nucleoid in living cells. Extensive studies have primarily emphasized the “histone-like” proteins including FIS, HU, H-NS, and IHF for their architectural roles in bending, looping, bridging and compacting DNA 25–36. The first three and RNA polymerase (RNAP) are the major nucleoid-associated proteins (NAPs) isolated from exponentially growing cells. Compared to the “histone-like” proteins, the binding of RNAP to DNA is much stronger. A prevailing view is that bacterial “histone-like proteins” are primarily responsible for the nucleoid organization and compaction in growing cells. Recent advances in the cell biology of E. coli RNAP and the nucleoid have shown that the distribution of RNAP, which is coupled to cell growth, plays an important role in the nucleoid dynamic structure. Emerging evidence indicates that formation of the transcription foci centered at the putative nucleolus structure is critical in nucleoid remodeling and influencing global gene expression. As other recent comprehensive reviews have dealt with the roles of other factors in bacterial nucleoid organization 37–43, this review provides an alternative and/or complementary perspective to the traditional views on bacterial nucleoid compaction and expansion.