Bacterial chromatin
Introduction
The bacterial nucleoid is a dynamic structure, the organization of which must adapt both to varying rates of replication and also to the different transcriptional requirements that are a consequence of changes in external environmental conditions. A single Escherichia coli chromosome comprises 4.6 Mb and must be compacted at least ∼1000-fold to fit inside the bacterial cell. The requirements of compaction and varying gene expression imply that bacterial chromatin, whether containing a replicating or a non-replicating chromosome, must, like eukaryotic chromatin, possess a high degree of spatial organization.
What is the nature of chromosomal organization and how is it imposed? In the past two years it has become apparent that the maintenance and use of negative supercoils in the DNA is central to both issues. Negative supercoiling can facilitate both DNA folding and compaction — as in the archetypal example of the eukaryotic nucleosome — and also the untwisting of DNA, which is required for the initiation of transcription and replication, in addition to DNA recombination. In the bacterial cell, the abundant nucleoid-associated proteins, including FIS (factor for inversion stimulation), H-NS (heat-stable [or histone-like] nucleoid-structuring), HU (heat-unstable), Dps (DNA-binding protein from starved cells) and IHF (integration host factor) (Table 1) function to package DNA and to dynamically constrain superhelicity.
In this review, we discuss recent developments linking the properties of superhelical domains to the spatial organisation of the bacterial chromosome.
Section snippets
Topological domains
There is abundant evidence that chromosomal DNA is organized into topological domains, which are insulated from their immediate neighbours. The extent of these domains has, until recently, been ill-defined but was initially believed to be approximately 50 to 100 kb [1]. One approach to a more precise determination of domain size is to alter local, rather than global, topology. Postow et al. [2••] accomplished this by the elegant technique of expressing the restriction enzyme SwaI in vivo to
Chromosome dynamics and the nature of topological barriers
The dynamic nature of topological domains implies that the barriers separating them must also be transient. Barriers are defined functionally as entities that prevent the free diffusion of supercoils. In principle a barrier could be created by tethering the DNA duplex either to RNA or to a protein, and thereby preventing free rotation. Another, not exclusive, possibility is that supercoils generated by transcription or a translocating enzyme could be dissipated by the binding of a topoisomerase
Macrodomain (and higher) organization
The correlation between the size of putative topological domains and the transcriptional activities has been emphasized by a recent study by Jeong et al. [10], who analysed the transcriptional properties of the E. coli genome as a function of the position of genes on the chromosome. These authors observed that the short-range pattern of transcriptional activity sensitive to gyrase function extended up to 16 kb. However, in addition, they detected two other patterns of transcriptional activity, a
Negative superhelicity and gene expression
Three independent lines of evidence now point to the important conclusion that negative supercoiling is a crucial determinant of the pattern of gene expression in the bacterial cell and that the available superhelicity is controlled by a homeostatic interconnected regulatory network that includes not only topoisomerases and the abundant nucleoid-associated proteins but also RNA polymerase and effectors that directly modify the properties of the enzyme. The implication is that, as in eukaryotes,
The role of nucleoid-associated proteins
Crucial to the organization of bacterial chromatin are the relative amounts of the different, abundant nucleoid-associated proteins. Not only do these amounts vary with growth phase [34] but also the expression of any one of these proteins is regulated by one or more of the others. In early exponential phase, FIS, HUα2 and H-NS predominate, to be succeeded by HUαβ and H-NS in the transition between exponential and stationary phase, and finally by IHF and Dps in late stationary phase. These
Conclusions and future directions
Despite the very different composition of bacterial and eukaryotic chromatin, there are some intriguing parallels. The delimitation of topological domains by DNA gyrase and topoisomerase IV in bacteria is reminiscent of the association of topoisomerase II with the eukaryotic nuclear matrix. Similarly, the occurrence of dynamic transcription factories in close spatial proximity appears to occur in both types of chromatin.
In bacteria, recent studies have emphasized the central role of DNA
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Glossary
- Counterions
- Positively charged ions that neutralize the negative charges of DNA phosphates.
- Pathogenicity islands
- Spatially separated regions of the genome that are enriched in genes associated with bacterial pathogenicity. These islands have a distinctive GC content and are usually flanked by mobile DNA elements.
- Plectonemic loops
- The loops generated by the intertwining of two DNA duplexes within a single supercoiled DNA molecule.
- Replichore
- The segment of the bacterial chromosome from origin to
References (46)
- et al.
Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium genome
Proc Natl Acad Sci USA
(2004) - et al.
Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function
Mol Microbiol
(1994) - et al.
Flexible DNA bending in HU–DNA cocrystal structures
EMBO J
(2003) - et al.
Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling
Proc Natl Acad Sci USA
(1981) - et al.
Topological domain structure of the Escherichia coli chromosome
Genes Dev
(2004) - et al.
Surveying a supercoil domain by using the γδ resolution system in Salmonella typhimurium
J Bacteriol
(1996) - et al.
Measuring chromosome dynamics on different time scales using resolvases with varying half lives
Mol Microbiol
(2005) Periodic transcriptional organization of the E. coli genome
J Mol Biol
(2004)- et al.
Gyrase and topo IV modulate chromosome domain size in vivo
Mol Microbiol
(1998) - et al.
The distribution of polymerase in Escherichia coli is dynamic and sensitive to environmental cues
Mol Microbiol
(2003)
Topological insulators inhibit diffusion of transcription-induced positive supercoils in the chromosome of Escherichia coli
Mol Microbiol
Spatial parameters of transcriptional activity in the chromosome
Genome Biol
Chromatin architecture and gene expression in Escherichia coli
Genome Biol
Dynamic organization of chromosomal DNA in Escherichia coli
Genes Dev
Macrodomain organization of the Escherichia coli chromosome
EMBO J
Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage λ integrase-mediated long-range rearrangements
Mol Microbiol
Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication
Proc Natl Acad Sci USA
The structure and function of the bacterial chromosome
Curr Opin Genet Dev
Linear ordering and dynamic segregation of the bacterial chromosome
Proc Natl Acad Sci USA
Bacillus subtilis actin-like protein MreB influences the positioning of the replication machinery and requires membrane proteins MreC/D and other actin-like proteins for proper localization
BMC Cell Biol
Nucleoid restructuring in stationary-state bacteria
Mol Microbiol
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
Genome Biol
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
Genetics
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Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome
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2019, Computational and Structural Biotechnology JournalCitation Excerpt :The former is transcriptionally activated when DNA becomes more negatively supercoiled, while the latter is activated when DNA is relaxed [83,170]. In this way, Fis is thought to act as a superhelicity monitor and topological buffer controller, with relevant effects in all physiology [131,159,160]. Through various positive vs. negative effects, direct vs. indirect mechanisms, as well as through the interaction with other NAPs and transcriptional regulators, Fis efficiently controls basic cellular processes and specific genetic programs including virulence, e.g. in pathogenic Salmonella carrying pathogenicity islands SPI-1 and SPI-2 [19,166] and several other bacteria (reviewed by Duprey et al. [46]).