Macromolecular crowding and the mandatory condensation of DNA in bacteria

Abstract

Cellular DNA in bacteria is localized into nucleoids enclosed by cytoplasm. The forces which cause condensation of the DNA into nucleoids are poorly understood. We suggest that direct and indirect macromolecular crowding forces from the surrounding cytoplasm are critical factors for nucleoid condensation, and that within a bacterial cell these crowding forces are always present at such high levels that the DNA is maintained in a condensed state. The DNA affected includes not only the preexisting genomic DNA but also DNA that is newly introduced by viral infection, replication or other means.Key words: Cytoplasmic macromolecule; DNA condensation; Escherichia coli; Macromolecular crowding; Mandatory condensation; Nucleoid DNA condensation in bacteria: general considerationsThe genomic DNA of bacteria is condensed into one or a few nucleoids per cell [1] that are in direct contact with a surrounding cytoplasm containing very high concentrations of macromolecules (e.g. ,~ 340 mg/ml of total RNA and protein [2]). The term 'condensation' is used to indicate adoption of a relatively concentrated, compact state occupying a fraction of the volume available. The DNA of the bacterial nucleoid is estimated to have a local concentration of ,'-50-100 mg DNA/ml (see footnote 6 of [3]) and to occupy 1/8 to 1/5 of the volume within the cell envelope [1].Condensation of DNA within bacterial ceils has been observed by light microscopy of both living and fixed cells, as well as by electron microscopy [4][5][6][7][8] (reviewed in [9,10]). Condensation of DNA in isolated nucleoids is indicated by microscopy as well as by hydrodynamic properties [11][12][13]. Condensation of DNA in model in vitro systems has been assayed by aggregation, as described below. Condensing forcesThe origins and magnitudes of the forces which cause DNA condensation are poorly understood. Supercoiling, macromolecular crowding and the binding of histone-like proteins and of polyamines have all been suggested to contribute to DNA condensation. It is unclear how important each of these fac-*Corresponding author: Fax: (1) (301) 496-0201.0014-5793196/$12.00 © 1996 Federation of European Biochemical Societies. PH SO0 1 4-5793(96)00725-9 tors is in causing DNA condensation in vivo. Model studies of the binding of histone-like proteins under dilute solution conditions indicate that the cellular amounts of DNA-binding proteins in bacteria are 5-10-fold lower than those required for condensation (see [14] for references and discussion). The polyamines putrescine and spermidine can occur in large amounts in E. coli [15]. Spermidine but not putrescine can condense DNA from aqueous solution [16], although the binding reaction is relatively salt-sensitive [17,18] and so may make a restricted contribution over much of the range of intracellular salt concentrations observed in growing cells [19,20]. Enzymatic supercoiling directly yields more compact forms [21].Macromolecular crowding ('crowding', reviewed in [22,23]) can cause DNA condensation by two distinctly dif...

The effect of macromolecular crowding on mobility of biomolecules, association kinetics, and gene expression in living cells

“…Intracellular macromolecular crowding is also expected to shrink solely the nucleoid to the observed in vivo volume due to purely entropic effects [124,125]. Indeed, the fast real-time compaction of chromosomes to native volumes [126] is observed in systems crowded by polymers.…”

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

“…It seems polyamines alone can not induce DNA condensation in cellular systems, and several other factors are involved in the stabilization of the compact forms of DNA such as specific proteins (histones in eukaryotes or histone-like proteins in prokaryotes), macromolecular crowding or DNA supercoiling. It appears that these different factors contribute to the stabilization of the compact forms of DNA (78). On the other hand, high concentrations of polyamines are generally found in the G 1 phase of the cell cycle (1).…”

Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

“…A well known example is the transition of DNA to a compact form (condensation) in the presence of overthreshold concentrations of simple neutral polymers and simple salts (2,3,4). It has been proposed that macromolecular crowding is the basis for phase separation in the cytoplasm (5) and condensation of DNA into the nucleoid of bacterial cells (6). The latter hypothesis is supported by the observation that DNA can be condensed by cytoplasmic extracts from Escherichia coli at extract concentrations corresponding to about 1 ⁄2 the cellular concentration (7).…”