Bacterial chromosome organization and segregation

Abstract

Bacterial chromosomes are generally approximately 1000 times longer than the cells in which they reside, and concurrent replication, segregation, and transcription/translation of this crowded mass of DNA poses a challenging organizational problem. Recent advances in cell-imaging technology with subdiffraction resolution have revealed that the bacterial nucleoid is reliably oriented and highly organized within the cell. Such organization is transmitted from one generation to the next by progressive segregation of daughter chromosomes and anchoring of DNA to the cell envelope. Active segregation by a mitotic machinery appears to be common; however, the mode of chromosome segregation varies significantly from species to species.

Figure 1.

The “rosette” model of DNA organization. Electron micrograph of isolated membrane-free chromosomes from E. coli. The central core, from which several tens of loops radiate, is sensitive to RNAse. Single strand cuts to any one loop will only affect the supercoiling of that particular domain, leaving the rest of the chromosome unaffected. Bar = 1 µm. (reprinted from Kavenoff and Bowen 1976, with permission).

Figure 2.

Chromosome organization in model bacteria. (A) The Caulobacter chromosome is linearly organized, and anchored to the flagellated pole via parS/ParB/PopZ. (B) In Vibrio cholerae, the origin region of the larger chromosome (chromosome I) is localized to the cell pole, whereas the origin of the smaller chromosome is localized to the cell center. The organization of the bulk of the chromosomes, as well as their separation or intermingling, are currently unknown. (C) Four loci have been localized in vegetative cells of Bacillus subtilis, and their organization is reminiscent of the linear order seen in Caulobacter. Although the origin region is localized near to one pole, it appears not to be anchored to the cell membrane. (D) Sporulating cells of B. subtilis, however, do anchor the origin region, through RacA/DivIVA, to the negatively curved membrane at the pole. RacA also binds all along the chromosome, compacting it into a long “axial filament” before sporulation. (E) The E. coli origin localizes to mid-cell, and the two replichores are separated into opposite cell halves. The terminus is broadly localized (arrows), and may be found on either side of the cell center.

Figure 3.

Chromosome organization in E. coli. The origin of replication of the E. coli chromosome (oriC) is located at midcell, and each arm is kept in a separate cell half (top). The terminus region is broadly distributed along the long axis of the cell (not shown). As replication proceeds (middle), each daughter oriC is segregated to the cell quarters and, when replication is complete, the daughter chromosomes adopt a translationally symmetric <L-R-L-R> configuration (bottom).

Figure 4.

Nonrandom segregation in E. coli. (A) A replicating mother cell is shown, highlighting the Left and Right replichores as well as the difference between leading-strand-replicated (solid black lines) and lagging-strand-replicated DNA (dashed black lines). The replication bubble (gray box) is also shown, and repeated above each example in B and C to illustrate the origin of each configuration. (B) To achieve the <L-R-L-R> configuration seen, it is necessary for both lagging strands or both leading strands to be segregated to the distal edges of the cell. Note that in ∼90% of cases, leading strand segregation to the distal edges (right) is observed. (C) If random segregation of leading and lagging strands is imposed, the <L-R-L-R> configuration cannot be achieved, and mirror symmetry appears (e.g., <L-R-R-L>).

Figure 5.

“Immortal strand” inheritance versus Leading strand segregation. Two generations of DNA replication and segregation are shown, to illustrate the association of an old DNA strand (colored) with the old cell pole. Note that in all cases, leading strand segregation to the distal cell edges is maintained. (A) After the first generation, both daughter cells carry one “new” and one “old” strand of DNA (black and colored, respectively). (B) During the second round of segregation, two scenarios are possible: (1) immortal strand segregation is kept, and the “old” pole stays associated with the “old” (colored) strand of DNA (top). Note that this is the case observed for E. coli cells in ∼70% of cases; (2) Immortal strand segregation is not kept, and the “old” pole received two “new” strands of DNA. In this case, the configuration of the chromosome changes from <L-R-L-R> to <R-L-R-L>.