Chromosome and replisome dynamics in E. coli: loss of sister cohesion triggers global chromosome movement and mediates chromosome segregation

Abstract

Chromosome and replisome dynamics were examined in synchronized E. coli cells undergoing a eukaryotic-like cell cycle. Sister chromosomes remain tightly colocalized for much of S phase and then separate, in a single coordinate transition. Origin and terminus regions behave differently, as functionally independent domains. During separation, sister loci move far apart and the nucleoid becomes bilobed. Origins and terminus regions also move. We infer that sisters are initially linked and that loss of cohesion triggers global chromosome reorganization. This reorganization creates the 2-fold symmetric, ter-in/ori-out conformation which, for E. coli, comprises sister segregation. Analogies with eukaryotic prometaphase suggest that this could be a primordial segregation mechanism to which microtubule-based processes were later added. We see no long-lived replication "factory"; replication initiation timing does not covary with cell mass, and we identify changes in nucleoid position and state that are tightly linked to cell division. We propose that cell division licenses the next round of replication initiation via these changes.

Figure 1. Chromosome Resymmetrization Mediates Chromosome Segregation

Slowly growing wild-type cells just prior to division (left) and just after birth (right); images are overlays of phase contrast, DAPI (gray) and ori (blue) and ter (red) FISH exposures. Dashed box: ori and ter movements required to convert polarized newborn cell into a dividing cell with mirror-image symmetry.

Figure 2. Landmark Cell Cycle Events

(A) Flow cytometry defines the distributions of DNA contents in a cell population, from which the percentage of cells in G1, S, and G2 phases can be calculated (Experimental Procedures). (B) Visible cell septation is detected by phase contrast microscopy (arrows, middle panel); presence of a septal membrane ring can be verified by staining with fluorescent dye FM4-64 (right panel). (C) Timing of landmark events at Td = 125min. (a) Percentages of cells undergoing DNA replication (gray) or cell septation (gold) and relative cell number (green) as a function of time. (b) Cumulative curves describing the kinetics of entry into (solid lines) and exit out of (dashed lines) the replication (gray) and septation (gold) stages. (c) Summary given by times at which 50% of cells have completed events in (b) plus timing of cell division from (a) and timing of cell birth, one division time earlier (text). Data from sample set I.

Figure 3. Sister Chromosome Cohesion and Separation

(A) Chromosomal positions of ori, gln, lac, and ter. (B) Loci in (A) were visualized by four-color FISH; each probed locus may present either one or two staining foci. Nucleoids were visualized by DAPI staining and may be single- or bilobed (arrow). (C) Percentage of cells containing two ori foci (top panel), two gln or two lac foci or two DAPI-staining bodies (middle panel), or two ter foci (bottom panel). Td = 125min. Closed circles—sample set II; open circles plus timing of replication and septation stages—sample set I, Figure 2C. (D) Cumulative entry and exit curves (solid and dashed lines) for each two-focus stage and the two-nucleoid stage. (E) Summary, with four stages in the evolution of sister chromosome relationships (text) indicated at bottom. (F) Frequencies of cells containing different numbers of ori (o) and ter (t) foci and nucleoid(s) (n) (sample set I). Cell classes represented by <5% of total cells (e.g., 1o, 1n, 2t) were excluded from the analysis. Yellow lines identify majority class at each time point.

Figure 4. Spatial Dynamics of the Chromosome and Replisome

Cellular positions of all ori and ter foci, all DnaX-GFP foci, and dimensional boundaries of all nucleoids and phase contrast cell outlines were recorded for each of 200 cells at 13 sequential time points (sample set I). (A) Absolute positions of each entity of interest were defined with respect to x and y coordinates centered at the middle of the cell (e.g., top, middle). Absolute positions were then normalized to total cell length and width, giving corresponding relative positions (bottom). (B) Cumulative curves describing occurrence of events of interest. Curves for DNA replication, septation, and division are from Figure 2. Data for numbers of foci and nucleoids from Figure 3F. For events involving focus position, an entity was defined as being “at” or “near” a particular location if it was ≤1/5 of the total cell length away from that location. The resolution of this approach is sufficient to resolve events separated in time by more than 5 min, as confirmed in several cases by individual cell analysis (e.g., Figures 5D and 5E). (C) Left: normalized focus positions for cells in the majority class at each time point (defined by Figure 3F), drawn within a nucleoid of average size for that class (error bars = 1 SD). Vertical black lines are drawn through the mean positions of split nucleoids (inner boundaries only) and of ori and ter foci. Right: Positions of DnaX foci in all cells at each time point. (D) Normalized positions of ori, gln, and lac foci in cells containing split nucleoids at t = 60 min in the four-color FISH experiment of Figure 3C. Bars represent the distance between the mean positions of the left (gray dots) and right (black dots) foci; “left” and “right” were defined arbitrarily. (E) Cell division is accompanied by nucleoid repositioning (text).

Figure 5. DnaX (Replisome) Dynamics

(A) DnaX-GFP localizes to midcell not only in wild-type cells (left) but in anucleate parC1215(Ts) cells arising after growth at 42°C for 1 hr (right). (B) Positions of DnaX-GFP and ori foci in cells containing a single focus of each type (from Figure 4C, t = 20 min; sample set I). (a) Overlay of DnaX and ori images from a typical cell. (b) All focus positions. (c) Inter-focus distances; mean = 0.3 μm. (C) Positions of DnaX foci in two-focus cells at t = 40 and 70 min. Each line represents the pair of foci seen in a single cell. Mean cell lengths shown at bottom (error bars = 1 SD). (D and E) Percentages of cells in different morphological categories plotted as a function of time; cells categorized by number of ori and DnaX foci (D) or ter and DnaX foci (E). Components of biphasic curves denoted by “(A)” and “(B).” *early classes reappearing after cell division.

Figure 6. Event Timing Under Varied Growth Conditions

(A) Timing of chromosome and replisome events in synchronized cells grown under three different conditions (text). Replication and septation are indicated by horizontal bars as above; splitting of ori, DnaX, ter, and the nucleoid and cell division, are indicated by vertical lines. Relative cell mass at birth was determined from average cell length at t = 0 (~birth) (L = 1.8, 2.5, and 2.0 μm for Td = 90, 125, and 300 min, respectively). Relative cell mass at the time of initiation was determined from average cell length at the time point corresponding to initiation of replication in each growth condition (L = 1.8, 2.7, and 2.1 μm, respectively). (B) Alternate representation of data in (A); slope of line indicates extent to which timing of event after birth varies with doubling time. Period of DNA replication is shaded. (C) Normalized positions of ori and ter FISH foci for Td = 90 min (A and B) as compared with those for Td = 125 min (above), described as in Figure 4C.

Figure 7. Summary and Implications

(A) Summary of events at Td = 125 min. ori and ter foci are depicted within nucleoids and cells of appropriate absolute sizes, prior to normalization (Figure 4). (B) Interchromosome pushing forces could promote sister separation. (Left) Sister chromosomes linked by cohesion molecules accumulate a tendency to push one another apart. (Right) Two chromosomes that push one another apart will become symmetrically displayed on either side of any region of residual linkage. (C) Features of late-stage eukaryotic chromosomes. (a) At pro-phase, sisters are tightly conjoined into a single unit; at prometaphase, sisters lie side-by-side (Sparrow et al., 1941, as cited in Kleckner et al., 2004). (b) Chromosome coils also arise at prometaphase and often exhibit opposite helical handedness (Boy de la Tour and Laemmli, 1988). (D) We propose (text) that cell division per se licenses initiation of the next round of DNA replication. Coupling at late-cell cycle stage precludes initiation until and unless cell progresses through critical step of cell division. Such a mechanism can explain one-to-one linkage of cell division and replication initiation at both slow and fast growth rates.