Coordination of Growth, Chromosome Replication/Segregation, and Cell Division in E. coli

Abstract

Bacterial cells growing in steady state maintain a 1:1:1 relationship between an appropriate mass increase, a round of DNA replication plus sister chromosome segregation, and cell division. This is accomplished without the cell cycle engine found in eukaryotic cells. We propose here a formal logic, and an accompanying mechanism, for how such coordination could be provided in E. coli. Completion of chromosomal and divisome-related events would lead, interactively, to a "progression control complex" (PCC) which provides integrated physical coupling between sister terminus regions and the nascent septum. When a cell has both (i) achieved a sufficient mass increase, and (ii) the PCC has developed, a conformational change in the PCC occurs. This change results in "progression permission," which triggers both onset of cell division and release of terminus regions. Release of the terminus region, in turn, directly enables a next round of replication initiation via physical changes transmitted through the nucleoid. Division and initiation are then implemented, each at its own rate and timing, according to conditions present. Importantly: (i) the limiting step for progression permission may be either completion of the growth requirement or the chromosome/divisome processes required for assembly of the PCC; and, (ii) the outcome of the proposed process is granting of permission to progress, not determination of the absolute or relative timings of downstream events. This basic logic, and the accompanying mechanism, can explain coordination of events in both slow and fast growth conditions; can accommodate diverse variations and perturbations of cellular events; and is compatible with existing mathematical descriptions of the E. coli cell cycle. Also, while our proposition is specifically designed to provide 1:1:1 coordination among basic events on a "per-cell cycle" basis, it is a small step to further envision permission progression is also the target of basic growth rate control. In such a case, the rate of mass accumulation (or its equivalent) would determine the length of the interval between successive permission events and, thus, successive cell divisions and successive replication initiations.

Keywords: DNA replication; E. coli; bacteria; cell cycle coordination; cell division; chromosome; licensing.

Figure 1

Progression permission model. (A) General logic for 1:1:1 coordination of cell growth, replication initiation and cell division. Note: in slow growth conditions, PCC development clearly precedes satisfaction of the growth requirement such that the two features operate in parallel. In fast growth conditions, it is less clear whether the growth input is independent of PCC development and/or feeds into development of the PCC. This ambiguity is indicated by the (^**); see text. (B) Development of the proposed PPC by integration of chromosome and divisome inputs.

Figure 2

The proposed model is compatible with diverse growth conditions. (A) Definition of classical Cooper-Helmstetter C and D periods (Helmstetter et al., 1968). (B) Natures of, and relationships among, slow and fast growth in terms of (C+D) sequences and the effect of coordination control in the two situations. Progression permission is indicated by a filled upward arrow; downward arrows indicate the corresponding permitted cell division and replication initiation. (C) (C+D) sequences for an E. coli K12 strain with non-canonical period lengths [Td = 55 min; (C+D) = 100 min, with a 55 min C period and a 45 minute D period; Nielsen et al., 2007]. (D) Synchronous cell analysis of chromosome and divisome events under several slow growth conditions show that replication (purple) always begins soon after division (from Bates and Kleckner, 2005). (E) Relationships between the length of (C+D) and doubling time (Td) as a function of doubling time (from Helmstetter et al., 1968).

Figure 3

Chromosomal and divisome events under slow growth conditions. (A). Cell division is accompanied by a change in nucleoid disposition, from sister nucleoids closely juxtaposed to mid-cell via their terminus regions to each nucleoid centrally positioned within its (future or existing) sister (daughter) cells. Note that septum closure and the nucleoid transition can occur in either order, implying that they are independent events. (B) The nucleoid transition in (A) involves a whole body movement of the nucleoid, with origin and terminus regions remaining in the same relative positions. (A,B) are from Bates and Kleckner (2005). (C) Sequence of chromosomal events including replication initiation; a prominent transition to nucleoid duality, accompanied by an exchange of places of one sister (marked by its origin) and the mother material (marked by its terminus), and ensuing terminus dynamics including splitting and transit of one terminus across midcell (from Joshi et al., based on data in Bates and Kleckner, 2005). (D). Divisome (FtsZ) assembly dynamics defined under slow growth conditions (from Coltharp et al., 2016) (middle and bottom) as compared to chromosomal events predicted by interpolation of data from similar conditions (Figure 1D) and the proposed progression permission/PCC model (Figures 1A,B).

Figure 4

Comparison of events in slow and fast growth conditions in the context of the progression permission model. Top: patterns of (C+D) sequences (bar) with corresponding events of coordination control including progression permission (upward filled arrows) and the corresponding permitted cell division and replication initiation events (downward arrows). Slow growth patterns correspond to conditions in Figures 3A–C (Bates and Kleckner, 2005); fast growth patterns correspond to conditions in Figure 2C (Nielsen et al., 2007). Bottom: patterns of events in slow (left) and fast (right) growth conditions. Events are color-coded in relation to the (C+D) period to which they correspond, as defined in the top panel. Bottom left side: patterns of nucleoid morphologies and terminus and origin dynamics observed experimentally in slow growth conditions [(Bates and Kleckner, 2005); Figure 3C] plus predicted events of the proposed progression permission process including PCC assembly, progression permission, and the ensuing permitted division and replication initiation. Note that replication begins after division in the study of Bates and Kleckner (Figure 3) but often begins just before division in a number of other slow growth conditions. Bottom right side: nucleoid and terminus morphologies extracted from live cell time-lapse movies of Youngren et al. (2014) and overlaid with predicted events of the proposed progression permission process as it would occur in the corresponding partially overlapping (C+D) periods. Origin numbers and dispositions predicted from “C+D” patterns (Nielsen et al., 2007) are superimposed. Events in slow and fast growth conditions are directly compared by the (C+D) sequences defined in green boxes, as described in the text. The replication initiations resulting from these sequences are shown at the bottom in green boxes, with origin colors of the corresponding (C+D) sequence. (Note that somewhat different replication timing was inferred by analysis of fluorescent foci of SSB; however, that inference failed to take into account the fact that sister replisomes tend to first cluster and then split, implying that SSB foci are not a reliable indicator of the number of replication forks. Indeed, data inspection shows that pairs of SSB foci tend to emerge at the same time as nucleoid duality, in accord with occurrence by splitting rather than as a reflection of the time of initiation).

Figure 5

The progression permission model can accommodate diverse situations. (A) Perturbations of chromosome/divisome events that delay PCC formation. (B) Growth rate transitions. It is well established that, in a given growth condition, replication initiation tends to occur at a particular cell mass (sometimes parameterized as the mass/origin ratio; Donachie, 1968). Thus, in some situations, a change in growth conditions can be implemented by the simple expedient of having replication initiation occur at the cell mass corresponding to the new growth rate (B). However, some situations, notably a dramatic increase in growth rate, require that replication initiate before the time at which it would normally be allowed to occur by a scheduled progression permission event. In such cases, the required adjustment can be made if PCC activity is compromised in such a way that it still forms in response to onset of a (C+D) sequence, and regulates the ensuing division, but is no longer able to regulate replication initiation. As a result, initiation can run free until such time as a properly constituted PCC has again formed (C). Open hexagon indicates the (C+D) period in which PCC control over replication intiation is abrogated. Orange circles denote the replication initiations that are determined independently of PCC control due to the combined effects of PCC control abrogation and timing relative to re-establishment of PCC control. This scenario corresponds to the Cooper-Helmstetter observations that ongoing C period(s) is/are completed before there is a change to a new interval between divisions [the phenomenon of “rate maintenance” Helmstetter et al., 1968]; compare orange and turquoise double-headed arrows in (B,C).

Figure 6

Possible relationship of progression permission to growth rate control. (A) Progression permission enables division and replication initiation in a particular growth regime. (B) In a given balanced growth condition, all indicated events occur in a 1:1:1:1:1 relationship with a particular relative timing (on a population average level). Thus, the ultimate determinant of cell division timing (e.g., by addition of a particular amount of cell mass Ho et al., 2018) could be progression permission (this work); cell division (Harris and Theriot, 2016) or replication initiation (Amir, 2017).