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.

Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations by triggering transient differentiation of a mutantgenerating cell subpopulation, using reactive oxygen species (ROS). Cipro-induced DNA breaks activate the Escherichia coli SOS DNA-damage response and error-prone DNA polymerases in all cells. However, mutagenesis is limited to a cell subpopulation in which electron transfer together with SOS induce ROS, which activate the sigma-S (s S ) general-stress response, which allows mutagenic DNA-break repair. When sorted, this small s S -response-''on'' subpopulation produces most antibiotic cross-resistant mutants. A U.S. Food and Drug Administration (FDA)-approved drug prevents s S induction, specifically inhibiting antibiotic-promoted mutagenesis. Further, SOS-inhibited cell division, which causes multi-chromosome cells, promotes mutagenesis. The data support a model in which within-cell chromosome cooperation together with development of a ''gambler'' cell subpopulation promote resistance evolution without risking most cells. RESULTS Cipro-Induced MutagenesisWe developed two assays for cipro-induced mutagenesis without cipro selection of the mutants (Figure 1A). In both assays, strains are grown in liquid, each with cipro at its minimum antibiotic concentration (MAC, final colony-forming units [CFU] are 10% of those of no-drug cultures) (Lorian and De Freitas, 1979). These are ''low-dose'' and ''sub-inhibitory'' relative to MICs (CFU %10 À4 of untreated cells). Table S1 shows MACs and MICs for all strains assayed (wild-type MAC, 8.5 ng/mL). Cells are then removed from cipro and plated selectively for colonies resistant to rifampicin (RifR) or ampicillin (AmpR) antibiotics (Figure 1A), and mutation rates are estimated (STAR Methods). RifR arises by specific base-substitutions in the rpoB gene (Figure S1A), and AmpR arises by ampD null mutations in engineered Escherichia coli (Petrosino et al., 2002) (Figures S1B and S1C; STAR Methods). Strikingly, cipro increased RifR and AmpR mutation rates 26-and 18-fold above no-cipro rates (Figure 1B; Table S2 for all mutation rates). The RifR or AmpR mutants are not selected in sub-inhibitory cipro and are at a slight but significant disadvantage (Figure 1C), implying that mutation, not selection of the mutants, is elevated by MAC cipro. Additional controls show negligible cell death in the lowdose cipro (Figures S1D and S2, other controls). ROS-Dependent Mutagenesis Is s S -Dependent Mutagenic Break RepairThe cipro-induced mutagenesis requires ROS and is inhibited by ROS scavenging or preventing agents thiourea (TU) and 2,2 0 -bipyridine (BP) (Figure 1D; Table S2). The following data indicate that the ROS instigate a s S -licensed mutagenic DNA breakrepair (MBR) mechanism triggered by cipro-induced DSBs.MBR is regulated mutagenesis during repair of DSBs, requiring the SOS and s S respon...

Spontaneous DNA breaks instigate genomic changes that fuel cancer and evolution, yet direct quantification of double-strand breaks (DSBs) has been limited. Predominant sources of spontaneous DSBs remain elusive. We report synthetic technology for quantifying DSBs using fluorescent-protein fusions of double-strand DNA end-binding protein, Gam of bacteriophage Mu. In Escherichia coli GamGFP forms foci at chromosomal DSBs and pinpoints their subgenomic locations. Spontaneous DSBs occur mostly one per cell, and correspond with generations, supporting replicative models for spontaneous breakage, and providing the first true breakage rates. In mammalian cells GamGFP—labels laser-induced DSBs antagonized by end-binding protein Ku; co-localizes incompletely with DSB marker 53BP1 suggesting superior DSB-specificity; blocks resection; and demonstrates DNA breakage via APOBEC3A cytosine deaminase. We demonstrate directly that some spontaneous DSBs occur outside of S phase. The data illuminate spontaneous DNA breakage in E. coli and human cells and illustrate the versatility of fluorescent-Gam for interrogation of DSBs in living cells.DOI: http://dx.doi.org/10.7554/eLife.01222.001

The basis for segregation of sister chromosomes in bacteria is not established. We show here that two discrete~150-kb regions, both located early in the right replichore, exhibit prolonged juxtaposition of sister loci, for 20 and 30 min, respectively, after replication. Flanking regions, meanwhile, separate. Thus, the two identified regions comprise specialized late-splitting intersister connections or snaps. Sister snap loci separate simultaneously in both snap regions, concomitant with a major global nucleoid reorganization that results in emergence of a bilobed nucleoid morphology. Split snap loci move rapidly apart to a separation distance comparable with one-half the length of the nucleoid. Concomitantly, at already split positions, sister loci undergo further separation to a comparable distance. The overall consequence of these and other effects is that thus far replicated sister chromosomes become spatially separated (individualized) into the two nucleoid lobes, while the terminus region (and likely, all unreplicated portions of the chromosome) moves to midcell. These and other findings imply that segregation of Escherichia coli sister chromosomes is not a smooth continuous process but involves at least one and likely, two major global transition(s). The presented patterns further suggest that accumulation of internal intranucleoid forces and constraining of these forces by snaps play central roles in global chromosome dynamics. They are consistent with and supportive of our previous proposals that individualization of sisters in E. coli is driven primarily by internally generated pushing forces and is directly analogous to sister individualization at the prophase to prometaphase transition of the eukaryotic cell cycle.E. coli chromosome | chromosome segregation | bacterial nucleoid I n bacteria, sister chromosomes segregate concomitant with DNA replication. We previously examined sister chromosome relationships over time in the Escherichia coli cell cycle (1). High temporal resolution (5-10 min) was achieved using synchronous populations (2). Sister relationships at individual loci were evaluated as in other studies. Also, uniquely, at a larger scale, whole nucleoid disposition and morphology were defined. This analysis identified a discrete transition, occurring part way through the replication process, in which the nucleoid becomes bilobed. This morphological change is accompanied by reciprocal repositioning of the replication origin (oriC) and terminus region (ter) and by strongly delayed splitting of one particular locus located near the replication origin (gln). These coordinate effects pointed to global reorganization of the nucleoid. We proposed that this reorganization resulted in spatial segregation of sister chromosomes and that it is analogous to the prophase to prometaphase transition of the eukaryotic cell cycle. We further proposed that, in both cases, sister individualization results from internally generated forces, more specifically, mechanical pushing effects (1, 3).Other models for seg...