Subcellular distribution of actively partitioning F plasmid during the cell division cycle in E. coli

Chromosome arrangement within a bacterium

BACKGROUND

The contour length of the circular chromosome of bacteria is greater than a millimeter but must be accommodated within a cell that is only a few micrometers in length. Bacteria do not have nucleosomes and little is known about the arrangement of the chromosome inside a prokaryotic cell.

RESULTS

We have investigated the arrangement of chromosomal DNA within the bacterium Bacillus subtilis by using fluorescence microscopy to visualize two sites on the chromosome simultaneously in the same cell. Indirect immunofluorescence with antibodies against the chromosome partition protein Spo0J were used to visualize the replication origin region of the chromosome. Green fluorescent protein fused to the lactose operon repressor Lacl was used to decorate tandem copies of the lactose operon operator lacO. A cassette of tandem operators was separately inserted into the chromosome near the origin (359 degrees), near the replication terminus (181 degrees), or at two points in between (90 degrees and 270 degrees). The results show that the layout of the chromosome is dynamic but is principally arranged with the origin and terminus maximally apart and the quarter points of the chromosome in between.

CONCLUSIONS

The use of cytological methods to visualize two chromosomal sites in the same cell has provided a glimpse of the arrangement of a bacterial chromosome. We conclude that, to a first approximation, the folding of the bacterial chromosome is consistent with, and may preserve, the linear order of genes on the DNA.

Mechanism of DNA segregation in prokaryotes: replicon pairing by parC of plasmid R1

Prokaryotic chromosomes and plasmids encode partitioning systems that are required for DNA segregation at cell division. The systems are thought to be functionally analogous to eukaryotic centromeres and to play a general role in DNA segregation. The parA system of plasmid R1 encodes two proteins ParM and ParR, and a cis-acting centromere-like site denoted parC. The ParR protein binds to parC in vivo and in vitro. The ParM protein is an ATPase that interacts with ParR specifically bound to parC. Using electron microscopy, we show here that parC mediates efficient pairing of plasmid molecules. The pairing requires binding of ParR to parC and is stimulated by the ParM ATPase. The ParM mediated stimulation of plasmid pairing is dependent on ATP hydrolysis by ParM. Using a ligation kinetics assay, we find that ParR stimulates ligation of parC-containing DNA fragments. The rate-of-ligation was increased by wild type ParM protein but not by mutant ParM protein deficient in the ATPase activity. Thus, two independent assays show that parC mediates pairing of plasmid molecules in vitro. These results are consistent with the proposal that replicon pairing is part of the mechanism of DNA segregation in prokaryotes.

A fixed distance for separation of newly replicated copies of oriC in Bacillus subtilis: implications for co-ordination of chromosome segregation and cell division

The Spo0J protein of Bacillus subtilis is required for normal chromosome segregation and forms discrete subcellular assemblies closely associated with the oriC region of the chromosome. Here we show that duplication of Spo0J foci occurs early in the DNA replication cycle and that this requires the initiation of DNA replication at oriC but not elongation beyond the nearby STer sites. Soon after duplication, sister oriC/Spo0J foci move rapidly apart to achieve a fixed separation of about 0.7 microm, reminiscent of the segregation of eukaryotic chromosomes on the mitotic spindle. The magnitude of the fixed separation distance may explain how chromosome segregation is kept in close register with cell growth and the initiation mass for DNA replication. It could also explain how segregation can proceed accurately in the absence of cell division. The kinetics of focal separation suggest that one role of Spo0J protein may be to facilitate formation of separate sister oriC complexes that can be segregated.

Use of time-lapse microscopy to visualize rapid movement of the replication origin region of the chromosome during the cell cycle in Bacillus subtilis

We describe the use of time-lapse fluorescence microscopy to visualize the movement of the DNA replication origin and terminus regions on the Bacillus subtilis chromosome during the course of the cell cycle. The origin and terminus regions were tagged with a cassette of tandem lac operator repeats and visualized through the use of a fusion of the green fluorescent protein to the LacI repressor. We have discovered that origin regions abruptly move apart towards the cell poles during a brief interval of the cell cycle. This movement was also seen in the absence of cell wall growth and in the absence of the product of the parB homologue spo0J. The origin regions moved apart an average distance of 1.4 microm in an 11 min period of abrupt movement, representing an average velocity of 0.17 microm min(-1), and reaching a maximum velocity of greater than 0.27 microm min(-1). The terminus region also exhibited a striking pattern of movement but not as far or a rapid as the origin region. These results provide evidence for a mitotic-like motor that is responsible for segregation of the origin regions of the chromosomes.

A green light for the bacterial cytoskeleton

Improved fluorescence techniques for visualizing proteins in whole bacterial cells have resulted in recent breakthroughs in our understanding of chromosome segregation and cytokinesis in prokaryotes. The dynamics and localization of some of these proteins reveal surprisingly cytoskeletal-like behavior.

Imaging techniques in microbiology

Recent advances in optical imaging have dramatically expanded the capabilities of the light microscope and its usefulness in microbiology research. Some of these advances include improved fluorescent probes, better cameras, new techniques such as confocal and deconvolution microscopy, and the use of computers in imaging and image analysis. These new technologies have now been applied to microbiological problems with resounding success.

Characterization of a prokaryotic SMC protein involved in chromosome partitioning

smc of Bacillus subtilis encodes a homolog of eukaryotic SMC proteins involved in chromosome condensation, pairing, and partitioning. A null mutation in B. subtilis smc caused a temperature-sensitive-lethal phenotype in rich medium. Under permissive conditions, the mutant had abnormal nucleoids, approximately 10% of the cells were anucleate, and assembly of foci of the chromosome partitioning protein Spo0J was altered. In combination with a null mutation in spo0J, the smc mutation caused a synthetic phenotype; cell growth was slower and approximately 25% of the cells were anucleate. Our results demonstrate that the B. subtilis Smc protein, like its eukaryotic counterpart, plays an important role in chromosome structure and partitioning.

Segregation of viral plasmids depends on tethering to chromosomes and is regulated by phosphorylation

Eukaryotic viruses can maintain latency in dividing cells as extrachromosomal nuclear plasmids. Segregation and nuclear retention of DNA is, therefore, a key issue in retaining copy number. The E2 enhancer protein of the papillomaviruses is required for viral DNA replication and transcription. Viral mutants that prevent phosphorylation of the bovine papillomavirus type 1 (BPV) E2 protein are transformation-defective, despite normal viral gene expression and replication function. Cell colonies harboring such mutants show sectoring of viral DNA and are unable to maintain the episome. We find that transforming viral DNA attaches to mitotic chromosomes, in contrast to the mutant genome encoding the E2 phosphorylation mutant. Second-site suppressor mutations were uncovered in both E1 and E2 genes that allow for transformation, maintenance, and chromosomal attachment. E2 protein was also found to colocalize to mitotic chromosomes, whereas the mutant did not, suggesting a direct role for E2 in viral attachment to chromosomes. Such viral hitch-hiking onto cellular chromosomes is likely to provide a general mechanism for maintaining nuclear plasmids.

The regulation of bacterial cell division: a time and place for it

Temporal and spatial regulation of cell division assures that each daughter cell receives a copy of the chromosome. Within the past year, the application of fluorescence microscopy to the cell biology of bacteria has revealed an increasing number of proteins that are localized within the bacterial cell to carry out DNA segregation and cell division. The localization of these proteins implies the existence of positional information in the cell, but how this information is established is unknown.

FtsZ dynamics during the division cycle of live Escherichia coli cells

The dynamics and assembly of bacterial cell division protein FtsZ were monitored in individual, growing and dividing Escherichia coli cells in real time by microculture of a merodiploid strain expressing green fluorescent protein (GFP)-tagged FtsZ. Cells expressing FtsZ-GFP at levels less than or equivalent to that of wild-type FtsZ were able to grow and divide over multiple generations, with their FtsZ rings visualized by fluorescence. During the late stages of cytokinesis, which constituted the last one-fourth of the cell cycle, the lumen of the FtsZ ring disappeared as the whole structure condensed. At this time, loops of FtsZ-GFP polymers emanated outward from the condensing ring structure and other unstable fluorescent structures elsewhere in the cell were also observed. Assembly of FtsZ rings at new division sites occurred within 1 min, from what appeared to be single points. Interestingly, this nucleation often took place in the predivisional cell at the same time the central FtsZ ring was in its final contraction phase. This demonstrates directly that, at least when FtsZ-GFP is being expressed, new division sites have the capacity to become fully functional for FtsZ targeting and assembly before cell division of the mother cell is completed. The results suggest that the timing of FtsZ assembly may be normally controlled in part by cellular FtsZ concentration. The use of wide-field optical sectioning microscopy to obtain sharp fluorescence images of FtsZ structures is also discussed.

Polar localization of the replication origin and terminus in Escherichia coli nucleoids during chromosome partitioning

We show the intracellular localization of the Escherichia coli replication origin (oriC) and chromosome terminus during the cell division cycle by FISH. In newborn cells, oriC is localized at the old-pole-proximal nucleoid border and the terminus at the new-pole-proximal nucleoid border. One copy of replicated oriC migrates rapidly to the opposite nucleoid border. These oriC copies are retained at both nucleoid borders, remaining at a constant distance from each cell pole. The terminus segment migrates from the nucleoid border to midcell and is retained there until the terminus is duplicated. The origin, terminus and other DNA regions show three migration patterns during active partitioning of daughter chromosomes.

Identification and characterization of a bacterial chromosome partitioning site

We have identified a DNA site involved in chromosome partitioning in B. subtilis. This site was identified in vivo as the binding site for the chromosome partitioning protein Spo0J, a member of the ParB family of partitioning proteins. Spo0J is a site-specific DNA-binding protein that recognizes a 16 bp sequence found in spo0J. Allowing two mismatches, this sequence occurs ten times in the entire B. subtilis chromosome, all in the origin-proximal approximately 20%. Eight of the ten sequences are bound to Spo0J in vivo. The presence of a site on an otherwise unstable plasmid stabilized the plasmid in a Spo0J-dependent manner, demonstrating that this site, called parS, can function as a partitioning site. This site and Spo0J are conserved in a wide range of bacterial species.

Localization of F plasmid SopB protein to positions near the poles of Escherichia coli cells

The subcellular localization of the SopB protein, which is encoded by the Escherichia coli F plasmid and is involved in the partition of the single-copy plasmid, was directly visualized through the expression of the protein fused to the jellyfish green fluorescent protein (GFP). The fusion protein, but not GFP itself, was found to localize to positions close but not at the poles of exponentially growing cells. Neither the presence of other F-encoded proteins nor the binding of SopB to its recognition sites within the sopC locus of F is required for this localization. Examination of derivatives of the fusion protein lacking various regions of SopB suggests that the signal for the cellular localization of SopB resides in a region close to its N terminus. It is plausible that the near polar localization of SopB may serve the function of keeping a segregated pair of F plasmids apart while the cell septum is being formed. The plausible relation between the specific location of SopB and its suppression of sopC-linked genes when overexpressed is also discussed.

Cell cycle-dependent duplication and bidirectional migration of SeqA-associated DNA-protein complexes in E. coli

Using immunofluorescence microscopy, we have found that SeqA protein, a regulator of replication initiation, is localized as discrete fluorescent foci in E. coli wild-type cells. Surprisingly, SeqA foci were observed also in an oriC deletion mutant. Statistical analysis revealed that a SeqA focus is localized at midcell in newborn cells. The SeqA focus is duplicated and tethered at midcell until an FtsZ ring is formed. Subsequently, these foci migrate in opposite directions toward cell quarter sites and remain tethered there until the cell divides. The cell cycle-dependent bidirectional migration of SeqA-DNA complexes is quite different from the migration pattern of oriC Dna copies. MukB protein is required for correct localization of SeqA complexes by an unknown mechanism.

Cell cycle: the bacterial approach to coordination

Despite the power of bacterial genetics, the prokaryotic cell cycle has remained poorly understood. But recent work with three different bacterial species has shed light on how chromosomes and plasmids are oriented and partitioned during the cell cycle, and on mechanisms regulating the initiation of DNA replication.