Super resolution microscopy reveals that ParF forms a meshwork of

Because of the limitation of resolution, confocal microscopy does not provide fine morphological details of the proteins hence three dimensional structured illumination microscopy (3D-SIM) was employed by using an OMX (Optical Microscopy eXperimental) microscope to investigate the features of the ParF structures in vivo. OMX set up includes isolated components for light source, imaging, microscope control and tracing the sample (Dobbie et al., 2011). In this microscopy, the lasers are beamed on the sample at multiple angles and in phases of the stripes to acquire and build up a compound image. The images have twice the resolution in the XY and Z planes after processing. Thus super resolution microscopy enhances resolution up to 100 nm in both axial and lateral directions. Approximately 50 cells were observed for each of wild type and mutant ParG containing plasmids. The images were analysed by 3D opacity using Volocity software (Perkin Elmer). As OMX microscope scans the sample for a longer interval, the photo-bleaching effect becomes a limiting factor.

The pattern of the ParF-eGFP localisation observed by OMX was found to be similar to those observed in the confocal images. When wild type ParG was present, the ParF-eGFP was distributed asymmetrically over the nucleoid (Figure 6.10). Images obtained from 3D-SIM showed ParF as a meshwork with various ParF polymers forming cable-like inter-wined structures distributed over the nucleoid. Wild type ParG-mCherry bound plasmids were located along the ParF cables. The co- localisation of multiple ParG-mCherry foci with ParF-eGFP appeared as beads on strings. A representative example of wild type ParG containing cells and the presence of ParF meshwork is given in Figure 6.10.

Figure 6.10. Structured illumination microscopy image of the ParF and ParG signal in

E. coli cells.

ParF-eGFP forms an asymmetric mesh of elongated structures over the nucleoid and ParG- mCherry bound plasmids appear as compact foci along the ParF cables. The filled white arrowheads show ParF cables. Empty arrowheads show co-localisation of ParF and ParG. The channels shown are ParF-eGFP (top-left), ParG-mCherry (top-right), DAPI (bottom- left) and merged (bottom-right). Scale bar, 1 unit = 0.415 µm.

Chapter 6

The cable-like ParF structures were also observed in the presence of ParG mutant proteins. ParG mutant proteins appeared as tight foci mainly at mid-cell position. ParG N-terminal partition deficient mutants were not impaired in promotion of ParF polymerization, hence it was not surprising to see the cable-like structure of ParF in the presence of these mutants in OMX images. Images of E. coli cells containing plasmids with ParG mutations were analysed by 3D opacity using Volocity software and representative examples are shown in Figure 6.11 and 6.12. Sometimes asymmetrical distribution was observed as shown for ParG-K12A. The images obtained using 3D-SIM are also shown as movies (Supplementary files, movies S10- S18). In the movies a rotation along the long axis suggests that the mesh forming cable-like ParF structures permeate the nucleoid.

Mutant ParG-mCherry bound plasmids were found at a fixed position. ParF-eGFP was evenly distributed over the nucleoid. The meshwork of ParF was visible in the presence of all the ParG mutant proteins except ParG-M13A and ParG-N18A. The absence of ParF meshwork in case of ParG-M13A cannot be established quantitatively as the sample size was small. In case of ParG-N18A, the compact focus of ParF-eGFP and lack of meshwork feature was frequently observed. This mirrors the observation made during the confocal imaging where ParF and ParG- N18A co-localised into a tight focus (Movie S7). In case of ParG-K11A sometimes two adjacent foci were observed at the mid-cell which might have arisen after replication. ParF-eGFP was spread around these ParG-K11A foci. In case of ParG- K5A and ParG-K12A, although ParF meshwork was observed over the nucleoid, the area around the plasmid was devoid of ParF-eGFP signal. During time-lapse experiment in confocal imaging, less overlap was observed between ParF-ParG-K5A and ParF-ParG-K12A (Movies S3 and S5). This might indicate towards the altered interaction between ParF and these ParG mutants. In case of ParG-R19A and ParG- L21A, co-localisation of ParF-ParG was observed. In the presence of ParG-R19A, long cables of ParF-eGFP were seen rather than a meshwork.

Movies legend

Movies S10-S18. The ParF-eGFP meshwork over the nucleoid shows variation depending upon the ParG mutants. E. coli cells containing plasmids pBAD-parF and

pBM20-parG/mutant were imaged on OMX microscope and displayed as a movie. (S10) ParG WT, Scale bar 1 unit = 0.316 µm; (S11) ParG-L3A, Scale bar 1 unit = 0.419 µm; (S12) ParG-K5A, Scale bar 1 unit = 0.581 µm; (S13) ParG-K11A, Scale bar 1 unit = 0.415 µm;

(S14) ParGK12A, Scale bar 1 unit = 0.45 µm; (S15) ParGM13A, Scale bar 1 unit = 0.478

µm; (S16) ParGN18A, Scale bar 1 unit = 0.577 µm; (S17) ParGR19A, Scale bar 1 unit = 0.233 µm; (S18) ParGL21A Scale bar 1 unit = 0.517 µm.

Chapter 6

Figure 6.11. Structured illumination microscopy images of the ParF distribution in the presence of ParG mutants inside E. coli cells.

The channels shown are green, red, DAPI and merged in all the images. A. ParG-L3A, B. ParG-K5A, C. ParG-K11A, D. ParG-K12A. In each pannel, the channels shown are ParF- eGFP (top-left), ParGmut-mCherry (top-right), DAPI (bottom-left) and merged (bottom- right). Scale bar, 1 unit = 0.415 µm.

Figure 6.12. Structured illumination microscopy images of the ParF distribution in the presence of ParG mutants inside E. coli cells.

The channels shown are green, red, DAPI and merged in all the images. A. ParG-M13A, B. ParG-N18A, C. ParG-R19A, D. ParG-L21A. In each pannel, the channels shown are ParF- eGFP (top-left), ParGmut-mCherry (top-right), DAPI (bottom-left) and merged (bottom- right). Scale bar, 1 unit = 0.415 µm.

Chapter 6

6.3 Conclusion

The orchestration of plasmid segregation was investigated by microscopy. ParF- eGFP appeared asymmetrically distributed over the nucleoid and ParG-mCherry appeared distinct but diffuse and located either at the mid-cell (in case of a single focus) or at 1/3 or 3/4 position. ParF-eGFP was visualised as an oscillating entity over the nucleoid during time-lapse experiment. While performing its dynamic movement ParF also transported the ParG-plasmid cargo and placed it at a site ready for segregation which indicates that ParF oscillation drives plasmid segregation. In the presence of ParG N-terminal mutants, ParF localisation was altered and it was distributed evenly throughout the nucleoid. ParG mutant proteins appeared as tight red foci and disorganised in the positioning compared to wild type ParG. The partition defective ParG N-terminal mutations caused detrimental effects on ParF oscillation. In the presence of the ParG mutant proteins, ParF polymers were locked and the oscillation was stalled. The compact nature of mutant foci pointed towards the inertness of the plasmid, as a consequence of lack of ParF oscillation. When bound to ATP, ParF dimerises and ParG stimulates the assembly of ParF into higher order structures. Partition deficient ParG N-terminal mutant proteins are able to promote ParF polymerization, hence the ParF-eGFP signal and localisation was similar in all cases. Polymeric ParF assembles onto the nucleoid, however, in the absence of stimulation of its ATPase activity by the ParG mutants, no dynamic relocation is observed. The enhancement of ParF ATP hydrolysis is likely to be a prerequisite for polymer remodelling and disassembly. Thus when this stimulation is missing, no turnover of ParF polymers and no oscillation are detected.

It was not possible to determine the effect of ParG-L21A on stimulation of ParF ATPase activity (Figure 5.10). However, as the ParF oscillation was abolished in the presence of ParG-L21A, it indicated that like other ParG mutants ParG-L21A might be impaired in stimulating ParF ATPase activity.

3D-SIM was instrumental in exploring the structural features of the ParF protein and showed ParF polymers as a mesh of inter-wined cables going through the nucleoid. The super resolution images displayed ParG mutants as tight foci.