E. coli bacterial strains, plasmids, and growth conditions
All E. coli strains used for the cell pole recruitment, Z-ring recruitment, and cytokinesis inhibition experiments were derivatives of BW25113 (CGSC #7636) strain and were grown in M9 + Glucose minimal media (recipe is provided in Supplementary Table 4). The DNA recruitment background strain was previously constructed by the Sherratt Lab30 (CGSC #12294) and was grown in EZ Rich Defined Media (EZRDM, Teknova Bio.) as described in Supplementary Table 4. Antibiotic requirements are specified in Supplementary Table 4 and the corresponding concentrations for each were chloramphenicol (150 µg/mL), streptomycin (50 µg/mL) and gentamycin (5 µg/mL). Inducer concentrations for respective strains and plasmid combinations are outlined in Supplementary Table 4 and described in more detail below. All bacterial cultures were grown in tubes covered in foil to minimize contact with ambient light. Plasmids expressing exogenous CRY2/CIBN fusion proteins with their associated sequences are described in Supplementary Table 4.
Recruitment of CRY2-mCherry to the DNA via TetR-CIBN in E. coli
Cultures were started from a single colony of the strain RM187 and grown in 6 mL EZ Rich Defined Medium (EZRDM, Teknova Bio.) containing chloramphenicol and gentamycin at 25 ºC with shaking until the cells entered early log-phase (OD600 between 0.1 and 0.2, ~ 19 hours). When the culture entered early log-phase the cells were induced with 60 µM IPTG and supplemented with 240 nM anhydrous-tetracycline (ATC) to avoid a replication block induced by binding of TetR-CIBN similarly as previously described. The cells were induced for 2 hours at 25 ºC with shaking. At the end of the induction period the cells were centrifuged for 10 minutes at 4110 rpm and the pellet was resuspended in 6 mL of EZRDM containing chloramphenicol and 240 nM ATC and grown for an additional 30 minutes at 25 ºC while shaking after which it was, again, centrifuged for 10 minutes at 4110 rpm and resuspended in 6 mL EZRDM containing chloramphenicol and gentamycin and allowed to grow an additional 2.5 hours at 25 ºC while shaking to allow the mCherry fluorophore to mature. Following the outgrowth period, the cells were prepared for imaging by centrifuging 1 mL of the culture at 13k rpm for 1 minute and then resuspending the pellet in 50 µL of fresh EZRDM. Following this, 0.5 µL of the resuspension was then placed on a gel pad and the pad and prepared for imaging as specified in the “Live cell imaging” section below.
Recruitment of CRY2-mCherry to the cell pole via CIBN-GFP-PopZ and the Z-ring via ZapA-CIBN in E. coli
Cultures were started from a single colony of the strain of interest and grown in M9 + Glucose minimal medium containing chloramphenicol and streptomycin at 37 ºC overnight until the cells reached stationary phase. The overnight culture was then diluted 1:100 in fresh of M9 + Glucose containing chloramphenicol and streptomycin and was allowed to grow at 37 ºC until it reached log-phase (OD600 between 0.1 and 0.2, ~ 3 hours) at which point the culture was induced with 0.4% arabinose and either 40 µM IPTG (ZapA fusion) or 100 µM IPTG (PopZ fusion). Following a 1-hour induction at 37 ºC the cells were prepared for imaging by centrifuging 1 mL of the culture at 13k rpm for 1 minute and then resuspending the pellet in 70 µL of fresh M9 + Glucose. Following this, 0.5 µL of the resuspension was then placed on a gel pad and the pad and prepared for imaging as specified in the “Live cell imaging” section below. The cells on the gel pad were then assembled into the imaging chamber and allowed to equilibrate on the microscope in the dark for 2 hours at ambient room temperature (RT).
Recruitment of CRY2-HaloTag to the cell pole via CIBN-GFP-PopZ using variable green (561nm) light in E. coli
Cultures were started from a single colony of the strain of interest and grown in M9 + Glucose minimal medium containing chloramphenicol and streptomycin at 37 ºC overnight until the cells reached stationary phase. The overnight culture was then diluted 1:100 in fresh of M9 + Glucose containing chloramphenicol and streptomycin and was allowed to grow at 37 ºC until it reached log-phase (OD600 between 0.1 and 0.2, ~ 3 hours) at which point the culture was induced. Following a 1-hour induction at 37 ºC the cells were prepared for imaging by centrifuging 1 mL of the culture at 13k rpm for 1 minute and then resuspending the pellet in 100 µL of fresh M9 + Glucose with 1 µM Janelia Fluor® 646 HaloTag® ligand (Promega Corp.) and allowed to incubate at RT for 2 hours covered in foil. Following this, 0.5 µL of the resuspension was then placed on a gel pad and the pad and prepared for imaging as specified in the “Live cell imaging” section below.
Rapid Z-ring decondensation experiments in E. coli
Cultures of strain RM077 and RM078 were started from a single colony and grown in LB at 37 ºC overnight until the cells reached stationary phase. The overnight LB culture was then diluted 1:200 in 3mL of M9 + Glucose and grown overnight at room temperature (RT, 25 ºC) until they reached log-phase (OD600 between 0.1 and 0.2) at which point the culture was induced with 10µM IPTG and 0.2% arabinose. Following a 2-hour induction at RT. Cells were prepared for imaging by centrifuging 1 mL of the culture at 13k rpm for 1 minute and then resuspending the pellet in 100 µL of fresh M9 + Glucose. Following resuspension, 0.5 µL of the resuspension was transferred to a 3% M9 + Glucose agarose gel pad containing 10µM IPTG and 0.2% arabinose for imaging.
Light induced inhibition of cytokinesis experiments in E. coli
Cultures were started from a single colony of the strain of interest (see Supplementary Table 4) and grown in LB containing chloramphenicol and/or streptomycin (depending on the strain background, see Supplementary Table 4) at 37 ºC overnight until the cells reached stationary phase. The overnight culture was then diluted 1:100 in fresh of M9 + Glucose containing chloramphenicol and streptomycin and was grown overnight at 25 ºC until it reached log-phase (OD600 between 0.1 and 0.2) at which point the culture was induced. Following a 2-hour induction at 25 ºC the cells were washed into fresh M9 + Glucose media lacking inducer and allowed to outgrow at 24 ºC for 2 hours. After the outgrowth, the cells were prepared for imaging by centrifuging 1 mL of the culture at 13k rpm for 1 minute and then resuspending the pellet in 40 µL of fresh M9 + Glucose. Following this, 0.5 µL of the resuspension was then placed on a gel pad and the pad and prepared for imaging as specified in the “Live cell imaging” section below. Control cells were placed in a chamber, wrapped in foil, left at RT in next to microscope for the duration of the experiment and imaged after the experiment ended.
B. subtilis culturing, sample preparation, and imaging
Cultures were started from a single colony of the strain SC757 grown on LB plates at 30 ºC for 16–20 hours. We note all the following culturing, sample preparation, and induction steps occurred in the dark to avoid pre-activation caused by ambient light.
For imaging in M9 + media (glucose minimal media with vitamins, see Supplementary Table 4), single colonies from fresh plates were then inoculated into M9 + with 100 µM IPTG to induce CRY2-tdTomato for 6–7 hours at 30 ºC shaking. When the culture entered early log phase between OD600 0.1 and 0.3, 500 µL of the cultures were harvested by centrifuging for 5 minutes at 5000 rpm and the pellet resuspended in 50 µL of M9 + by vortexing. 1 µL of the resuspended culture was spotted on 3% (w/v) M9 + agarose pad supplemented with 100 µM IPTG. The sample was allowed to equilibrate at the imaging temperature of 25 ⁰C for 1 hour prior to imaging.
For imaging in B. subtilis casein hydrolysate (CH) media74 (B. subtilis rich media commonly used for imaging75), single colonies from fresh plates were inoculated into CH media with 50 µM IPTG to induce CRY2-tdTomato for 16–20 hours at 25 ºC shaking in 10-fold dilution series. 500 µL of the cultures in early log phase between OD600 0.1 and 0.3, were harvested by centrifuging for 5 minutes at 5000 rpm and the pellet resuspended in 50 µL of CH media by vortexing. 1 µL of the resuspended culture was spotted on 3% (w/v) CH agarose pad supplemented with 50 µM IPTG. The sample was allowed to equilibrate at the imaging temperature of 25 ⁰C for 1 hour prior to imaging.
To image the cells, cells were placed into focus using the 561 nm imaging laser that was also used for image acquisition at 1.63 W/cm2 measured 1 cm from the objective. The 488 nm laser power used to activate CRY2/CIBN system was 1.28 W/cm2 measured 1 cm from the objective in an area 200 x 200 pixels (160 nm/pixel). Every 3 seconds, cells were pulsed with blue light for 500 ms to activate the system followed by 50 ms green light to acquire image for a total of 160 frames (8 min).
C. crescentus culturing, sample preparation, and imaging
Cultures were started from single colony of EG3979 and EG3988 grown on PYE supplemented with both 5 µg/mL gentamycin and 25 µg/mL kanamycin or only kanamycin, respectively, at 30 ºC for 48-72h. Colonies from fresh plates were then inoculated into PYE supplemented with appropriate antibiotics (1 µg/mL gentamycin and/or 5 µg/mL kanamycin) and grown overnight to an OD600 of ~ 0.3–0.6. Cultures were diluted to an OD600 of ~ 0.08 in 2 mL of appropriate media supplemented with 0.3% xylose and 0.5 mM vanillate for EG3979 or just xylose for EG3988 and induced for 2 hours. Control samples were left growing in appropriate media lacking inducers. All culture tubes were protected from ambient light.
500 µL of cells were concentrated 10X by spinning for 5 minutes at 5000 rpm, removing 450µL of media, and resuspending in left over 50 µL, 1 µL was spotted on PYE agarose pad containing gentamycin and kanamycin for EG3979 or just kanamycin for EG3988. Samples were allowed to equilibrate at the imaging temperature of 25 ºC for 30 minutes prior to image acquisition at 25 ºC.
Live cell imaging
Live cell imaging was performed on a custom-built optical setup routed to an Olympus IX71 inverted microscope with a 100X 1.49 NA oil-immersion objective (Olympus Inc.). The light was focused onto the chip of an EMCCD camera (iXon Ultra 897, Andor Technology) with a final pixel size of 160 x 160 nm. The imaging focal plane was controlled by a piezo-driven stage (ASI, Eugene, OR). The EMCCD camera, lasers and shutters were controlled by Metamorph™ software (Molecular Devices).
Excitation light was provided by solid state 488 nm (Coherent OBIS), 561 nm (Toptica Photonics) or 647 nm (Coherent OBIS) lasers. The fluorescence emission signal was collected using either a ZET 488/561 nm (Chroma Technology) or ZET 488/561/647 nm (Chroma Technology) dual-band dichroic depending on the imaging conditions used. For two-color experiments, the emission light from the RFP and GFP channels were split using a 525/50 (Chroma Technology) and 650/50 (Chroma Technology) filter set mounted inside of an Optosplit II beam-splitter system (Cairn Research) prior to focusing on the EMCCD camera chip. The 488 nm laser power used to activate the CRY2/CIBN system was the same as what was used to image GFP fusions at 8.08 W/cm2 measured 1 cm from the objective for PopZ and ZapA experiments and 80.8 W/cm2 measured 1 cm from the objective for the TetR experiments measured using a Thor Labs Inc. Power Meter). The 561 nm laser power used to image the mCherry fusions was 8.71 W/cm2 measured 1 cm from the objective for the PopZ and ZapA experiments and 93.3 W/cm2 measured 1 cm from the objective for the TetR experiments unless otherwise noted in the text.
For two-color experiments using the 647 nm laser, the emission light from the RFP and GFP channels were split using a 556 nm long-pass filter (T556lpxr, Chroma Technology) in the Optosplitter followed by 700/75 (Chroma Technology) filter for the RFP emission light prior to focusing on the EMCCD camera chip.
To avoid activation of the CRY2/CIBN system by the LED bright-field lamp (LDB100F System, Prior Scientific Inc.), we placed a 715nm long-pass filter (RG715, Thor Labs Inc.) or a 665nm long-pass filter (ET665lp, Chroma Technology) filter after the condenser and the BF lamp intensity was adjusted such that the measured 488 nm light after the filter was measured to be ~ 200 nW at 1 cm from the sample plane.
Gel pads used to support the living bacteria cells were prepared by melting 3% w/v solution of agarose powder (SeaPlaque™ GTG™, Lonza Scientific) and either EZRDM or M9 + Glucose for 0.5-1 hour at 70 ºC. The melted gel was then transferred to a gasketed, cover-glass (FCS2, Bioptechs Inc.) and allowed to polymerize while sandwiched between the cover-glass and a cleaned coverslip (40 CIR-1, VWR Inc.) for 4 hours at 25 ºC (room temperature). 0.5 µL of the cells to be imaged were placed on the gel pad and allowed to dry (~ 3 minutes) before a fresh coverslip was placed on top and the imaging chamber (FCS2, Bioptechs) was assembled.
Generally, the blue light intensities and pulse sequences used to activate CRY2/CIBN in various imaging configurations were chosen to minimize phototoxicity of cells to blue light while maximizing the amount of activated CRY2. Whenever possible, we tried to minimize both the intensity and the number of blue pulses we delivered over the course of an acquisition. However, if the observed level of complex formation was not sufficient under a particular blue light induction scheme, we increased the number of pulses and or the intensity of blue light used to activate the system accordingly.
For the DNA recruitment experiments, the cells were irradiated with 30 ms pulses of 488 nm and 561 nm light delivered consecutively every 5 seconds using a 30 ms exposure time for each.
For the cell pole and Z-ring recruitment experiments the cells were first imaged for 2.5 seconds with 561 nm light after which they were irradiated with 488nm light for 100ms and then imaged with 56 nm light by streaming for 15 seconds using a 50ms exposure time.
For the cell pole recruitment experiments where the green (561 nm) light was varied: the cells were first imaged for 2.5 seconds with both 647 nm and 561 nm light after which they were irradiated with 488 nm light for 100 ms and then imaged with 647 nm and 561 nm light by streaming for 15 seconds using a 50 ms exposure time.
For the fast Z-ring decondensation experiments, cells were initially imaged with 561 nm light after which they were irradiated with 50 ms pulses of 488 nm light delivered consecutively every 10 seconds for a 5-minute period. The cells were then imaged again with 561 nm light at the end of the 5-minute period.
For the Light-induced Inhibition of Cytokinesis (LInC) experiments, cells were irradiated with alternating 100 ms pulses of 488 nm and 561 nm every five minutes for a period of 12 hours.
Quantifying the percentage increase in the DNA recruitment experiments in E. coli
To quantitatively characterize the accumulation of CRY2-mCherry at chromosomal sites, we calculated the increase in the Weber contrast77 of single cells. This calculation was used because chromosomal DNA spots were diffusive in both the lateral and azimuthal directions (relative to the z-axis of our objective) over the course of the experiments. This type of movement made it difficult to track individual spots and accurately estimate their intensities using the method we applied to our cell pole and midcell platforms (see above). Since the accumulation of CRY2-mCherry from a uniform distribution to a single concentrated location inside the cell body is equivalent to an increase in the Weber Contrast of a single cell image, we estimated the accumulation using the following method. First, we segmented the cells with observable spots in the last frame of the time lapse movie. There are normally 1 or 2 spots in a segmented cell region. Then we subtracted the background intensity of each image using ImageJ78. Finally, the normalized contrast for a single cell, j, in frame i is defined as:
$$\:{C}_{norm}\left(i,j\right)=\:\frac{{I}_{\text{max}i,j}-{I}_{\text{min}i,j}}{⟨{I}_{i,j}⟩-{I}_{\text{min}i,j}}$$
Where \(\:{C}_{norm}(i,j)\) reflects the extended accumulation of CRY2-mCherry in the DNA spot and \(\:{I}_{\text{max}i,j}\) and \(\:{I}_{\text{min}i,j}\) are the intensity of the brightest and darkest pixels in the cells, respectively. The contrast is normalized by the mean intensity, 〈Ii,j ⟩, of all the pixels in this region considering cell-to-cell variations in expression levels. Figure 2d and 2e were calculated using this method with the y-axis in Fig. 2e converted to percent increase (\(\:\%\:Inc)\) by:
$$\:\%\:Inc\:\left(t\right)=\:\left(\frac{{C}_{norm}\left(t\right)}{{C}_{norm}(t=0)}-1\right)\times\:100$$
for ease of comparison with other experiments.
Quantifying the RFP and/or GFP signal in cell pole and Z-ring recruitment experiments
A variation on a previously published custom MATLAB script76 used to quantify FRAP data was created to measure the GFP and RFP signals in the live-cell recruitment experiments. Briefly, cells were manually selected and cropped using a maximum intensity projection image of the entire recruitment stream (created in ImageJ) to avoid any selection bias. The max intensity image was also used to manually crop both the total cell area as well as the recruitment site area (either Z-ring or cell pole). For the Z-ring experiments the selected area was cropped manually using a rectangular selection. For the cell pole experiments the PopZ region was cropped using a fixed circle with a 2-pixel radius. To calculate the percent increase at target loci, we first calculated the fraction \(\:Frac\left(t\right)\:\)of the fluorescence intensity \(\:{I}_{target}\left(t\right)\:\)at the target site at a given time t\(\:\:\)versus that of the whole cell \(\:{I}_{cell}\left(t\right)\):
$$\:Frac\left(t\right)=\frac{{I}_{target}\left(t\right)}{{I}_{cell}\left(t\right)}\:$$
We then converted this fraction to percent increase (\(\:\%\:Inc)\) by:
$$\:\%\:Inc\:\left(t\right)=\:\left(\frac{Frac\left(t\right)}{Frac(t=0)}-1\right)\times\:100$$
The percentage increase curves of all cells were then averaged to obtain the mean and the associated standard error.
We noticed that our experimental setup introduced a slight variation in the time between activation with blue light and acquisition with either green or far-red light. This variation was because in some experiments (Fig. 2i and 3d), the CRY2/CIBN association kinetics were too fast that the microscope hardware speed of switching blue-light activation to green-light was not fast enough to capture the true time 0 after switching, and hence the first datapoint did not start at true time 0. To account for this delay, we created a custom MATLAB script to determine the true time delay between activation and acquisition frames using the imaging metadata obtained by Metamorph. We then used the actual time of switching when aggregating data and/or making measurements. Therefore, some of the time traces did not start at precisely time 0.
Quantifying the Halo signal in cell pole dissociation experiments in E. coli
Individual well-isolated cells were cropped from whole field of view time-course image stacks starting 5 minutes after CRY2/CIBN association was activated using blue light. The individual cell image stacks were then registered in x-y space using the ImageJ StackReg79 plug-in to minimize the shifting of the cells over long timescales due to growth. The depletion of cell pole foci was then measured using the Weber contrast-based methodology employed for the TetR recruitment platform described above. The resulting traces for individual cells were averaged together and the exponential decay curve was fit to
$$\:f\left(t\right)=A{e}^{-\left(\frac{1}{{\tau\:}_{off}}\right)(t-5)}+C$$
to extract the dissociation time constant (𝜏off).
Quantification of Z-ring decondensation in E. coli
Cells were segmented using the MiSiC deep learning-based cell segmentation algorithm80. After segmentation, the resulting cell masks were fed into MicrobeJ81 to quantify the mean ZapA-mCherry intensity at across the long axis of the cell and cell lengths. All cells were visually inspected to remove any cells that lacked a Z-ring at the start of the experiment. The midcell localization fraction of the Z-ring was measured by dividing the integrated ZapA-mCherry fluorescence intensity within a 3-pixel window (480 nm width) about the midcell maximum (approximate Z-ring position) by the total integrated ZapA-mCherry fluorescence intensity of the whole cell both before and after a 5-minute blue light induction. The change in the midcell localization fraction before and after blue light induction was calculated, normalized by the midcell fraction before induction and multiplied by a factor of 100 to obtain the percent change in Z-ring intensity at midcell. The percentage of cells that both harbored a Z-ring prior to induction with blue light and showed a reduction in the midcell fraction of ZapA-mCherry intensity at midcell greater than 4% were deemed as “decondensed”. This decondensation threshold was applied to every cell in each experimental population to determine the fraction of cell that underwent significant decondensation in each experimental condition. Bootstrapping was employed to estimate the standard error of the mean. Briefly, a subpopulation of cells (500 for the induced cells and 300 for the uninduced cells) were randomly sampled and used to calculate the percentage of cells that underwent decondensation. This calculation was repeated 100 times to obtain the standard error of the mean.
Quantification of inhibition of cytokinesis in E. coli
Cells were manually tracked throughout the duration of the experiment to determine if and when a successful division occurred. Cells were cropped and the average midcell intensity across the long-axis of the cells (long-axis projection) was calculated using a custom MATLAB script.
Quantification of maximal enrichment and reduction of CRY2-mCherry and CRY2-HaloTag
In order to reduce the effects of noise on the maximal fold enrichment and maximal fold reduction of CRY2-HaloTag signal at the cell poles (i.e., estimation of the plateau value), the final plateau value was calculated by taking the mean of the last ten datapoints of individual cell trajectories.
Statistics
All experimental replicates (N) were noted in the main text along with the number of data points used in the analysis where applicable. All error bars and significance values were calculated using MATLAB by a statistical test specified in the figure legend. p-values < 0.05 were accepted as statistically significant. The different significance levels indicated as stars in figures correspond to *p value < 0.05, **p < 0.01, ***p < 0.001 and ****p < 0.0001 or n.s. where no significant difference was observed.